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transient", ".


transient transfection", "transfection experiments", "experiments in", "in human", "human embryonic", "embryonic kidney", "293 cells", "cells revealed", "revealed that", "that traf6", "traf6 associates", "associates with", "with ips", "ikki and", "and tank", "2009 .", ". traf3", "traf3 was", "was also", "also shown", "shown to", "to form", "form complexes", "complexes with", "tbk1 and", "and ikki", "alff pj", "pj et", "al 2008", "saha sk", "sk et", "activated ips", "ips 1 recruits", "1 recruits trafs", "trafs tnf", "tnf receptor associated", "receptor associated factor", "associated factor protein", "factor protein family", "protein family members", "members to", "to the rig", "the rig 1/mda5", "rig 1/mda5 receptor", "1/mda5 receptor complex.", "receptor complex. traf3", "complex. traf3 and", "traf3 and traf6", "and traf6 act", "traf6 act as", "act as a", "as a scaffold", "a scaffold for", "scaffold for the", "for the assembly", "the assembly of", "assembly of the", "of the signaling", "the signaling complex", "signaling complex composed", "complex composed of", "composed of tbk1/", "of tbk1/ ikk", "tbk1/ ikk epsilon", "epsilon leading", "leading to the", "to the activation", "the activation of", "activation of transcription", "of transcription factors", "transcription factors irf3", "factors irf3 and", "irf3 and irf7.", "and irf7. traf6", "irf7. traf6 induced", "traf6 induced activation", "induced activation of", "of irf is", "irf is likely", "is likely to", "likely to be", "to be specific", "be specific for", "specific for irf7", "irf7 while", "while traf3 is", "traf3 is thought", "is thought to", "thought to activate", "to activate both", "activate both irf3", "both irf3 and", "irf3 and irf7", "irf7 konno", "konno h et", "h et al", "et al 2009", "2009 oganesyan", "oganesyan g et", "g et al", "et al 2006", "al 2006 .


transient", "2006 .


transient transfection", ".


transient transfection experiments", "transfection experiments in", "experiments in human", "in human embryonic", "human embryonic kidney", "kidney hek", "hek 293", "293 cells revealed", "cells revealed that", "revealed that traf6", "that traf6 associates", "traf6 associates with", "associates with ips", "with ips 1", "tbk1 ikki", "ikki and tank", "tank konno", "al 2009 .", "2009 . traf3", ". traf3 was", "traf3 was also", "was also shown", "also shown to", "shown to form", "to form complexes", "form complexes with", "complexes with ips", "1 tbk1", "tbk1 and ikki", "ikki oganesyan", "2006 alff", "alff pj et", "pj et al", "et al 2008", "2008 saha", "saha sk et", "sk et al", "once activated ips", "activated ips 1", "ips 1 recruits trafs", "recruits trafs tnf", "trafs tnf receptor", "tnf receptor associated factor", "receptor associated factor protein", "associated factor protein family", "factor protein family members", "family members to", "members to the", "to the rig 1/mda5", "the rig 1/mda5 receptor", "rig 1/mda5 receptor complex.", "1/mda5 receptor complex. traf3", "receptor complex. traf3 and", "complex. traf3 and traf6", "traf3 and traf6 act", "and traf6 act as", "traf6 act as a", "act as a scaffold", "as a scaffold for", "a scaffold for the", "scaffold for the assembly", "for the assembly of", "the assembly of the", "assembly of the signaling", "of the signaling complex", "the signaling complex composed", "signaling complex composed of", "complex composed of tbk1/", "composed of tbk1/ ikk", "of tbk1/ ikk epsilon", "ikk epsilon leading", "epsilon leading to", "leading to the activation", "to the activation of", "the activation of transcription", "activation of transcription factors", "of transcription factors irf3", "transcription factors irf3 and", "factors irf3 and irf7.", "irf3 and irf7. traf6", "and irf7. traf6 induced", "irf7. traf6 induced activation", "traf6 induced activation of", "induced activation of irf", "activation of irf is", "of irf is likely", "irf is likely to", "is likely to be", "likely to be specific", "to be specific for", "be specific for irf7", "for irf7 while", "irf7 while traf3", "while traf3 is thought", "traf3 is thought to", "is thought to activate", "thought to activate both", "to activate both irf3", "activate both irf3 and", "both irf3 and irf7", "and irf7 konno", "irf7 konno h", "konno h et al", "h et al 2009", "al 2009 oganesyan", "2009 oganesyan g", "oganesyan g et al", "g et al 2006", "et al 2006 .


transient", "al 2006 .


transient transfection", "2006 .


transient transfection experiments", ".


transient transfection experiments in", "transfection experiments in human", "experiments in human embryonic", "in human embryonic kidney", "embryonic kidney hek", "hek 293 cells", "293 cells revealed that", "cells revealed that traf6", "revealed that traf6 associates", "that traf6 associates with", "traf6 associates with ips", "associates with ips 1", "tbk1 ikki and", "and tank konno", "tank konno h", "et al 2009 .", "al 2009 . traf3", "2009 . traf3 was", ". traf3 was also", "traf3 was also shown", "was also shown to", "also shown to form", "shown to form complexes", "to form complexes with", "form complexes with ips", "complexes with ips 1", "ips 1 tbk1", "1 tbk1 and", "and ikki oganesyan", "ikki oganesyan g", "al 2006 alff", "2006 alff pj", "alff pj et al", "pj et al 2008", "al 2008 saha", "2008 saha sk", "saha sk et al", "sk et al 2006", "once activated ips 1", "activated ips 1 recruits", "1 recruits trafs tnf", "recruits trafs tnf receptor", "trafs tnf receptor associated", "tnf receptor associated factor protein", "receptor associated factor protein family", "associated factor protein family members", "protein family members to", "family members to the", "members to the rig", "to the rig 1/mda5 receptor", "the rig 1/mda5 receptor complex.", "rig 1/mda5 receptor complex. traf3", "1/mda5 receptor complex. traf3 and", "receptor complex. traf3 and traf6", "complex. traf3 and traf6 act", "traf3 and traf6 act as", "and traf6 act as a", "traf6 act as a scaffold", "act as a scaffold for", "as a scaffold for the", "a scaffold for the assembly", "scaffold for the assembly of", "for the assembly of the", "the assembly of the signaling", "assembly of the signaling complex", "of the signaling complex composed", "the signaling complex composed of", "signaling complex composed of tbk1/", "complex composed of tbk1/ ikk", "composed of tbk1/ ikk epsilon", "tbk1/ ikk epsilon leading", "ikk epsilon leading to", "epsilon leading to the", "leading to the activation of", "to the activation of transcription", "the activation of transcription factors", "activation of transcription factors irf3", "of transcription factors irf3 and", "transcription factors irf3 and irf7.", "factors irf3 and irf7. traf6", "irf3 and irf7. traf6 induced", "and irf7. traf6 induced activation", "irf7. traf6 induced activation of", "traf6 induced activation of irf", "induced activation of irf is", "activation of irf is likely", "of irf is likely to", "irf is likely to be", "is likely to be specific", "likely to be specific for", "to be specific for irf7", "specific for irf7 while", "for irf7 while traf3", "irf7 while traf3 is", "while traf3 is thought to", "traf3 is thought to activate", "is thought to activate both", "thought to activate both irf3", "to activate both irf3 and", "activate both irf3 and irf7", "irf3 and irf7 konno", "and irf7 konno h", "irf7 konno h et", "konno h et al 2009", "et al 2009 oganesyan", "al 2009 oganesyan g", "2009 oganesyan g et", "oganesyan g et al 2006", "g et al 2006 .


transient", "et al 2006 .


transient transfection", "al 2006 .


transient transfection experiments", "2006 .


transient transfection experiments in", ".


transient transfection experiments in human", "transfection experiments in human embryonic", "experiments in human embryonic kidney", "human embryonic kidney hek", "kidney hek 293", "hek 293 cells revealed", "293 cells revealed that traf6", "cells revealed that traf6 associates", "revealed that traf6 associates with", "that traf6 associates with ips", "traf6 associates with ips 1", "tbk1 ikki and tank", "ikki and tank konno", "and tank konno h", "tank konno h et", "h et al 2009 .", "et al 2009 . traf3", "al 2009 . traf3 was", "2009 . traf3 was also", ". traf3 was also shown", "traf3 was also shown to", "was also shown to form", "also shown to form complexes", "shown to form complexes with", "to form complexes with ips", "form complexes with ips 1", "with ips 1 tbk1", "ips 1 tbk1 and", "1 tbk1 and ikki", "tbk1 and ikki oganesyan", "and ikki oganesyan g", "ikki oganesyan g et", "et al 2006 alff", "al 2006 alff pj", "2006 alff pj et", "alff pj et al 2008", "et al 2008 saha", "al 2008 saha sk", "2008 saha sk et", "saha sk et al 2006" ] }, { "record_id": "GLY_000968_1_34", "filename": "chicken_protein_pathways_reactome", "fieldtype": "id", "phraselist": [ "gly_000968", "gga", "1227887", "r gga", "gga 1227887", "r gga 1227887" ] }, { "record_id": "GLY_000968_1_34", "filename": "chicken_protein_pathways_reactome", "fieldtype": "text", "phraselist": [ "rig like", "like receptor", "mediated induction", "induction of", "of ifn", "ifn alpha/beta", "rlr rig", "rig like receptor", "receptor mediated", "mediated induction of", "induction of ifn", "of ifn alpha/beta", "rlr rig like", "like receptor mediated", "receptor mediated induction", "mediated induction of ifn", "induction of ifn alpha/beta", "rlr rig like receptor", "rig like receptor mediated", "like receptor mediated induction", "receptor mediated induction of", "mediated induction of ifn alpha/beta", "in human", "rig i", "i like", "family is", "is crucial", "crucial for", "for triggering", "triggering response", "response to", "to cytosolic", "cytosolic viral", "viral rna.", "rna. rlr", "rlr family", "is composed", "composed of", "of retinoic", "retinoic acid", "acid inducible", "inducible gene", "gene 1", "1 protein", "melanoma differentiation", "differentiation associated", "associated protein", "protein 5", "and laboratory", "laboratory of", "of genetics", "genetics and", "and physiology", "physiology 2", "yoneyama et", "et al", "al 2005", "2005 .

rig1", "mda5 and", "and lgp2", "lgp2 are", "are cytosolic", "cytosolic multidomain", "multidomain proteins.", "proteins. they", "they all", "all contain", "contain a", "a central", "central dexd/h", "dexd/h box", "box rna", "rna helicase/adenosine", "helicase/adenosine triphosphatase", "domain that", "that can", "can bind", "bind viral", "viral rna", "and a", "a c", "c terminal", "terminal regulatory", "regulatory domain", "that prevents", "prevents signaling", "signaling in", "in the", "the absence", "absence of", "of viral", "rna. rig", "i and", "and mda5", "but not", "not lgp2", "also encode", "encode two", "two n", "n terminal", "terminal caspase", "caspase activation", "activation and", "and recruitment", "recruitment domains", "that transmit", "transmit the", "the signal", "signal by", "by binding", "binding to", "to card", "card domain", "domain of", "of mitochondrial", "mitochondrial ifn", "ifn beta", "beta promoter", "promoter stimulator", "stimulator protein", "ips 1", "also known", "known as", "as mavs", "visa or", "or cardif", "cardif .", ". this", "this card", "card card", "interaction leads", "leads to", "to production", "production of", "alpha/beta and", "and pro", "pro inflammatory", "inflammatory cytokines.", "cytokines. lgp2", "lgp2 that", "that lacks", "lacks card", "card motifs", "motifs but", "but binds", "binds viral", "rna is", "is believed", "believed to", "to regulate", "regulate rlr", "rlr signaling", "however the", "the mechanism", "mechanism of", "of the", "the regulation", "regulation remains", "remains unclear", "lgp2 was", "was reported", "reported to", "to act", "act as", "as negative", "negative regulator", "komuro and", "and horvath", "horvath 2006", "saito et", "al 2007", "while other", "other studies", "studies suggested", "suggested that", "that lgp2", "lgp2 may", "may cooperate", "cooperate with", "with rig", "rig 1", "1 and", "mda5 in", "in sensing", "sensing certain", "certain viral", "venkataraman et", "satoh et", "al 2010", "2010 .

primary", ".

primary chick", "chick embryo", "embryo cells", "cells produced", "produced ifn", "ifn alpha", "alpha in", "in response", "to newcastle", "newcastle disease", "disease virus", "and produced", "produced both", "both ifn", "ifn alpfa", "alpfa and", "and ifn", "beta in", "to vaccinia", "vaccinia virus", "virus or", "or influenza", "influenza a", "shwartz h", "h et", "al 2004", "2004 .", ". those", "those viruses", "viruses have", "have been", "been reported", "to induce", "induce tlr3", "mda5 signaling", "in mammals", "delaloye j", "j et", "al 2009", "kato h", "al 2006", "childs et", "2007 .", ". although", "although rlr", "signaling is", "is conserved", "conserved among", "among vertebrates", "vertebrates sarkar", "sarkar d", "d et", "al 2008", "zou j", "2009 and", "and feng", "feng h", "al 2011", "analysis of", "of chicken", "chicken genome", "genome revealed", "revealed only", "only orthologs", "orthologs for", "for mammalian", "mammalian mda5", "while rig", "1 gene", "gene was", "was not", "not identified", "and barber", "barber mr", "mr et", "2010 .", "human rig", "rig i like", "i like receptor", "receptor rlr", "family is crucial", "is crucial for", "crucial for triggering", "for triggering response", "triggering response to", "response to cytosolic", "to cytosolic viral", "cytosolic viral rna.", "viral rna. rlr", "rna. rlr family", "rlr family is", "family is composed", "is composed of", "composed of retinoic", "of retinoic acid", "retinoic acid inducible", "acid inducible gene", "inducible gene 1", "gene 1 protein", "protein rig", "melanoma differentiation associated", "differentiation associated protein", "associated protein 5", "5 mda5", "and laboratory of", "laboratory of genetics", "of genetics and", "genetics and physiology", "and physiology 2", "2 lgp2", "yoneyama et al", "et al 2005", "al 2005 .

rig1", ".

rig1 mda5", "mda5 and lgp2", "and lgp2 are", "lgp2 are cytosolic", "are cytosolic multidomain", "cytosolic multidomain proteins.", "multidomain proteins. they", "proteins. they all", "they all contain", "all contain a", "contain a central", "a central dexd/h", "central dexd/h box", "dexd/h box rna", "box rna helicase/adenosine", "rna helicase/adenosine triphosphatase", "triphosphatase atpase", "atpase domain", "domain that can", "that can bind", "can bind viral", "bind viral rna", "rna and", "and a c", "a c terminal", "c terminal regulatory", "terminal regulatory domain", "domain rd", "rd that", "that prevents signaling", "prevents signaling in", "signaling in the", "in the absence", "the absence of", "absence of viral", "of viral rna.", "viral rna. rig", "rna. rig i", "rig i and", "i and mda5", "mda5 but", "but not lgp2", "lgp2 also", "also encode two", "encode two n", "two n terminal", "n terminal caspase", "terminal caspase activation", "caspase activation and", "activation and recruitment", "and recruitment domains", "domains cards", "cards that", "that transmit the", "transmit the signal", "the signal by", "signal by binding", "by binding to", "binding to card", "to card domain", "card domain of", "domain of mitochondrial", "of mitochondrial ifn", "mitochondrial ifn beta", "ifn beta promoter", "beta promoter stimulator", "promoter stimulator protein", "protein ips", "1 also", "also known as", "known as mavs", "mavs visa", "visa or cardif", "or cardif .", "cardif . this", ". this card", "this card card", "card interaction", "interaction leads to", "leads to production", "to production of", "production of ifn", "ifn alpha/beta and", "alpha/beta and pro", "and pro inflammatory", "pro inflammatory cytokines.", "inflammatory cytokines. lgp2", "cytokines. lgp2 that", "lgp2 that lacks", "that lacks card", "lacks card motifs", "card motifs but", "motifs but binds", "but binds viral", "binds viral rna", "viral rna is", "rna is believed", "is believed to", "believed to regulate", "to regulate rlr", "regulate rlr signaling", "signaling however", "however the mechanism", "the mechanism of", "mechanism of the", "of the regulation", "the regulation remains", "regulation remains unclear", "unclear lgp2", "lgp2 was reported", "was reported to", "reported to act", "to act as", "act as negative", "as negative regulator", "regulator yoneyama", "2005 komuro", "komuro and horvath", "and horvath 2006", "2006 saito", "saito et al", "et al 2007", "while other studies", "other studies suggested", "studies suggested that", "suggested that lgp2", "that lgp2 may", "lgp2 may cooperate", "may cooperate with", "cooperate with rig", "with rig 1", "rig 1 and", "1 and mda5", "and mda5 in", "mda5 in sensing", "in sensing certain", "sensing certain viral", "certain viral rna", "rna venkataraman", "venkataraman et al", "2007 satoh", "satoh et al", "et al 2010", "al 2010 .

primary", "2010 .

primary chick", ".

primary chick embryo", "chick embryo cells", "embryo cells produced", "cells produced ifn", "produced ifn alpha", "ifn alpha in", "alpha in response", "in response to", "response to newcastle", "to newcastle disease", "newcastle disease virus", "virus ndv", "ndv and", "and produced both", "produced both ifn", "both ifn alpfa", "ifn alpfa and", "alpfa and ifn", "and ifn beta", "ifn beta in", "beta in response", "response to vaccinia", "to vaccinia virus", "vaccinia virus or", "virus or influenza", "or influenza a", "a shwartz", "shwartz h et", "h et al", "et al 2004", "al 2004 .", "2004 . those", ". those viruses", "those viruses have", "viruses have been", "have been reported", "been reported to", "reported to induce", "to induce tlr3", "tlr3 rig", "and mda5 signaling", "mda5 signaling in", "signaling in mammals", "mammals delaloye", "delaloye j et", "j et al", "et al 2009", "2009 kato", "kato h et", "et al 2006", "2006 childs", "childs et al", "al 2007 .", "2007 . although", ". although rlr", "although rlr signaling", "rlr signaling is", "signaling is conserved", "is conserved among", "conserved among vertebrates", "among vertebrates sarkar", "vertebrates sarkar d", "sarkar d et", "d et al", "et al 2008", "2008 zou", "zou j et", "al 2009 and", "2009 and feng", "and feng h", "feng h et", "et al 2011", "analysis of chicken", "of chicken genome", "chicken genome revealed", "genome revealed only", "revealed only orthologs", "only orthologs for", "orthologs for mammalian", "for mammalian mda5", "mammalian mda5 and", "lgp2 while", "while rig 1", "rig 1 gene", "1 gene was", "gene was not", "was not identified", "identified sarkar", "and barber mr", "barber mr et", "mr et al", "al 2010 .", "in human rig", "human rig i", "rig i like receptor", "like receptor rlr", "family is crucial for", "is crucial for triggering", "crucial for triggering response", "for triggering response to", "triggering response to cytosolic", "response to cytosolic viral", "to cytosolic viral rna.", "cytosolic viral rna. rlr", "viral rna. rlr family", "rna. rlr family is", "rlr family is composed", "family is composed of", "is composed of retinoic", "composed of retinoic acid", "of retinoic acid inducible", "retinoic acid inducible gene", "acid inducible gene 1", "inducible gene 1 protein", "1 protein rig", "protein rig i", "i melanoma", "melanoma differentiation associated protein", "differentiation associated protein 5", "protein 5 mda5", "and laboratory of genetics", "laboratory of genetics and", "of genetics and physiology", "genetics and physiology 2", "physiology 2 lgp2", "lgp2 yoneyama", "yoneyama et al 2005", "et al 2005 .

rig1", "2005 .

rig1 mda5", ".

rig1 mda5 and", "mda5 and lgp2 are", "and lgp2 are cytosolic", "lgp2 are cytosolic multidomain", "are cytosolic multidomain proteins.", "cytosolic multidomain proteins. they", "multidomain proteins. they all", "proteins. they all contain", "they all contain a", "all contain a central", "contain a central dexd/h", "a central dexd/h box", "central dexd/h box rna", "dexd/h box rna helicase/adenosine", "box rna helicase/adenosine triphosphatase", "helicase/adenosine triphosphatase atpase", "atpase domain that", "domain that can bind", "that can bind viral", "can bind viral rna", "viral rna and", "rna and a", "and a c terminal", "a c terminal regulatory", "c terminal regulatory domain", "regulatory domain rd", "rd that prevents", "that prevents signaling in", "prevents signaling in the", "signaling in the absence", "in the absence of", "the absence of viral", "absence of viral rna.", "of viral rna. rig", "viral rna. rig i", "rna. rig i and", "rig i and mda5", "and mda5 but", "mda5 but not", "not lgp2 also", "lgp2 also encode", "also encode two n", "encode two n terminal", "two n terminal caspase", "n terminal caspase activation", "terminal caspase activation and", "caspase activation and recruitment", "activation and recruitment domains", "recruitment domains cards", "cards that transmit", "that transmit the signal", "transmit the signal by", "the signal by binding", "signal by binding to", "by binding to card", "binding to card domain", "to card domain of", "card domain of mitochondrial", "domain of mitochondrial ifn", "of mitochondrial ifn beta", "mitochondrial ifn beta promoter", "ifn beta promoter stimulator", "beta promoter stimulator protein", "stimulator protein ips", "protein ips 1", "ips 1 also", "1 also known", "also known as mavs", "as mavs visa", "mavs visa or", "visa or cardif .", "or cardif . this", "cardif . this card", ". this card card", "card card interaction", "card interaction leads", "interaction leads to production", "leads to production of", "to production of ifn", "production of ifn alpha/beta", "of ifn alpha/beta and", "ifn alpha/beta and pro", "alpha/beta and pro inflammatory", "and pro inflammatory cytokines.", "pro inflammatory cytokines. lgp2", "inflammatory cytokines. lgp2 that", "cytokines. lgp2 that lacks", "lgp2 that lacks card", "that lacks card motifs", "lacks card motifs but", "card motifs but binds", "motifs but binds viral", "but binds viral rna", "binds viral rna is", "viral rna is believed", "rna is believed to", "is believed to regulate", "believed to regulate rlr", "to regulate rlr signaling", "rlr signaling however", "signaling however the", "however the mechanism of", "the mechanism of the", "mechanism of the regulation", "of the regulation remains", "the regulation remains unclear", "remains unclear lgp2", "unclear lgp2 was", "lgp2 was reported to", "was reported to act", "reported to act as", "to act as negative", "act as negative regulator", "negative regulator yoneyama", "regulator yoneyama et", "al 2005 komuro", "2005 komuro and", "komuro and horvath 2006", "horvath 2006 saito", "2006 saito et", "saito et al 2007", "2007 while", "while other studies suggested", "other studies suggested that", "studies suggested that lgp2", "suggested that lgp2 may", "that lgp2 may cooperate", "lgp2 may cooperate with", "may cooperate with rig", "cooperate with rig 1", "with rig 1 and", "rig 1 and mda5", "1 and mda5 in", "and mda5 in sensing", "mda5 in sensing certain", "in sensing certain viral", "sensing certain viral rna", "viral rna venkataraman", "rna venkataraman et", "venkataraman et al 2007", "al 2007 satoh", "2007 satoh et", "satoh et al 2010", "et al 2010 .

primary", "al 2010 .

primary chick", "2010 .

primary chick embryo", ".

primary chick embryo cells", "chick embryo cells produced", "embryo cells produced ifn", "cells produced ifn alpha", "produced ifn alpha in", "ifn alpha in response", "alpha in response to", "in response to newcastle", "response to newcastle disease", "to newcastle disease virus", "disease virus ndv", "ndv and produced", "and produced both ifn", "produced both ifn alpfa", "both ifn alpfa and", "ifn alpfa and ifn", "alpfa and ifn beta", "and ifn beta in", "ifn beta in response", "beta in response to", "in response to vaccinia", "response to vaccinia virus", "to vaccinia virus or", "vaccinia virus or influenza", "virus or influenza a", "influenza a shwartz", "a shwartz h", "shwartz h et al", "h et al 2004", "et al 2004 .", "al 2004 . those", "2004 . those viruses", ". those viruses have", "those viruses have been", "viruses have been reported", "have been reported to", "been reported to induce", "reported to induce tlr3", "induce tlr3 rig", "tlr3 rig 1", "1 and mda5 signaling", "and mda5 signaling in", "mda5 signaling in mammals", "in mammals delaloye", "mammals delaloye j", "delaloye j et al", "j et al 2009", "al 2009 kato", "2009 kato h", "kato h et al", "h et al 2006", "al 2006 childs", "2006 childs et", "childs et al 2007", "et al 2007 .", "al 2007 . although", "2007 . although rlr", ". although rlr signaling", "although rlr signaling is", "rlr signaling is conserved", "signaling is conserved among", "is conserved among vertebrates", "conserved among vertebrates sarkar", "among vertebrates sarkar d", "vertebrates sarkar d et", "sarkar d et al", "d et al 2008", "al 2008 zou", "2008 zou j", "zou j et al", "et al 2009 and", "al 2009 and feng", "2009 and feng h", "and feng h et", "feng h et al", "h et al 2011", "2011 analysis", "analysis of chicken genome", "of chicken genome revealed", "chicken genome revealed only", "genome revealed only orthologs", "revealed only orthologs for", "only orthologs for mammalian", "orthologs for mammalian mda5", "for mammalian mda5 and", "mammalian mda5 and lgp2", "and lgp2 while", "lgp2 while rig", "while rig 1 gene", "rig 1 gene was", "1 gene was not", "gene was not identified", "not identified sarkar", "identified sarkar d", "2009 and barber", "and barber mr et", "barber mr et al", "mr et al 2010", "et al 2010 .", "in human rig i", "human rig i like", "i like receptor rlr", "receptor rlr family", "rlr family is crucial", "family is crucial for triggering", "is crucial for triggering response", "crucial for triggering response to", "for triggering response to cytosolic", "triggering response to cytosolic viral", "response to cytosolic viral rna.", "to cytosolic viral rna. rlr", "cytosolic viral rna. rlr family", "viral rna. rlr family is", "rna. rlr family is composed", "rlr family is composed of", "family is composed of retinoic", "is composed of retinoic acid", "composed of retinoic acid inducible", "of retinoic acid inducible gene", "retinoic acid inducible gene 1", "acid inducible gene 1 protein", "gene 1 protein rig", "1 protein rig i", "rig i melanoma", "i melanoma differentiation", "melanoma differentiation associated protein 5", "associated protein 5 mda5", "mda5 and laboratory", "and laboratory of genetics and", "laboratory of genetics and physiology", "of genetics and physiology 2", "and physiology 2 lgp2", "lgp2 yoneyama et", "yoneyama et al 2005 .

rig1", "al 2005 .

rig1 mda5", "2005 .

rig1 mda5 and", ".

rig1 mda5 and lgp2", "mda5 and lgp2 are cytosolic", "and lgp2 are cytosolic multidomain", "lgp2 are cytosolic multidomain proteins.", "are cytosolic multidomain proteins. they", "cytosolic multidomain proteins. they all", "multidomain proteins. they all contain", "proteins. they all contain a", "they all contain a central", "all contain a central dexd/h", "contain a central dexd/h box", "a central dexd/h box rna", "central dexd/h box rna helicase/adenosine", "dexd/h box rna helicase/adenosine triphosphatase", "rna helicase/adenosine triphosphatase atpase", "triphosphatase atpase domain", "atpase domain that can", "domain that can bind viral", "that can bind viral rna", "bind viral rna and", "viral rna and a", "rna and a c", "and a c terminal regulatory", "a c terminal regulatory domain", "terminal regulatory domain rd", "domain rd that", "rd that prevents signaling", "that prevents signaling in the", "prevents signaling in the absence", "signaling in the absence of", "in the absence of viral", "the absence of viral rna.", "absence of viral rna. rig", "of viral rna. rig i", "viral rna. rig i and", "rna. rig i and mda5", "i and mda5 but", "and mda5 but not", "mda5 but not lgp2", "but not lgp2 also", "not lgp2 also encode", "lgp2 also encode two", "also encode two n terminal", "encode two n terminal caspase", "two n terminal caspase activation", "n terminal caspase activation and", "terminal caspase activation and recruitment", "caspase activation and recruitment domains", "and recruitment domains cards", "domains cards that", "cards that transmit the", "that transmit the signal by", "transmit the signal by binding", "the signal by binding to", "signal by binding to card", "by binding to card domain", "binding to card domain of", "to card domain of mitochondrial", "card domain of mitochondrial ifn", "domain of mitochondrial ifn beta", "of mitochondrial ifn beta promoter", "mitochondrial ifn beta promoter stimulator", "ifn beta promoter stimulator protein", "promoter stimulator protein ips", "stimulator protein ips 1", "ips 1 also known", "1 also known as", "known as mavs visa", "as mavs visa or", "mavs visa or cardif", "visa or cardif . this", "or cardif . this card", "cardif . this card card", "this card card interaction", "card card interaction leads", "card interaction leads to", "interaction leads to production of", "leads to production of ifn", "to production of ifn alpha/beta", "production of ifn alpha/beta and", "of ifn alpha/beta and pro", "ifn alpha/beta and pro inflammatory", "alpha/beta and pro inflammatory cytokines.", "and pro inflammatory cytokines. lgp2", "pro inflammatory cytokines. lgp2 that", "inflammatory cytokines. lgp2 that lacks", "cytokines. lgp2 that lacks card", "lgp2 that lacks card motifs", "that lacks card motifs but", "lacks card motifs but binds", "card motifs but binds viral", "motifs but binds viral rna", "but binds viral rna is", "binds viral rna is believed", "viral rna is believed to", "rna is believed to regulate", "is believed to regulate rlr", "believed to regulate rlr signaling", "regulate rlr signaling however", "rlr signaling however the", "signaling however the mechanism", "however the mechanism of the", "the mechanism of the regulation", "mechanism of the regulation remains", "of the regulation remains unclear", "regulation remains unclear lgp2", "remains unclear lgp2 was", "unclear lgp2 was reported", "lgp2 was reported to act", "was reported to act as", "reported to act as negative", "to act as negative regulator", "as negative regulator yoneyama", "negative regulator yoneyama et", "regulator yoneyama et al", "et al 2005 komuro", "al 2005 komuro and", "2005 komuro and horvath", "and horvath 2006 saito", "horvath 2006 saito et", "2006 saito et al", "al 2007 while", "2007 while other", "while other studies suggested that", "other studies suggested that lgp2", "studies suggested that lgp2 may", "suggested that lgp2 may cooperate", "that lgp2 may cooperate with", "lgp2 may cooperate with rig", "may cooperate with rig 1", "cooperate with rig 1 and", "with rig 1 and mda5", "rig 1 and mda5 in", "1 and mda5 in sensing", "and mda5 in sensing certain", "mda5 in sensing certain viral", "in sensing certain viral rna", "certain viral rna venkataraman", "viral rna venkataraman et", "rna venkataraman et al", "et al 2007 satoh", "al 2007 satoh et", "2007 satoh et al", "satoh et al 2010 .

primary", "et al 2010 .

primary chick", "al 2010 .

primary chick embryo", "2010 .

primary chick embryo cells", ".

primary chick embryo cells produced", "chick embryo cells produced ifn", "embryo cells produced ifn alpha", "cells produced ifn alpha in", "produced ifn alpha in response", "ifn alpha in response to", "alpha in response to newcastle", "in response to newcastle disease", "response to newcastle disease virus", "newcastle disease virus ndv", "virus ndv and", "ndv and produced both", "and produced both ifn alpfa", "produced both ifn alpfa and", "both ifn alpfa and ifn", "ifn alpfa and ifn beta", "alpfa and ifn beta in", "and ifn beta in response", "ifn beta in response to", "beta in response to vaccinia", "in response to vaccinia virus", "response to vaccinia virus or", "to vaccinia virus or influenza", "vaccinia virus or influenza a", "or influenza a shwartz", "influenza a shwartz h", "a shwartz h et", "shwartz h et al 2004", "h et al 2004 .", "et al 2004 . those", "al 2004 . those viruses", "2004 . those viruses have", ". those viruses have been", "those viruses have been reported", "viruses have been reported to", "have been reported to induce", "been reported to induce tlr3", "to induce tlr3 rig", "induce tlr3 rig 1", "tlr3 rig 1 and", "rig 1 and mda5 signaling", "1 and mda5 signaling in", "and mda5 signaling in mammals", "signaling in mammals delaloye", "in mammals delaloye j", "mammals delaloye j et", "delaloye j et al 2009", "et al 2009 kato", "al 2009 kato h", "2009 kato h et", "kato h et al 2006", "et al 2006 childs", "al 2006 childs et", "2006 childs et al", "childs et al 2007 .", "et al 2007 . although", "al 2007 . although rlr", "2007 . although rlr signaling", ". although rlr signaling is", "although rlr signaling is conserved", "rlr signaling is conserved among", "signaling is conserved among vertebrates", "is conserved among vertebrates sarkar", "conserved among vertebrates sarkar d", "among vertebrates sarkar d et", "vertebrates sarkar d et al", "sarkar d et al 2008", "et al 2008 zou", "al 2008 zou j", "2008 zou j et", "zou j et al 2009", "j et al 2009 and", "et al 2009 and feng", "al 2009 and feng h", "2009 and feng h et", "and feng h et al", "feng h et al 2011", "al 2011 analysis", "2011 analysis of", "analysis of chicken genome revealed", "of chicken genome revealed only", "chicken genome revealed only orthologs", "genome revealed only orthologs for", "revealed only orthologs for mammalian", "only orthologs for mammalian mda5", "orthologs for mammalian mda5 and", "for mammalian mda5 and lgp2", "mda5 and lgp2 while", "and lgp2 while rig", "lgp2 while rig 1", "while rig 1 gene was", "rig 1 gene was not", "1 gene was not identified", "was not identified sarkar", "not identified sarkar d", "identified sarkar d et", "al 2009 and barber", "2009 and barber mr", "and barber mr et al", "barber mr et al 2010", "mr et al 2010 ." ] }, { "record_id": "GLY_000968_1_35", "filename": "chicken_protein_pathways_reactome", "fieldtype": "id", "phraselist": [ "gly_000968", "gga", "1227888", "r gga", "gga 1227888", "r gga 1227888" ] }, { 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nf kb activation", "traf6 mediated nf kb activation", "although rlr", "rlr mediated", "mediated signaling", "signaling to", "to nfkb", "nfkb and", "and mapk", "mapk shares", "shares similarity", "similarity with", "with better", "better characterized", "characterized tlr", "tlr and", "and tnf", "tnf signaling", "signaling pathways", "many of", "of the", "the details", "details need", "need to", "to be", "be clarified.", "clarified. thus", "tgf beta", "beta activated", "activated kinase", "kinase 1", "1 tak1", "also known", "known as", "as map3k7", "an essential", "essential mediator", "mediator in", "in tlr", "tlr signaling", "signaling downstream", "downstream of", "of traf6", "was shown", "shown to", "to associate", "associate with", "with ips", "ips 1", "xu lg", "lg et", "et al", "al 2005", "2005 .", ". however", "there are", "are conflicting", "conflicting reports", "reports on", "on the", "the role", "role of", "of tak1", "tak1 in", "in rig", "rig 1/ips", "1/ips 1", "1 mediated", "mediated nfkb", "nfkb activation", "konno h", "h et", "al 2009", "yoshida r", "r et", "al 2008", "mikkelsen ss", "ss et", "2009 .", ".

another", "

another map3k", "has been", "been reported", "reported to", "to induce", "induce ikk", "ikk and", "mapk activation", "activation in", "in rig1", "rig1 signaling", "signaling pathway", "pathway in", "in response", "response to", "to dsrna.", "dsrna. yoshida", "2008 .", "although rlr mediated", "rlr mediated signaling", "mediated signaling to", "signaling to nfkb", "to nfkb and", "nfkb and mapk", "and mapk shares", "mapk shares similarity", "shares similarity with", "similarity with better", "with better characterized", "better characterized tlr", "characterized tlr and", "tlr and tnf", "and tnf signaling", "tnf signaling pathways", "pathways many", "many of the", "of the details", "the details need", "details need to", "need to be", "to be clarified.", "be clarified. thus", "thus tgf", "tgf beta activated", "beta activated kinase", "activated kinase 1", "kinase 1 tak1", "tak1 also", "also known as", "known as map3k7", "an essential mediator", "essential mediator in", "mediator in tlr", "in tlr signaling", "tlr signaling downstream", "signaling downstream of", "downstream of traf6", "traf6 was", "was shown to", "shown to associate", "to associate with", "associate with ips", "with ips 1", "1 xu", "xu lg et", "lg et al", "et al 2005", "al 2005 .", "2005 . however", "however there", "there are conflicting", "are conflicting reports", "conflicting reports on", "reports on the", "on the role", "the role of", "role of tak1", "of tak1 in", "tak1 in rig", "in rig 1/ips", "rig 1/ips 1", "1/ips 1 mediated", "1 mediated nfkb", "mediated nfkb activation", "activation konno", "konno h et", "h et al", "et al 2009", "2009 yoshida", "yoshida r et", "r et al", "et al 2008", "2008 mikkelsen", "mikkelsen ss et", "ss et al", "al 2009 .", "2009 .

another", ".

another map3k", "map3k mekk1", "mekk1 has", "has been reported", "been reported to", "reported to induce", "to induce ikk", "induce ikk and", "ikk and mapk", "and mapk activation", "mapk activation in", "activation in rig1", "in rig1 signaling", "rig1 signaling pathway", "signaling pathway in", "pathway in response", "in response to", "response to dsrna.", "to dsrna. yoshida", "dsrna. yoshida r", "al 2008 .", "although rlr mediated signaling", "rlr mediated signaling to", "mediated signaling to nfkb", "signaling to nfkb and", "to nfkb and mapk", "nfkb and mapk shares", "and mapk shares similarity", "mapk shares similarity with", "shares similarity with better", "similarity with better characterized", "with better characterized tlr", "better characterized tlr and", "characterized tlr and tnf", "tlr and tnf signaling", "and tnf signaling pathways", "signaling pathways many", "pathways many of", "many of the details", "of the details need", "the details need to", "details need to be", "need to be clarified.", "to be clarified. thus", "clarified. thus tgf", "thus tgf beta", "tgf beta activated kinase", "beta activated kinase 1", "activated kinase 1 tak1", "1 tak1 also", "tak1 also known", "also known as map3k7", "an essential mediator in", "essential mediator in tlr", "mediator in tlr signaling", "in tlr signaling downstream", "tlr signaling downstream of", "signaling downstream of traf6", "of traf6 was", "traf6 was shown", "was shown to associate", "shown to associate with", "to associate with ips", "associate with ips 1", "ips 1 xu", "1 xu lg", "xu lg et al", "lg et al 2005", "et al 2005 .", "al 2005 . however", ". however there", "however there are", "there are conflicting reports", "are conflicting reports on", "conflicting reports on the", "reports on the role", "on the role of", "the role of tak1", "role of tak1 in", "of tak1 in rig", "tak1 in rig 1/ips", "in rig 1/ips 1", "rig 1/ips 1 mediated", "1/ips 1 mediated nfkb", "1 mediated nfkb activation", "nfkb activation konno", "activation konno h", "konno h et al", "h et al 2009", "al 2009 yoshida", "2009 yoshida r", "yoshida r et al", "r et al 2008", "al 2008 mikkelsen", "2008 mikkelsen ss", "mikkelsen ss et al", "ss et al 2009", "et al 2009 .", "al 2009 .

another", "2009 .

another map3k", "

another map3k mekk1", "mekk1 has been", "has been reported to", "been reported to induce", "reported to induce ikk", "to induce ikk and", "induce ikk and mapk", "ikk and mapk activation", "and mapk activation in", "mapk activation in rig1", "activation in rig1 signaling", "in rig1 signaling pathway", "rig1 signaling pathway in", "signaling pathway in response", "pathway in response to", "in response to dsrna.", "response to dsrna. yoshida", "to dsrna. yoshida r", "dsrna. yoshida r et", "et al 2008 .", "although rlr mediated signaling to", "rlr mediated signaling to nfkb", "mediated signaling to nfkb and", "signaling to nfkb and mapk", "to nfkb and mapk shares", "nfkb and mapk shares similarity", "and mapk shares similarity with", "mapk shares similarity with better", "shares similarity with better characterized", "similarity with better characterized tlr", "with better characterized tlr and", "better characterized tlr and tnf", "characterized tlr and tnf signaling", "tlr and tnf signaling pathways", "tnf signaling pathways many", "signaling pathways many of", "pathways many of the", "many of the details need", "of the details need to", "the details need to be", "details need to be clarified.", "need to be clarified. thus", "be clarified. thus tgf", "clarified. thus tgf beta", "thus tgf beta activated", "tgf beta activated kinase 1", "beta activated kinase 1 tak1", "kinase 1 tak1 also", "1 tak1 also known", "tak1 also known as", "map3k7 an", "an essential mediator in tlr", "essential mediator in tlr signaling", "mediator in tlr signaling downstream", "in tlr signaling downstream of", "tlr signaling downstream of traf6", "downstream of traf6 was", "of traf6 was shown", "traf6 was shown to", "was shown to associate with", "shown to associate with ips", "to associate with ips 1", "with ips 1 xu", "ips 1 xu lg", "1 xu lg et", "xu lg et al 2005", "lg et al 2005 .", "et al 2005 . however", "2005 . however there", ". however there are", "however there are conflicting", "there are conflicting reports on", "are conflicting reports on the", "conflicting reports on the role", "reports on the role of", "on the role of tak1", "the role of tak1 in", "role of tak1 in rig", "of tak1 in rig 1/ips", "tak1 in rig 1/ips 1", "in rig 1/ips 1 mediated", "rig 1/ips 1 mediated nfkb", "1/ips 1 mediated nfkb activation", "mediated nfkb activation konno", "nfkb activation konno h", "activation konno h et", "konno h et al 2009", "et al 2009 yoshida", "al 2009 yoshida r", "2009 yoshida r et", "yoshida r et al 2008", "et al 2008 mikkelsen", "al 2008 mikkelsen ss", "2008 mikkelsen ss et", "mikkelsen ss et al 2009", "ss et al 2009 .", "et al 2009 .

another", "al 2009 .

another map3k", ".

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analysis of", "of genome", "genome data", "data revealed", "revealed that", "that mammals", "mammals and", "and aves", "aves seem", "seem to", "to share", "share practically", "practically the", "same set", "set of", "of complement", "complement genes", "nonaka m", "m and", "and kimura", "kimura a", "a 2006", "2006 .", ". indeed", "most of", "the components", "components of", "classical and", "alternative complement", "pathways have", "been found", "found in", "the chicken", "chicken genome.", "genome. however", "an absence", "absence of", "of some", "some components", "components such", "such as", "as chicken", "chicken c9", "factor d", "masp 1", "1 has", "has been", "been also", "also reported", "barta o", "o and", "and hubbert", "hubbert nl", "nl 1978", "lynch et", "koch c", "c 1986", "mikrou a", "a and", "and zarkadis", "zarkadis ik.", "ik. 2010", "2010 .", ". in", "in this", "this project", "project we", "we assume", "assume that", "that antimicrobial", "antimicrobial functions", "functions of", "of chicken", "chicken complement", "complement are", "are similar", "similar to", "to those", "those of", "of human", "although the", "the mechanism", "mechanism of", "activation remains", "remains to", "to be", "be clarified.

this", "clarified.

this reactome", "reactome module", "module refers", "refers to", "to the", "the larger", "larger complement", "complement fragments", "fragments as", "as \\b\\", "\\b\\ and", "and the", "the smaller", "smaller \\a\\", "based on", "the nomenclature", "nomenclature of", "complement proteins", "proteins .", "the complement system", "complement system is", "system is the", "is the first", "the first line", "first line of", "line of defense", "of defense against", "defense against invading", "against invading microbes.", "invading microbes. it", "microbes. it consists", "it consists of", "consists of a", "of a large", "a large number", "large number of", "number of distinct", "of distinct proteins", "proteins which", "which circulate in", "circulate in the", "in the blood", "the blood stream", "blood stream in", "stream in functionally", "in functionally inactive", "functionally inactive states.", "inactive states. when", "states. when activated", "activated complement", "complement components assemble", "components assemble on", "assemble on the", "on the surface", "the surface of", "surface of a", "of a target", "a target cell.", "target cell. the", "cell. the activation", "the activation of", "activation of one", "of one component", "one component induces", "component induces its", "induces its proteolytic", "its proteolytic function", "proteolytic function that", "function that acts", "that acts on", "acts on the", "on the next", "the next component", "next component in", "component in the", "in the cascade", "cascade cleaving", "cleaving it into", "it into biologically", "into biologically active", "biologically active fragments.", "active fragments. in", "fragments. in mammals", "mammals the", "system is activated", "is activated via", "activated via three", "via three distinct", "three distinct pathways:", "distinct pathways: the", "pathways: the classical", "classical lectin", "lectin and alternative", "and alternative pathways.", "alternative pathways. all", "pathways. all three", "all three pathways", "three pathways merge", "pathways merge at", "merge at the", "at the proteolytic", "the proteolytic cleavage", "proteolytic cleavage of", "cleavage of component", "of component c3", "component c3 to", "c3 to form", "to form the", "form the key", "the key molecule", "key molecule c3b.", "molecule c3b. the", "c3b. the activation", "activation of the", "of the complement", "complement system leads", "system leads to", "leads to four", "to four principal", "four principal outcomes:", "outcomes: 1", "1 opsonization", "opsonization of target", "of target cells", "target cells to", "cells to enhance", "to enhance phagocytosis", "phagocytosis 2", "2 lysis", "lysis of target", "target cells via", "cells via an", "via an assembly", "an assembly of", "assembly of the", "of the membrane", "the membrane attack", "membrane attack complex", "complex mac", "mac on", "on the pathogen", "the pathogen surface", "surface 3", "3 production", "production of anaphylatoxins", "of anaphylatoxins that", "anaphylatoxins that are", "that are involved", "are involved in", "involved in the", "in the host", "the host inflammatory", "host inflammatory response", "response 4", "4 clearance", "clearance of antibody", "of antibody antigen", "antibody antigen complexes.

avian", "antigen complexes.

avian species", "species chicken", "chicken turkey", "turkey and duck", "duck have", "have been reported", "been reported to", "reported to induce", "to induce functional", "induce functional complement", "functional complement pathways", "complement pathways in", "pathways in response", "in response to", "response to immunization", "to immunization with", "immunization with sheep", "with sheep red", "sheep red blood", "red blood cells", "cells srbc", "ellis mg et", "mg et al", "et al 1989", "1989 koppenheffer", "koppenheffer tl et", "tl et al", "et al 1999", "1999 baelmans", "baelmans r et", "r et al", "et al 2005", "al 2005 .", "2005 . complement", ". complement activation", "complement activation in", "activation in chicken", "in chicken was", "chicken was also", "was also shown", "also shown to", "shown to mediate", "to mediate host", "mediate host response", "host response against", "response against bacterial", "against bacterial and", "bacterial and viral", "and viral infections", "infections skeeles", "skeeles jk et", "jk et al", "et al 1979a", "1979a b", "b ohta", "ohta h et", "h et al", "et al 1983", "1983 laursen", "laursen sb and", "sb and nielsen", "and nielsen ol", "nielsen ol 2000", "ol 2000 .", "2000 . immune", ". immune competence", "immune competence of", "competence of the", "of the distinct", "the distinct chicken", "distinct chicken ecotypes", "chicken ecotypes was", "ecotypes was assessed", "was assessed by", "assessed by measuring", "by measuring complement", "measuring complement hemolytic", "complement hemolytic activity", "hemolytic activity after", "activity after immunization", "after immunization with", "immunization with srbc", "srbc baelmans", "et al 2004", "2004 baelmans", "2005 . both", ". both classical", "both classical ca2+", "classical ca2+ dependent", "ca2+ dependent complement", "dependent complement pathway", "pathway cpw", "cpw and", "and alternative calcium", "alternative calcium independent", "calcium independent complement", "independent complement pathway", "pathway apw", "as well as", "well as total", "as total ig", "ig igg", "igg and igm", "and igm antibody", "antibody responses", "responses were detected.", "were detected. however", "however the", "the type and", "type and magnitude", "and magnitude of", "magnitude of immune", "of immune response", "immune response varied", "response varied for", "varied for individual", "for individual chickens", "individual chickens even", "chickens even within", "even within the", "within the same", "the same ecotype.

analysis", "same ecotype.

analysis of", "ecotype.

analysis of genome", "of genome data", "genome data revealed", "data revealed that", "revealed that mammals", "that mammals and", "mammals and aves", "and aves seem", "aves seem to", "seem to share", "to share practically", "share practically the", "practically the same", "the same set", "same set of", "set of complement", "of complement genes", "genes nonaka", "nonaka m and", "m and kimura", "and kimura a", "kimura a 2006", "a 2006 .", "2006 . indeed", "indeed most", "most of the", "of the components", "the components of", "components of the", "of the classical", "the classical and", "classical and alternative", "and alternative complement", "alternative complement pathways", "complement pathways have", "pathways have been", "have been found", "been found in", "found in the", "in the chicken", "the chicken genome.", "chicken genome. however", "however an", "an absence of", "absence of some", "of some components", "some components such", "components such as", "such as chicken", "as chicken c9", "c9 factor", "d properdin", "properdin masp", "masp 1 has", "1 has been", "has been also", "been also reported", "reported barta", "barta o and", "o and hubbert", "and hubbert nl", "hubbert nl 1978", "1978 lynch", "lynch et al", "2005 koch", "koch c 1986", "1986 mikrou", "mikrou a and", "a and zarkadis", "and zarkadis ik.", "zarkadis ik. 2010", "ik. 2010 .", "2010 . in", ". in this", "in this project", "this project we", "project we assume", "we assume that", "assume that antimicrobial", "that antimicrobial functions", "antimicrobial functions of", "functions of chicken", "of chicken complement", "chicken complement are", "complement are similar", "are similar to", "similar to those", "to those of", "those of human", "human although", "although the mechanism", "the mechanism of", "mechanism of the", "of the chicken", "the chicken complement", "chicken complement activation", "complement activation remains", "activation remains to", "remains to be", "to be clarified.

this", "be clarified.

this reactome", "clarified.

this reactome module", "reactome module refers", "module refers to", "refers to the", "to the larger", "the larger complement", "larger complement fragments", "complement fragments as", "fragments as \\b\\", "as \\b\\ and", "\\b\\ and the", "and the smaller", "the smaller \\a\\", "\\a\\ based", "based on the", "on the nomenclature", "the nomenclature of", "nomenclature of the", "the complement proteins", "complement proteins .", "the complement system is", "complement system is the", "system is the first", "is the first line", "the first line of", "first line of defense", "line of defense against", "of defense against invading", "defense against invading microbes.", "against invading microbes. it", "invading microbes. it consists", "microbes. it consists of", "it consists of a", "consists of a large", "of a large number", "a large number of", "large number of distinct", "number of distinct proteins", "distinct proteins which", "proteins which circulate", "which circulate in the", "circulate in the blood", "in the blood stream", "the blood stream in", "blood stream in functionally", "stream in functionally inactive", "in functionally inactive states.", "functionally inactive states. when", "inactive states. when activated", "when activated complement", "activated complement components", "complement components assemble on", "components assemble on the", "assemble on the surface", "on the surface of", "the surface of a", "surface of a target", "of a target cell.", "a target cell. the", "target cell. the activation", "cell. the activation of", "the activation of one", "activation of one component", "of one component induces", "one component induces its", "component induces its proteolytic", "induces its proteolytic function", "its proteolytic function that", "proteolytic function that acts", "function that acts on", "that acts on the", "acts on the next", "on the next component", "the next component in", "next component in the", "component in the cascade", "the cascade cleaving", "cascade cleaving it", "cleaving it into biologically", "it into biologically active", "into biologically active fragments.", "biologically active fragments. in", "active fragments. in mammals", "in mammals the", "mammals the complement", "complement system is activated", "system is activated via", "is activated via three", "activated via three distinct", "via three distinct pathways:", "three distinct pathways: the", "distinct pathways: the classical", "the classical lectin", "classical lectin and", "lectin and alternative pathways.", "and alternative pathways. all", "alternative pathways. all three", "pathways. all three pathways", "all three pathways merge", "three pathways merge at", "pathways merge at the", "merge at the proteolytic", "at the proteolytic cleavage", "the proteolytic cleavage of", "proteolytic cleavage of component", "cleavage of component c3", "of component c3 to", "component c3 to form", "c3 to form the", "to form the key", "form the key molecule", "the key molecule c3b.", "key molecule c3b. the", "molecule c3b. the activation", "c3b. the activation of", "the activation of the", "activation of the complement", "of the complement system", "the complement system leads", "complement system leads to", "system leads to four", "leads to four principal", "to four principal outcomes:", "principal outcomes: 1", "1 opsonization of", "opsonization of target cells", "of target cells to", "target cells to enhance", "cells to enhance phagocytosis", "enhance phagocytosis 2", "2 lysis of", "lysis of target cells", "of target cells via", "target cells via an", "cells via an assembly", "via an assembly of", "an assembly of the", "assembly of the membrane", "of the membrane attack", "the membrane attack complex", "attack complex mac", "mac on the", "on the pathogen surface", "pathogen surface 3", "3 production of", "production of anaphylatoxins that", "of anaphylatoxins that are", "anaphylatoxins that are involved", "that are involved in", "are involved in the", "involved in the host", "in the host inflammatory", "the host inflammatory response", "inflammatory response 4", "4 clearance of", "clearance of antibody antigen", "of antibody antigen complexes.

avian", "antibody antigen complexes.

avian species", "complexes.

avian species chicken", "chicken turkey and", "and duck have", "duck have been", "have been reported to", "been reported to induce", "reported to induce functional", "to induce functional complement", "induce functional complement pathways", "functional complement pathways in", "complement pathways in response", "pathways in response to", "in response to immunization", "response to immunization with", "to immunization with sheep", "immunization with sheep red", "with sheep red blood", "sheep red blood cells", "blood cells srbc", "srbc ellis", "ellis mg et al", "mg et al 1989", "al 1989 koppenheffer", "1989 koppenheffer tl", "koppenheffer tl et al", "tl et al 1999", "al 1999 baelmans", "1999 baelmans r", "baelmans r et al", "r et al 2005", "et al 2005 .", "al 2005 . complement", "2005 . complement activation", ". complement activation in", "complement activation in chicken", "activation in chicken was", "in chicken was also", "chicken was also shown", "was also shown to", "also shown to mediate", "shown to mediate host", "to mediate host response", "mediate host response against", "host response against bacterial", "response against bacterial and", "against bacterial and viral", "bacterial and viral infections", "viral infections skeeles", "infections skeeles jk", "skeeles jk et al", "jk et al 1979a", "al 1979a b", "b ohta h", "ohta h et al", "h et al 1983", "al 1983 laursen", "1983 laursen sb", "laursen sb and nielsen", "sb and nielsen ol", "and nielsen ol 2000", "nielsen ol 2000 .", "ol 2000 . immune", "2000 . immune competence", ". immune competence of", "immune competence of the", "competence of the distinct", "of the distinct chicken", "the distinct chicken ecotypes", "distinct chicken ecotypes was", "chicken ecotypes was assessed", "ecotypes was assessed by", "was assessed by measuring", "assessed by measuring complement", "by measuring complement hemolytic", "measuring complement hemolytic activity", "complement hemolytic activity after", "hemolytic activity after immunization", "activity after immunization with", "after immunization with srbc", "with srbc baelmans", "srbc baelmans r", "r et al 2004", "al 2004 baelmans", "2004 baelmans r", "al 2005 . both", "2005 . both classical", ". both classical ca2+", "both classical ca2+ dependent", "classical ca2+ dependent complement", "ca2+ dependent complement pathway", "complement pathway cpw", "cpw and alternative", "and alternative calcium independent", "alternative calcium independent complement", "calcium independent complement pathway", "complement pathway apw", "apw as", "as well as total", "well as total ig", "total ig igg", "ig igg and", "igg and igm antibody", "igm antibody responses", "antibody responses were", "responses were detected. however", "detected. however the", "however the type", "the type and magnitude", "type and magnitude of", "and magnitude of immune", "magnitude of immune response", "of immune response varied", "immune response varied for", "response varied for individual", "varied for individual chickens", "for individual chickens even", "individual chickens even within", "chickens even within the", "even within the same", "within the same ecotype.

analysis", "the same ecotype.

analysis of", "same ecotype.

analysis of genome", "ecotype.

analysis of genome data", "of genome data revealed", "genome data revealed that", "data revealed that mammals", "revealed that mammals and", "that mammals and aves", "mammals and aves seem", "and aves seem to", "aves seem to share", "seem to share practically", "to share practically the", "share practically the same", "practically the same set", "the same set of", "same set of complement", "set of complement genes", "complement genes nonaka", "genes nonaka m", "nonaka m and kimura", "m and kimura a", "and kimura a 2006", "kimura a 2006 .", "a 2006 . indeed", ". indeed most", "indeed most of", "most of the components", "of the components of", "the components of the", "components of the classical", "of the classical and", "the classical and alternative", "classical and alternative complement", "and alternative complement pathways", "alternative complement pathways have", "complement pathways have been", "pathways have been found", "have been found in", "been found in the", "found in the chicken", "in the chicken genome.", "the chicken genome. however", "genome. however an", "however an absence", "an absence of some", "absence of some components", "of some components such", "some components such as", "components such as chicken", "such as chicken c9", "chicken c9 factor", "c9 factor d", "factor d properdin", "properdin masp 1", "masp 1 has been", "1 has been also", "has been also reported", "also reported barta", "reported barta o", "barta o and hubbert", "o and hubbert nl", "and hubbert nl 1978", "nl 1978 lynch", "1978 lynch et", "lynch et al 2005", "al 2005 koch", "2005 koch c", "c 1986 mikrou", "1986 mikrou a", "mikrou a and zarkadis", "a and zarkadis ik.", "and zarkadis ik. 2010", "zarkadis ik. 2010 .", "ik. 2010 . in", "2010 . in this", ". in this project", "in this project we", "this project we assume", "project we assume that", "we assume that antimicrobial", "assume that antimicrobial functions", "that antimicrobial functions of", "antimicrobial functions of chicken", "functions of chicken complement", "of chicken complement are", "chicken complement are similar", "complement are similar to", "are similar to those", "similar to those of", "to those of human", "of human although", "human although the", "although the mechanism of", "the mechanism of the", "mechanism of the chicken", "of the chicken complement", "the chicken complement activation", "chicken complement activation remains", "complement activation remains to", "activation remains to be", "remains to be clarified.

this", "to be clarified.

this reactome", "be clarified.

this reactome module", "clarified.

this reactome module refers", "reactome module refers to", "module refers to the", "refers to the larger", "to the larger complement", "the larger complement fragments", "larger complement fragments as", "complement fragments as \\b\\", "fragments as \\b\\ and", "as \\b\\ and the", "\\b\\ and the smaller", "and the smaller \\a\\", "smaller \\a\\ based", "\\a\\ based on", "based on the nomenclature", "on the nomenclature of", "the nomenclature of the", "nomenclature of the complement", "of the complement proteins", "the complement proteins .", "the complement system is the", "complement system is the first", "system is the first line", "is the first line of", "the first line of defense", "first line of defense against", "line of defense against invading", "of defense against invading microbes.", "defense against invading microbes. it", "against invading microbes. it consists", "invading microbes. it consists of", "microbes. it consists of a", "it consists of a large", "consists of a 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pathways: the classical", "pathways: the classical lectin", "the classical lectin and", "classical lectin and alternative", "lectin and alternative pathways. all", "and alternative pathways. all three", "alternative pathways. all three pathways", "pathways. all three pathways merge", "all three pathways merge at", "three pathways merge at the", "pathways merge at the proteolytic", "merge at the proteolytic cleavage", "at the proteolytic cleavage of", "the proteolytic cleavage of component", "proteolytic cleavage of component c3", "cleavage of component c3 to", "of component c3 to form", "component c3 to form the", "c3 to form the key", "to form the key molecule", "form the key molecule c3b.", "the key molecule c3b. the", "key molecule c3b. the activation", "molecule c3b. the activation of", "c3b. the activation of the", "the activation of the complement", "activation of the complement system", "of the complement system leads", "the complement system leads to", "complement system leads to four", "system leads to four principal", "leads to four principal outcomes:", "four principal outcomes: 1", "outcomes: 1 opsonization", "1 opsonization of target", "opsonization of target cells to", "of target cells to enhance", "target cells to enhance phagocytosis", "to enhance phagocytosis 2", "phagocytosis 2 lysis", "2 lysis of target", "lysis of target cells via", "of target cells via an", "target cells via an assembly", "cells via an assembly of", "via an assembly of the", "an assembly of the membrane", "assembly of the membrane attack", "of the membrane attack complex", "membrane attack complex mac", "complex mac on", "mac on the pathogen", "the pathogen surface 3", "surface 3 production", "3 production of anaphylatoxins", "production of anaphylatoxins that are", "of anaphylatoxins that are involved", "anaphylatoxins that are involved in", "that are involved in the", "are involved in the host", "involved in the host inflammatory", "in the host inflammatory response", "host inflammatory response 4", "response 4 clearance", "4 clearance of antibody", "clearance of antibody antigen complexes.

avian", "of antibody antigen complexes.

avian species", "antigen complexes.

avian species chicken", "species chicken turkey", "chicken turkey and duck", "turkey and duck have", "and duck have been", "duck have been reported", "have been reported to induce", "been reported to induce functional", "reported to induce functional complement", "to induce functional complement pathways", "induce functional complement pathways in", "functional complement pathways in response", "complement pathways in response to", "pathways in response to immunization", "in response to immunization with", "response to immunization with sheep", "to immunization with sheep red", "immunization with sheep red blood", "with sheep red blood cells", "red blood cells srbc", "srbc ellis mg", "ellis mg et al 1989", "et al 1989 koppenheffer", "al 1989 koppenheffer tl", "1989 koppenheffer tl et", "koppenheffer tl et al 1999", "et al 1999 baelmans", "al 1999 baelmans r", "1999 baelmans r et", "baelmans r et al 2005", "r et al 2005 .", "et al 2005 . complement", "al 2005 . complement activation", "2005 . complement activation in", ". complement activation in chicken", "complement activation in chicken was", "activation in chicken was also", "in chicken was also shown", "chicken was also shown to", "was also shown to mediate", "also shown to mediate host", "shown to mediate host response", "to mediate host response against", "mediate host response against bacterial", "host response against bacterial and", "response against bacterial and viral", "against bacterial and viral infections", "and viral infections skeeles", "viral infections skeeles jk", "infections skeeles jk et", "skeeles jk et al 1979a", "et al 1979a b", "1979a b ohta", "b ohta h et", "ohta h et al 1983", "et al 1983 laursen", "al 1983 laursen sb", "1983 laursen sb and", "laursen sb and nielsen ol", "sb and nielsen ol 2000", "and nielsen ol 2000 .", "nielsen ol 2000 . immune", "ol 2000 . immune competence", "2000 . immune competence of", ". immune competence of the", "immune competence of the distinct", "competence of the distinct chicken", "of the distinct chicken ecotypes", "the distinct chicken ecotypes was", "distinct chicken ecotypes was assessed", "chicken ecotypes was assessed by", "ecotypes was assessed by measuring", "was assessed by measuring complement", "assessed by measuring complement hemolytic", "by measuring complement hemolytic activity", "measuring complement hemolytic activity after", "complement hemolytic activity after immunization", "hemolytic activity after immunization with", "activity after immunization with srbc", "immunization with srbc baelmans", "with srbc baelmans r", "srbc baelmans r et", "baelmans r et al 2004", "et al 2004 baelmans", "al 2004 baelmans r", "2004 baelmans r et", "et al 2005 . both", "al 2005 . both classical", "2005 . both classical ca2+", ". both classical ca2+ dependent", "both classical ca2+ dependent complement", "classical ca2+ dependent complement pathway", "dependent complement pathway cpw", "pathway cpw and", "cpw and alternative calcium", "and alternative calcium independent complement", "alternative calcium independent complement pathway", "independent complement pathway apw", "apw as well", "as well as total ig", "as total ig igg", "total ig igg and", "ig igg and igm", "and igm antibody responses", "igm antibody responses were", "antibody responses were detected.", "were detected. however the", "detected. however the type", "however the type and", "the type and magnitude of", "type and magnitude of immune", "and magnitude of immune response", "magnitude of immune response varied", "of immune response varied for", "immune response varied for individual", "response varied for individual chickens", "varied for individual chickens even", "for individual chickens even within", "individual chickens even within the", "chickens even within the same", "even within the same ecotype.

analysis", "within the same ecotype.

analysis of", "the same ecotype.

analysis of genome", "same ecotype.

analysis of genome data", "ecotype.

analysis of genome data revealed", "of genome data revealed that", "genome data revealed that mammals", "data revealed that mammals and", "revealed that mammals and aves", "that mammals and aves seem", "mammals and aves seem to", "and aves seem to share", "aves seem to share practically", "seem to share practically the", "to share practically the same", "share practically the same set", "practically the same set of", "the same set of complement", "same set of complement genes", "of complement genes nonaka", "complement genes nonaka m", "genes nonaka m and", "nonaka m and kimura a", "m and kimura a 2006", "and kimura a 2006 .", "kimura a 2006 . indeed", "2006 . indeed most", ". indeed most of", "indeed most of the", "most of the components of", "of the components of the", "the components of the classical", "components of the classical and", "of the classical and alternative", "the classical and alternative complement", "classical and alternative complement pathways", "and alternative complement pathways have", "alternative complement pathways have been", "complement pathways have been found", "pathways have been found in", "have been found in the", "been found in the chicken", "found in the chicken genome.", "in the chicken genome. however", "chicken genome. however an", "genome. however an absence", "however an absence of", "an absence of some components", "absence of some components such", "of some components such as", "some components such as chicken", "components such as chicken c9", "as chicken c9 factor", "chicken c9 factor d", "d properdin masp", "properdin masp 1 has", "masp 1 has been also", "1 has been also reported", "been also reported barta", "also reported barta o", "reported barta o and", "barta o and hubbert nl", "o and hubbert nl 1978", "hubbert nl 1978 lynch", "nl 1978 lynch et", "1978 lynch et al", "et al 2005 koch", "al 2005 koch c", "2005 koch c 1986", "koch c 1986 mikrou", "c 1986 mikrou a", "1986 mikrou a and", "mikrou a and zarkadis ik.", "a and zarkadis ik. 2010", "and zarkadis ik. 2010 .", "zarkadis ik. 2010 . in", "ik. 2010 . in this", "2010 . in this project", ". in this project we", "in this project we assume", "this project we assume that", "project we assume that antimicrobial", "we assume that antimicrobial functions", "assume that antimicrobial functions of", "that antimicrobial functions of chicken", "antimicrobial functions of chicken complement", "functions of chicken complement are", "of chicken complement are similar", "chicken complement are similar to", "complement are similar to those", "are similar to those of", "similar to those of human", "those of human although", "of human although the", "human although the mechanism", "although the mechanism of the", "the mechanism of the chicken", "mechanism of the chicken complement", "of the chicken complement activation", "the chicken complement activation remains", "chicken complement activation remains to", "complement activation remains to be", "activation remains to be clarified.

this", "remains to be clarified.

this reactome", "to be clarified.

this reactome module", "be clarified.

this reactome module refers", "clarified.

this reactome module refers to", "reactome module refers to the", "module refers to the larger", "refers to the larger complement", "to the larger complement fragments", "the larger complement fragments as", "larger complement fragments as \\b\\", "complement fragments as \\b\\ and", "fragments as \\b\\ and the", "as \\b\\ and the smaller", "\\b\\ and the smaller \\a\\", "the smaller \\a\\ based", "smaller \\a\\ based on", "\\a\\ based on the", "based on the nomenclature of", "on the nomenclature of the", "the nomenclature of the complement", "nomenclature of the complement proteins", "of the complement proteins ." ] }, { "record_id": "GLY_000968_1_255", "filename": "chicken_protein_pathways_reactome", "fieldtype": "id", "phraselist": [ "gly_000968", "gga", "2132286", "r gga", "gga 2132286", "r gga 2132286" ] }, { "record_id": "GLY_000968_1_255", "filename": "chicken_protein_pathways_reactome", "fieldtype": "text", "phraselist": [ "classical antibody", "antibody mediated", "mediated 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"target cell", "cell surface.", "surface. the", "complex then", "then cleaves", "cleaves and", "and activates", "activates c2", "c2 which", "which has", "has bound", "bound to", "to c4b", "yielding a", "a c4b:c2a", "c4b:c2a complex", "c3 convertase", "convertase .", ". c3", "in turn", "cleaves the", "the third", "third component", "component of", "complement c3", "c3 to", "form c3a", "c3a and", "and c3b.", "c3b. a", "a single", "single c3", "convertase can", "can generate", "generate hundreds", "hundreds molecules", "molecules of", "of c3b", "which can", "can directly", "directly bind", "to the", "the target", "target surface.", "surface. opsonization", "opsonization with", "with c3b", "c3b fragments", "fragments mark", "mark the", "cell for", "for phagocytosis.", "phagocytosis. c3b", "c3b can", "can also", "also bind", "the c3", "convertase yielding", "yielding c5", "c5 convertase", "which cleaves", "cleaves c5", "c5 into", "into c5a", "c5a and", "and c5b.", "c5b. c5b", "c5b is", "is 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"formation janeway", "janeway ca et", "ca et al.", "et al. 2001", "al. 2001 .", "in mammals the", "mammals the classical", "the classical pathway is", "classical pathway is initiated", "pathway is initiated by", "is initiated by binding", "initiated by binding of", "by binding of antibody", "binding of antibody molecules", "antibody molecules igm", "molecules igm or", "or igg to", "igg to an", "an antigen followed", "antigen followed by", "followed by binding of", "by binding of complement", "binding of complement protein", "of complement protein c1q.", "complement protein c1q. two", "protein c1q. two molecules", "c1q. two molecules each", "two molecules each of", "molecules each of c1r", "each of c1r and", "of c1r and c1s", "c1r and c1s bind", "and c1s bind to", "c1s bind to c1q", "bind to c1q to", "to c1q to form", "c1q to form an", "to form an active", "form an active c1", "an active c1 complex.", "active c1 complex. the", "c1 complex. the activated", "complex. the activated c1", 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c3b", "for phagocytosis. c3b can", "phagocytosis. c3b can also", "c3b can also bind", "can also bind to", "also bind to the", "bind to the c3", "to the c3 convertase", "the c3 convertase yielding", "c3 convertase yielding c5", "convertase yielding c5 convertase", "c5 convertase c4b:c2a:c3b", "c4b:c2a:c3b which", "which cleaves c5 into", "cleaves c5 into c5a", "c5 into c5a and", "into c5a and c5b.", "c5a and c5b. c5b", "and c5b. c5b is", "c5b. c5b is an", "c5b is an active", "is an active fragment", "an active fragment which", "active fragment which initiates", "fragment which initiates a", "which initiates a membrane", "initiates a membrane attack", "a membrane attack complex", "attack complex mac", "formation janeway ca", "janeway ca et al.", "ca et al. 2001", "et al. 2001 .", "in mammals the classical", "mammals the classical pathway", "the classical pathway is initiated", "classical pathway is initiated by", "pathway is initiated by binding", "is initiated by binding of", "initiated 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"activated c1 complex cleaves c4", "c1 complex cleaves c4 to", "complex cleaves c4 to generate", "cleaves c4 to generate c4a", "c4 to generate c4a and", "to generate c4a and c4b.", "generate c4a and c4b. c4b", "c4a and c4b. c4b fragment", "and c4b. c4b fragment binds", "c4b. c4b fragment binds the", "c4b fragment binds the nearby", "fragment binds the nearby target", "binds the nearby target cell", "the nearby target cell surface.", "nearby target cell surface. the", "target cell surface. the activated", "cell surface. the activated c1", "surface. the activated c1 complex", "the activated c1 complex then", "activated c1 complex then cleaves", "c1 complex then cleaves and", "complex then cleaves and activates", "then cleaves and activates c2", "cleaves and activates c2 which", "and activates c2 which has", "activates c2 which has bound", "c2 which has bound to", "which has bound to c4b", "bound to c4b yielding", "to c4b yielding a", "c4b yielding a c4b:c2a", "a c4b:c2a complex c3", "c4b:c2a complex c3 convertase", "complex c3 convertase .", "c3 convertase . c3 convertase", ". c3 convertase in", "c3 convertase in turn", "in turn cleaves the", "turn cleaves the third", "cleaves the third component of", "the third component of complement", "third component of complement c3", "component of complement c3 to", "of complement c3 to form", "complement c3 to form c3a", "c3 to form c3a and", "to form c3a and c3b.", "form c3a and c3b. a", "c3a and c3b. a single", "and c3b. a single c3", "c3b. a single c3 convertase", "a single c3 convertase can", "single c3 convertase can generate", "c3 convertase can generate hundreds", "convertase can generate hundreds molecules", "can generate hundreds molecules of", "generate hundreds molecules of c3b", "molecules of c3b which", "of c3b which can", "c3b which can directly", "which can directly bind to", "can directly bind to the", "directly bind to the target", "bind to the target surface.", "to the target surface. opsonization", "the target surface. opsonization with", "target surface. opsonization with c3b", "surface. opsonization with c3b fragments", "opsonization with c3b fragments mark", "with c3b fragments mark the", "c3b fragments mark the target", "fragments mark the target cell", "mark the target cell for", "the target cell for phagocytosis.", "target cell for phagocytosis. c3b", "cell for phagocytosis. c3b can", "for phagocytosis. c3b can also", "phagocytosis. c3b can also bind", "c3b can also bind to", "can also bind to the", "also bind to the c3", "bind to the c3 convertase", "to the c3 convertase yielding", "the c3 convertase yielding c5", "c3 convertase yielding c5 convertase", "yielding c5 convertase c4b:c2a:c3b", "c4b:c2a:c3b which cleaves", "which cleaves c5 into c5a", "cleaves c5 into c5a and", "c5 into c5a and c5b.", "into c5a and c5b. c5b", "c5a and c5b. c5b is", "and c5b. c5b is an", "c5b. c5b is an active", "c5b is an active fragment", "is an active fragment which", "an active fragment which initiates", "active fragment which initiates a", "fragment which initiates a membrane", "which initiates a membrane attack", "initiates a membrane attack complex", "membrane attack complex mac", "complex mac formation", "mac formation janeway", "formation janeway ca et", "janeway ca et al. 2001", "ca et al. 2001 ." ] }, { "record_id": "GLY_000968_1_256", "filename": "chicken_protein_pathways_reactome", "fieldtype": "id", "phraselist": [ "gly_000968", "gga", "2132293", "r gga", "gga 2132293", "r gga 2132293" ] }, { "record_id": "GLY_000968_1_256", "filename": "chicken_protein_pathways_reactome", "fieldtype": "text", "phraselist": [ "formation of", "of fluid", "fluid phase", "phase convertase", "convertase c3", "formation of fluid", "of fluid phase", "fluid phase convertase", "phase convertase c3", "formation of fluid phase", "of fluid phase convertase", "fluid phase convertase c3", "formation of fluid phase convertase", "of fluid phase convertase c3", "in human", "small amounts", 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chicken", "

chicken factor", "b like", "like protease", "protease was", "was shown", "shown to", "to create", "create a", "a functional", "functional c3", "jensen lb", "lb &", "& koch", "koch c", "c 1991", "1991 .", ". although", "although an", "an orthologue", "orthologue of", "of human", "human factor", "d has", "has not", "not been", "been identified", "identified in", "the chicken", "chicken genome", "this chicken", "chicken module", "module describes", "describes a", "a cleavage", "cleavage of", "of factor", "protease as", "as an", "an essential", "essential step", "step of", "chicken alternative", "alternative complement", "complement pathway.", "human small", "small amounts of", "amounts of hydrolyzed", "of hydrolyzed c3", "c3 c3", "h20 or", "c3i are", "are continuously formed", "continuously formed in", "formed in the", "in the fluid", "the fluid phase", "fluid phase following", "phase following spontaneous", "following spontaneous hydrolysis", "spontaneous hydrolysis of", "hydrolysis of the", "of the internal", "the internal thioester", "internal thioester bond", "thioester bond of", "bond of c3.", "of c3. c3i", "c3. c3i can", "c3i can bind", "can bind to", "bind to factor", "to factor b", "factor b which", "which in", "turn is", "is cleaved by", "cleaved by factor", "by factor d", "factor d yielding", "d yielding an", "yielding an alternative", "an alternative fluid", "alternative fluid phase", "fluid phase c3", "phase c3 convertase", "convertase c3i:bb.", "c3i:bb.

chicken factor", "

chicken factor b", "factor b like", "b like protease", "like protease was", "protease was shown", "was shown to", "shown to create", "to create a", "create a functional", "a functional c3", "functional c3 convertase", "convertase jensen", "jensen lb &", "lb & koch", "& koch c", "koch c 1991", "c 1991 .", "1991 . although", ". although an", "although an orthologue", "an orthologue of", "orthologue of human", "of human factor", "human factor d", "factor d has", "d has not", "has not been", "not been identified", "been identified in", "identified in the", "in the chicken", "the chicken genome", "genome this", "this chicken module", "chicken module describes", "module describes a", "describes a cleavage", "a cleavage of", "cleavage of factor", "of factor b", "like protease as", "protease as an", "as an essential", "an essential step", "essential step of", "step of the", "of the chicken", "the chicken alternative", "chicken alternative complement", "alternative complement pathway.", "in human small", "human small amounts", "small amounts of hydrolyzed", "amounts of hydrolyzed c3", "hydrolyzed c3 c3", "c3 c3 h20", "c3 h20 or", "h20 or c3i", "or c3i are", "c3i are continuously", "are continuously formed in", "continuously formed in the", "formed in the fluid", "in the fluid phase", "the fluid phase following", "fluid phase following spontaneous", "phase following spontaneous hydrolysis", "following spontaneous hydrolysis of", "spontaneous hydrolysis of the", "hydrolysis of the internal", "of the internal thioester", "the internal thioester bond", "internal thioester bond of", "thioester bond of c3.", "bond of c3. c3i", "of c3. c3i can", "c3. c3i can bind", "c3i can bind to", "can bind to factor", "bind to factor b", "to factor b which", "b which in", "which in turn", "in turn is", "turn is cleaved", "is cleaved by factor", "cleaved by factor d", "by factor d yielding", "factor d yielding an", "d yielding an alternative", "yielding an alternative fluid", "an alternative fluid phase", "alternative fluid phase c3", "fluid phase c3 convertase", "c3 convertase c3i:bb.", "convertase c3i:bb.

chicken", "c3i:bb.

chicken factor b", "

chicken factor b like", "factor b like protease", "b like protease was", "like protease was shown", "protease was shown to", "was shown to create", "shown to create a", "to create a functional", "create a functional c3", "a functional c3 convertase", "c3 convertase jensen", "convertase jensen lb", "jensen lb & koch", "lb & koch c", "& koch c 1991", "koch c 1991 .", "c 1991 . although", "1991 . although an", ". although an orthologue", "although an orthologue of", "an orthologue of human", "orthologue of human factor", "of human factor d", "human factor d has", "factor d has not", "d has not been", "has not been identified", "not been identified in", "been identified in the", "identified in the chicken", "in the chicken genome", "chicken genome this", "genome this chicken", "this chicken module describes", "chicken module describes a", "module describes a cleavage", "describes a cleavage of", "a cleavage of factor", "cleavage of factor b", "of factor b like", "b like protease as", "like protease as an", "protease as an essential", "as an essential step", "an essential step of", "essential step of the", "step of the chicken", "of the chicken alternative", "the chicken alternative complement", "chicken alternative complement pathway.", "in human small amounts", "human small amounts of", "small amounts of hydrolyzed c3", "of hydrolyzed c3 c3", "hydrolyzed c3 c3 h20", "c3 h20 or c3i", "or c3i are continuously", "c3i are continuously formed", "are continuously formed in the", "continuously formed in the fluid", "formed in the fluid phase", "in the fluid phase following", "the fluid phase following spontaneous", "fluid phase following spontaneous hydrolysis", "phase following spontaneous hydrolysis of", "following spontaneous hydrolysis of the", "spontaneous hydrolysis of the internal", "hydrolysis of the internal thioester", "of the internal thioester bond", "the internal thioester bond of", "internal thioester bond of c3.", "thioester bond of c3. c3i", "bond of c3. c3i can", "of c3. c3i can bind", "c3. c3i can bind to", "c3i can bind to factor", "can bind to factor b", "bind to factor b which", "factor b which in", "b which in turn", "in turn is cleaved", "turn is cleaved by", "is cleaved by factor d", "cleaved by factor d yielding", "by factor d yielding an", "factor d yielding an alternative", "d yielding an alternative fluid", "yielding an alternative fluid phase", "an alternative fluid phase c3", "alternative fluid phase c3 convertase", "phase c3 convertase c3i:bb.", "c3 convertase c3i:bb.

chicken", "convertase c3i:bb.

chicken factor", "c3i:bb.

chicken factor b like", "

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in", "1990 .

in all", ".

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in", "of cytosolic reactions.

in the", "cytosolic reactions.

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in", "al. 1990 .

in all", "1990 .

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in", "one from gtp.

in the", "from gtp.

in the second", "gtp.

in the second part", "the second part of", "second part of gluconeogenesis", "of gluconeogenesis cytosolic", "gluconeogenesis cytosolic phosphoenolpyruvate", "cytosolic phosphoenolpyruvate however", "phosphoenolpyruvate however derived", "however derived is", "derived is converted", "is converted to fructose", "converted to fructose 1", "to fructose 1 6", "fructose 1 6 bisphosphate", "1 6 bisphosphate by", "6 bisphosphate by reactions", "bisphosphate by reactions that", "by reactions that are", "reactions that are the", "that are the reverse", "are the reverse of", "the reverse of steps", "reverse of steps of", "of steps of glycolysis.", "steps of glycolysis. hydrolysis", "of glycolysis. hydrolysis of", "glycolysis. hydrolysis of fructose", "hydrolysis of fructose 1", "of fructose 1 6", "1 6 bisphosphate to", "6 bisphosphate to fructose", "bisphosphate to fructose 6", "to fructose 6 phosphate", "fructose 6 phosphate is", "6 phosphate is catalyzed", "phosphate is catalyzed by", "is catalyzed by fructose", "catalyzed by fructose 1", "by fructose 1 6", "fructose 1 6 bisphosphatase", "6 bisphosphatase and", "bisphosphatase and fructose", "and fructose 6 phosphate", "6 phosphate is reversibly", "phosphate is reversibly isomerized", "is reversibly isomerized to", "reversibly isomerized to glucose", "isomerized to glucose 6", "to glucose 6 phosphate.", "the reactions of gluconeogenesis convert", "reactions of gluconeogenesis convert mitochondrial", "of gluconeogenesis convert mitochondrial pyruvate", "gluconeogenesis convert mitochondrial pyruvate to", "convert mitochondrial pyruvate to cytosolic", "mitochondrial pyruvate to cytosolic glucose", "pyruvate to cytosolic glucose 6", "to cytosolic glucose 6 phosphate", "cytosolic glucose 6 phosphate which", "glucose 6 phosphate which in", "6 phosphate which in turn", "phosphate which in turn can", "which in turn can be", "in turn can be hydrolyzed", "turn can be hydrolyzed to", "can be hydrolyzed to glucose", "be hydrolyzed to glucose and", "hydrolyzed to glucose and exported", "to glucose and exported from", "glucose and exported from the", "and exported from the cell.", "exported from the cell. gluconeogenesis", "from the cell. gluconeogenesis is", "the cell. gluconeogenesis is confined", "cell. gluconeogenesis is confined to", "gluconeogenesis is confined to cells", "is confined to cells of", "confined to cells of the", "to cells of the liver", "cells of the liver and", "of the liver and kidney", "the liver and kidney and", "liver and kidney and enables", "and kidney and enables glucose", "kidney and enables glucose synthesis", "and enables glucose synthesis from", "enables glucose synthesis from molecules", "glucose synthesis from molecules such", "synthesis from molecules such as", "from molecules such as lactate", "molecules such as lactate and", "such as lactate and alanine", "as lactate and alanine and", "lactate and alanine and other", "and alanine and other amino", "alanine and other amino acids", "and other amino acids when", "other amino acids when exogenous", "amino acids when exogenous glucose", "acids when exogenous glucose is", "when exogenous glucose is not", "exogenous glucose is not available.", "glucose is not available. the", "is not available. the process", "not available. the process of", "available. the process of gluconeogenesis", "the process of gluconeogenesis as", "process of gluconeogenesis as diagrammed", "of gluconeogenesis as diagrammed below", "gluconeogenesis as diagrammed below occurs", "as diagrammed below occurs in", "diagrammed below occurs in two", "below occurs in two parts:", "occurs in two parts: a", "in two parts: a network", "two parts: a network of", "parts: a network of possible", "a network of possible reactions", "network of possible reactions mediates", "of possible reactions mediates the", "possible reactions mediates the conversion", "reactions mediates the conversion of", "mediates the conversion of mitochondrial", "the conversion of mitochondrial pyruvate", "conversion of mitochondrial pyruvate to", "of mitochondrial pyruvate to cytosolic", "mitochondrial pyruvate to cytosolic phosphoenolpyruvate", "to cytosolic phosphoenolpyruvate which", "cytosolic phosphoenolpyruvate which in", "which in turn is converted", "in turn is converted to", "turn is converted to glucose", "is converted to glucose 6", "converted to glucose 6 phosphate", "to glucose 6 phosphate in", "glucose 6 phosphate in a", "6 phosphate in a single", "phosphate in a single sequence", "in a single sequence of", "a single sequence of cytosolic", "single sequence of cytosolic reactions.

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in the", "of cytosolic reactions.

in the chicken", "reactions.

in the chicken three", "the chicken three variants", "chicken three variants of", "three variants of the process", "variants of the process can", "of the process can be", "the process can be distinguished", "can be distinguished two", "be distinguished two restricted", "distinguished two restricted to", "two restricted to the kidney", "restricted to the kidney and", "to the kidney and one", "the kidney and one that", "kidney and one that takes", "and one that takes place", "one that takes place in", "that takes place in both", "takes place in both kidney", "place in both kidney and", "in both kidney and liver.", "both kidney and liver. 1", "and liver. 1 in", "liver. 1 in the", "1 in the kidney", "in the kidney carbon", "the kidney carbon atoms", "kidney carbon atoms from", "carbon atoms from mitochondrial oxaloacetate", "from mitochondrial oxaloacetate via", "mitochondrial oxaloacetate via a", "oxaloacetate via a series", "via a series of transport", "a series of transport and", "series of transport and transamination", "of transport and transamination reactions", "and transamination reactions are", "transamination reactions are used", "reactions are used to", "are used to generate cytosolic", "used to generate cytosolic oxaloacetate", "generate cytosolic oxaloacetate which", "cytosolic oxaloacetate which is", "oxaloacetate which is converted", "which is converted to phosphoenolpyruvate", "is converted to phosphoenolpyruvate by", "converted to phosphoenolpyruvate by a", "to phosphoenolpyruvate by a cytosolic", "by a cytosolic hormonally", "a cytosolic hormonally regulated", "cytosolic hormonally regulated form", "hormonally regulated form of phosphoenolpyruvate", "regulated form of phosphoenolpyruvate carboxykinase", "of phosphoenolpyruvate carboxykinase pck1.", "phosphoenolpyruvate carboxykinase pck1. this", "carboxykinase pck1. this variant", "pck1. this variant allows regulated", "this variant allows regulated glucose", "variant allows regulated glucose synthesis", "allows regulated glucose synthesis from", "regulated glucose synthesis from lactate.", "glucose synthesis from lactate. 2", "from lactate. 2 in", "lactate. 2 in the", "2 in the kidney", "in the kidney mitochondrial", "the kidney mitochondrial oxaloacetate", "kidney mitochondrial oxaloacetate is", "mitochondrial oxaloacetate is reduced to", "oxaloacetate is reduced to malate", "reduced to malate which", "to malate which is", "malate which is exported", "which is exported to the", "is exported to the cytosol", "exported to the cytosol and", "to the cytosol and re", "the cytosol and re oxidized", "cytosol and re oxidized to", "and re oxidized to oxaloacetate.", "re oxidized to oxaloacetate. this", "oxidized to oxaloacetate. this variant", "to oxaloacetate. this variant provides", "oxaloacetate. this variant provides reducing", "this variant provides reducing equivalents", "variant provides reducing equivalents to", "provides reducing equivalents to the", "reducing equivalents to the cytosol", "to the cytosol needed", "the cytosol needed for", "cytosol needed for glucose", "needed for glucose synthesis from", "for glucose synthesis from amino", "glucose synthesis from amino acids", "synthesis from amino acids such", "from amino acids such as", "amino acids such as alanine", "acids such as alanine and", "such as alanine and glutamine.", "as alanine and glutamine. 3", "and glutamine. 3 in", "glutamine. 3 in both", "3 in both liver", "in both liver and kidney", "liver and kidney constitutively", "and kidney constitutively expressed", "kidney constitutively expressed mitochondrial", "constitutively expressed mitochondrial phosphoenolpyruvate carboxykinase", "mitochondrial phosphoenolpyruvate carboxykinase pck2", "carboxykinase pck2 catalyzes", "pck2 catalyzes the conversion", "catalyzes the conversion of mitochondrial", "the conversion of mitochondrial oxaloacetate", "conversion of mitochondrial oxaloacetate to", "of mitochondrial oxaloacetate to phosphoenolpyruvate", "mitochondrial oxaloacetate to phosphoenolpyruvate which", "oxaloacetate to phosphoenolpyruvate which in", "to phosphoenolpyruvate which in turn", "phosphoenolpyruvate which in turn is", "which in turn is transported", "in turn is transported to", "turn is transported to the", "is transported to the cytosol.", "transported to the cytosol. this", "to the cytosol. this third", "the cytosol. this third variant", "cytosol. this third variant also", "this third variant also allows", "third variant also allows glucose", "variant also allows glucose synthesis", "also allows glucose synthesis from", "allows glucose synthesis from lactate", "synthesis from lactate soling", "from lactate soling et", "lactate soling et al.", "et al. 1973 wallace", "al. 1973 wallace and", "1973 wallace and newsholme", "and newsholme 1967 watford", "newsholme 1967 watford et", "1967 watford et al.", "et al. 1981 weldon", "al. 1981 weldon et", "1981 weldon et al.", "weldon et al. 1990 .

in", "et al. 1990 .

in all", "al. 1990 .

in all cases", ".

in all cases the", "all cases the metabolism", "cases the metabolism of", "the metabolism of a molecule", "metabolism of a molecule of", "of a molecule of pyruvate", "a molecule of pyruvate requires", "molecule of pyruvate requires the", "of pyruvate requires the generation", "pyruvate requires the generation and", "requires the generation and consumption", "the generation and consumption of", "generation and consumption of one", "and consumption of one reducing", "consumption of one reducing equivalent", "of one reducing equivalent as", "one reducing equivalent as cytosolic", "reducing equivalent as cytosolic nadh", "equivalent as cytosolic nadh +", "as cytosolic nadh + h+.", "cytosolic nadh + h+. for", "nadh + h+. for pyruvate", "+ h+. for pyruvate derived", "h+. for pyruvate derived from", "for pyruvate derived from lactate", "derived from lactate variants", "from lactate variants 1", "lactate variants 1 and", "and 3 nadh", "3 nadh +", "nadh + h+ is generated", "+ h+ is generated with", "h+ is generated with the", "is generated with the oxidation", "generated with the oxidation of", "with the oxidation of lactate", "the oxidation of lactate to", "oxidation of lactate to pyruvate", "of lactate to pyruvate in", "lactate to pyruvate in the", "to pyruvate in the cytosol", "in the cytosol a", "the cytosol a reaction", "cytosol a reaction of", "a reaction of pyruvate metabolism", "reaction of pyruvate metabolism not", "of pyruvate metabolism not shown", "pyruvate metabolism not shown in", "metabolism not shown in the", "not shown in the diagram", "shown in the diagram .", "in the diagram . for", "the diagram . for pyruvate", "diagram . for pyruvate derived", ". for pyruvate derived from", "for pyruvate derived from amino", "pyruvate derived from amino acids", "from amino acids variant", "amino acids variant 2", "variant 2 mitochondrial", "2 mitochondrial nadh", "mitochondrial nadh + h+ generated", "nadh + h+ generated by", "+ h+ generated by glutamate", "h+ generated by glutamate dehydrogenase", "by glutamate dehydrogenase a", "glutamate dehydrogenase a reaction", "dehydrogenase a reaction of", "a reaction of amino acid", "reaction of amino acid metabolism", "amino acid metabolism not", "acid metabolism not shown", "not shown is used", "shown is used to", "is used to reduce oxaloacetate", "used to reduce oxaloacetate to", "to reduce oxaloacetate to malate", "oxaloacetate to malate which", "malate which is transported", "which is transported to the", "is transported to the cytosol", "transported to the cytosol and", "and re oxidized generating", "re oxidized generating cytosolic", "oxidized generating cytosolic nadh", "generating cytosolic nadh + h+.", "cytosolic nadh + h+. the", "nadh + h+. the metabolism", "+ h+. the metabolism of", "h+. the metabolism of each", "the metabolism of each molecule", "metabolism of each molecule of", "of each molecule of pyruvate", "each molecule of pyruvate also", "molecule of pyruvate also requires", "of pyruvate also requires the", "pyruvate also requires the consumption", "also requires the consumption of", "requires the consumption of three", "the consumption of three high", "consumption of three high energy", "of three high energy phosphates", "high energy phosphates two", "energy phosphates two from", "phosphates two from atp", "two from atp and one", "from atp and one from", "atp and one from gtp.

in", "and one from gtp.

in the", "one from gtp.

in the second", "from gtp.

in the second part", "gtp.

in the second part of", "the second part of gluconeogenesis", "part of gluconeogenesis cytosolic", "of gluconeogenesis cytosolic phosphoenolpyruvate", "cytosolic phosphoenolpyruvate however derived", "however derived is converted", "derived is converted to", "is converted to fructose 1", "converted to fructose 1 6", "to fructose 1 6 bisphosphate", "fructose 1 6 bisphosphate by", "1 6 bisphosphate by reactions", "6 bisphosphate by reactions that", "bisphosphate by reactions that are", "by reactions that are the", "reactions that are the reverse", "that are the reverse of", "are the reverse of steps", "the reverse of steps of", "reverse of steps of glycolysis.", "of steps of glycolysis. hydrolysis", "steps of glycolysis. hydrolysis of", "of glycolysis. hydrolysis of fructose", "glycolysis. hydrolysis of fructose 1", "hydrolysis of fructose 1 6", "of fructose 1 6 bisphosphate", "fructose 1 6 bisphosphate to", "1 6 bisphosphate to fructose", "6 bisphosphate to fructose 6", "bisphosphate to 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damage", "error prone damage bypass", "prone damage bypass has", "damage bypass has been", "bypass has been identified.", "cell nuclear antigen pcna", "antigen pcna is", "pcna is a dna", "is a dna polymerase cofactor", "a dna polymerase cofactor and", "dna polymerase cofactor and regulator", "polymerase cofactor and regulator of", "cofactor and regulator of replication", "and regulator of replication linked", "regulator of replication linked functions.", "of replication linked functions. upon", "replication linked functions. upon dna", "linked functions. upon dna damage", "upon dna damage vertebrate", "dna damage vertebrate pcna", "damage vertebrate pcna is", "vertebrate pcna is modified at", "pcna is modified at the", "is modified at the conserved", "modified at the conserved k164", "at the conserved k164 residue", "the conserved k164 residue by", "conserved k164 residue by ubiquitin.", "k164 residue by ubiquitin. ubiquitinated", "residue by ubiquitin. ubiquitinated pcna", "by 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deamination", "transcription coupled cytidine deamination in", "coupled cytidine deamination in the", "cytidine deamination in the ig", "deamination in the ig loci.", "in the ig loci. rad6/rad18", "the ig loci. rad6/rad18 mediated", "ig loci. rad6/rad18 mediated ubiquitination", "loci. rad6/rad18 mediated ubiquitination of", "rad6/rad18 mediated ubiquitination of pcna", "ubiquitination of pcna thus", "pcna thus is", "thus is a major", "is a major regulatory point", "a major regulatory point controlling", "major regulatory point controlling the", "regulatory point controlling the fidelity", "point controlling the fidelity of", "controlling the fidelity of dna", "the fidelity of dna lesions", "fidelity of dna lesions for", "of dna lesions for immunoglobulin", "dna lesions for immunoglobulin hypermutation", "lesions for immunoglobulin hypermutation during", "for immunoglobulin hypermutation during the", "immunoglobulin hypermutation during the mutagenesis", "hypermutation during the 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the telomerase ribonucleoprotein complex", ".

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ruvbl1", "al. 2007 .

ruvbl1 pontin", ".

ruvbl1 pontin and", "ruvbl2 reptin are", "reptin are found associated", "are found associated with human", "found associated with human telomerase", "associated with human telomerase purified", "with human telomerase purified from", "human telomerase purified from hela", "telomerase purified from hela cells", "purified from hela cells and", "from hela cells and activities", "hela cells and activities of", "cells and activities of these", "and activities of these proteins", "activities of these proteins are", "of these proteins are required", "these proteins are required for", "proteins are required for telomerase", "are required for telomerase assembly", "required for telomerase assembly in", "for telomerase assembly in vitro", "assembly in vitro venteicher", "in vitro venteicher et", "vitro venteicher et al.", "venteicher et al. 2008 .", "et al. 2008 . their", "al. 2008 . their exact", "2008 . their exact roles", ". their exact roles in", "their exact roles in the", "exact roles in the assembly", "roles in the assembly and", "in the assembly and function", "the assembly and function of", "assembly and function of in", "and function of in vivo", "function of in vivo telomerase", "of in vivo telomerase remain", "in vivo telomerase remain unclear.", "vivo telomerase remain unclear. a", "telomerase remain unclear. a potential", "remain unclear. a potential chicken", "unclear. a potential chicken ortholog", "a potential chicken ortholog for", "potential chicken ortholog for ruvbl1", "ortholog for ruvbl1 pontin", "ruvbl1 pontin has", "pontin has been identified.

nhp2", "has been identified.

nhp2 nola2", "identified.

nhp2 nola2 is", "nola2 is likewise associated", "is likewise associated with telomerase", "likewise associated with telomerase ribonucleoprotein", "associated with telomerase ribonucleoprotein complexes", "telomerase ribonucleoprotein complexes pogacic", "ribonucleoprotein complexes pogacic et", "complexes pogacic et al.", "et al. 2000 and", "al. 2000 and homozygous", "2000 and homozygous nhp2", "and homozygous nhp2 mutations are", "homozygous nhp2 mutations are associated", "nhp2 mutations are associated with", "mutations are associated with telomerase", "are associated with telomerase failure", "associated with telomerase failure in", "with telomerase failure in humans", "failure in humans vuillamy", "humans vuillamy et", "vuillamy et al. 2008", "et al. 2008 . a", "al. 2008 . a potential", "2008 . a potential chicken", ". a potential chicken ortholog", "potential chicken ortholog for nhp2", "chicken ortholog for nhp2 has", "ortholog for nhp2 has been", "for nhp2 has been identified." ] }, { "record_id": "GLY_000968_1_393", "filename": "chicken_protein_pathways_reactome", "fieldtype": "id", "phraselist": [ "gly_000968", "gga", "417957", "r gga", "gga 417957", "r gga 417957" ] }, { "record_id": "GLY_000968_1_393", "filename": "chicken_protein_pathways_reactome", "fieldtype": "text", "phraselist": [ "p2y receptors", "this event", "event has", "has been", "been computationally", "computationally inferred", "inferred from", "from an", "an event", "event that", "that has", "been demonstrated", "demonstrated in", "in another", "another species.

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the", ".

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in", ".

in both", "both chicken", "activity in", "in vivo", "vivo is", "is robust", "robust early", "early in", "in development", "declines thereafter", "thereafter in", "in most", "most somatic", "somatic tissues", "yet remains", "remains active", "active in", "in renewable", "renewable tissues", "taylor and", "delany 2000", ". telomerase", "activity is", "is also", "also present", "present in", "most transformed", "transformed cells", "cells examined", "examined thus", "thus far", "far in", "in both", "both human", "newbold 2002", "swanberg and", "delany 2003", "delany 2005", "2005 .", "telomerase component", "component transcript", "transcript analysis", "gene expression", "was examined", "examined and", "and cterc", "cterc down", "down regulation", "regulation correlates", "correlates with", "with absence", "absence of", "in telomerase", "telomerase negative", "negative cells", "suggesting that", "that cterc", "cterc may", "be the", "the rate", "rate limiting", "limiting component", "component in", "in some", "some cell", ". telomere", "shortening occurs", "occurs in", "in somatic", "tissues in", "vivo and", "and correlates", "with age", ". division", "shortening is", "is observed", "observed in", "in non", "non immortalized", "non transformed", "transformed chicken", "chicken cells", "cells in", "in vitro", "2003 .

", ".

in", "in human", "proteins involved", "involved in", "the protection", "protection of", "of telomeres", "telomeres include", "include the", "the shelterin", "shelterin complex", "complex composed", "composed of", "of trf1", "trf2 and", "and pot1", "pot1 all", "all of", "of which", "which recognize", "n sequence", "sequence repeats", "repeats and", "and tin2", "tpp1 and", "and rap1", "rap1 which", "which are", "are thought", "thought to", "to interconnect", "interconnect with", "with trf1", "de lange", "lange 2005", "palm and", "and de", "lange 2008", "2008 .", ". known", "known telomere", "telomere related", "related proteins", "proteins found", "chicken include:", "include: trf1", "cooley et", "al. 2009", "konrad et", "al. 1999", "wei and", "and price", "price 2004", "chicken homolog", "homolog of", "of rap1", "tan and", "price 2003", "and tankyrases", "tankyrases 1", "1 and", "and 2", "de rycker", "rycker et", "2003 .

the", ".

the figure", "figure shows", "shows mitotic", "mitotic metaphase", "metaphase chromosomes", "chromosomes from", "from a", "a ucd", "ucd 001", "red jungle", "jungle fowl", "illustrating the", "chicken telomeric", "dna profile.", "profile. ucd", "001 is", "is the", "the sequenced", "sequenced chicken", "dapi stained", "stained mitotic", "with autosomes", "autosomes 1", "1 4", "and zw", "zw sex", "sex chromosomes", "chromosomes indicated.", "the same", "same metaphase", "metaphase displaying", "displaying a", "a fitc", "fitc labeled", "labeled telomeric", "telomeric probe", "probe showing", "showing the", "the telomeric", "dna locations", "including interstitial", "gga 1", "1 arrays", "arrays located", "located within", "within chromosome", "chromosome arms", "arms and", "and near", "the centromere", "the typical", "typical terminal", "and mega", "telomeres on", "on gga", "gga 9", "9 and", "and w.", "chicken and human", "and human telomeres", "human telomeres share", "telomeres share many", "share many features", "many features including", "features including the", "including the sequence", "the sequence of", "sequence of telomeric", "of telomeric repeats", "the structure and", "structure and function", "and function of", "function of telomerase", "of telomerase and", "telomerase and its", "and its components", "components differential", "differential telomerase activity", "telomerase activity profiles", "activity profiles among", "profiles among cell", "among cell types", "types age", "age related and", "related and division", "and division dependent", "division dependent telomere", "dependent telomere shortening", "shortening the", "the complement of", "complement of binding", "of binding proteins", "binding proteins associated", "proteins associated with", "associated with the", "with the telomere", "the telomere and", "telomere and the", "and the role", "the role of", "role of telomerase", "of telomerase in", "telomerase in immortalization", "in immortalization and", "immortalization and cellular", "and cellular transformation.

three", "cellular transformation.

three to", "transformation.

three to five", "to five percent", "five percent of", "percent of the", "of the chicken", "the chicken genome", "chicken genome is", "genome is telomeric", "is telomeric dna", "telomeric dna including", "dna including both", "including both terminal", "both terminal and", "terminal and interstitial", "and interstitial telomeric", "interstitial telomeric repeats", "repeats which", "which is ten", "is ten times", "ten times that", "times that found", "that found in", "found in the", "in the human", "the human genome", "genome delany", "delany et al.", "et al. 2000", "2000 nanda", "nanda et al.", "et al. 2002", "2002 o'hare", "o'hare and delany", "and delany 2009", "delany 2009 .", "2009 . the", ". the quantity", "the quantity of", "quantity of telomeric", "of telomeric dna", "telomeric dna is", "dna is striking", "is striking because", "striking because the", "because the chicken", "genome is one", "is one third", "one third the", "third the size", "the size of", "size of human", "human 1.25", "1.25 pg versus", "pg versus 3", "versus 3 pg", "3 pg per", "pg per haploid", "per haploid genome", "genome and", "and the sequencing", "the sequencing and", "sequencing and assembly", "and assembly of", "assembly of the", "chicken genome indicate", "genome indicate an", "indicate an overall", "an overall reduction", "overall reduction of", "reduction of repetitive", "of repetitive dna", "dna international", "international chicken genome", "chicken genome sequencing", "genome sequencing consortium", "sequencing consortium 2004", "consortium 2004 .", ". there", "there are three", "are three classes", "three classes of", "classes of telomeric", "of telomeric arrays", "telomeric arrays in", "arrays in chicken:", "in chicken: interstitial", "chicken: interstitial arrays", "interstitial arrays of", "arrays of ~2", "of ~2 to", "~2 to 10", "to 10 kb", "kb terminal", "terminal arrays ranging", "arrays ranging from", "ranging from 10", "from 10 40", "10 40 kb", "kb and", "and a second", "a second class", "second class of", "class of terminal", "of terminal arrays", "terminal arrays called", "arrays called mega", "called mega telomeres", "telomeres also", "also known as", "known as ultra", "as ultra long", "long ranging", "ranging from 50", "from 50 kb", "50 kb to", "kb to several", "to several mb", "mb delany", "al. 2000 .", "the mega telomeres", "mega telomeres show", "telomeres show evidence", "show evidence of", "evidence of a", "of a high", "a high meiotic", "high meiotic recombination", "meiotic recombination rate", "recombination rate and", "rate and genotype", "and genotype specific", "genotype specific variation", "variation delany", "et al. 2003", "2003 rodrigue", "rodrigue et al.", "et al. 2005", "2005 o'hare", ". despite", "despite these extremes", "these extremes in", "extremes in size", "in size and", "size and abundance", "abundance shown", "shown in the", "in the photomicrograph", "the photomicrograph below", "below chicken", "chicken telomeres closely", "telomeres closely resemble", "closely resemble their", "resemble their human", "their human counterparts", "human counterparts in", "counterparts in sequence", "in sequence and", "sequence and organization", "organization nanda", "nanda and schmid", "and schmid 1994", "1994 nikitina", "nikitina and woodcock", "and woodcock 2004", "woodcock 2004 .

telomerase", "2004 .

telomerase genes", ".

telomerase genes characterized", "genes characterized in", "characterized in chicken", "in chicken include", "chicken include telomerase", "include telomerase rna", "rna cterc", "cterc also known", "known as ctr", "ctr and", "and telomerase reverse", "telomerase reverse transcriptase", "transcriptase ctert", "delany and daniels", "and daniels 2003", "2003 delany", "and daniels 2004", "daniels 2004 .", "2004 . chicken", ". chicken terc", "chicken terc maps", "terc maps to", "maps to gga", "to gga 9q", "gga 9q and", "9q and displays", "and displays conservation", "displays conservation of", "conservation of sequence", "sequence regulatory", "regulatory elements and", "elements and synteny", "and synteny among", "synteny among viral", "viral avian", "avian and mammalian", "and mammalian genomes", "genomes delany", "2003 fragnet", "fragnet et al.", "al. 2003 .", "2003 . the", ". the template", "template cr1", "cr1 region", "region of terc", "of terc is", "terc is conserved", "is conserved between", "conserved between human", "between human and", "human and chicken", "chicken chen", "chen et al.", "2000 . in", ". in addition", "in addition to", "addition to its", "to its role", "its role as", "role as the", "as the template", "the template for", "template for addition", "for addition of", "addition of telomeric", "of telomeric sequence", "sequence terc", "terc may be", "may be required", "be required for", "required for proliferation", "for proliferation in", "proliferation in dt40", "in dt40 cells", "dt40 cells as", "cells as faure", "as faure et", "faure et al.", "al. 2008", "2008 were", "were unable to", "unable to generate", "to generate terc", "generate terc null", "terc null dt40", "null dt40 cells", "dt40 cells by", "cells by gene", "by gene targeting.", "gene targeting. the", "targeting. the chicken", "the chicken dt40", "chicken dt40 cell", "dt40 cell line", "cell line was", "line was derived", "was derived from", "derived from an", "from an alv", "an alv transformed", "alv transformed b", "transformed b cell", "b cell lymphoma", "lymphoma baba", "baba et al.1985", "al.1985 and", "and possesses a", "possesses a high", "a high rate", "high rate of", "rate of homologous", "of homologous recombination.", "homologous recombination. therefore", "therefore it", "it is widely", "is widely used", "widely used for", "used for transfection", "for transfection of", "transfection of genes", "of genes or", "genes or knockdown", "or knockdown of", "knockdown of expression", "of expression to", "expression to explore", "to explore vertebrate", "explore vertebrate gene", "vertebrate gene function", "function buerstedde", "buerstedde et al.", "et al. 1991", "1991 winding", "winding and berchtold", "and berchtold 2001", "2001 arakawa", "arakawa and buerstedde", "and buerstedde 2006", "2006 bachl", "bachl et al.", "et al. 2007", "al. 2007 .

the", "2007 .

the sequence", ".

the sequence and", "sequence and structure", "and structure of", "structure of the", "of the catalytic", "the catalytic subunit", "catalytic subunit ctert", "ctert which", "which maps to", "to gga 2q", "2q is", "is highly conserved", "highly conserved with", "conserved with regions", "with regions and", "regions and motifs", "and motifs in", "motifs in common", "in common with", "common with human", "human xenopus", "xenopus mouse", "mouse rat", "rat and hamster", "and hamster terts", "terts delany", ". chicken tert", "tert 1346", "1346 amino acids", "acids shares", "shares 45% amino", "45% amino acid", "amino acid identity", "acid identity with", "identity with human", "with human tert", "tert 1132", "1132 amino acids", "2004 . interesting", ". interesting differences", "interesting differences include", "differences include a", "include a substantially", "a substantially larger", "substantially larger region", "larger region of", "region of the", "of the protein", "the protein termed", "protein termed the", "termed the flexible", "the flexible linker", "flexible linker which", "linker which is", "which is located", "is located near", "located near the", "near the n", "the n terminus", "n terminus and", "terminus and includes", "and includes 298", "includes 298 amino", "298 amino acids", "amino acids in", "acids in chicken", "in chicken and", "chicken and only", "and only 155", "only 155 in", "155 in human.", "in human. comparisons", "human. comparisons between", "comparisons between human", "and chicken 5'", "chicken 5' regulatory", "5' regulatory motifs", "regulatory motifs are", "motifs are reviewed", "are reviewed further", "reviewed further in", "further in delany", "in delany and", "2004 . both", ". both full", "both full length", "full length ctert", "length ctert mrna", "ctert mrna and", "mrna and numerous", "and numerous shorter", "numerous shorter mrnas", "shorter mrnas generated", "mrnas generated by", "generated by alternative", "by alternative splicing", "alternative splicing have", "splicing have been", "have been described", "been described although", "described although the", "although the function", "the function of", "function of these", "of these splice", "these splice variants", "splice variants remains", "variants remains to", "remains to be", "to be clarified", "clarified chang", "chang and delany", "and delany 2006", "2006 hrdlickova", "hrdlickova et al.", "et al. 2006", "al. 2006 .

in", "2006 .

in both", ".

in both chicken", "both chicken and", "human telomerase", "telomerase activity in", "activity in vivo", "in vivo is", "vivo is robust", "is robust early", "robust early in", "early in development", "development declines", "declines thereafter in", "thereafter in most", "in most somatic", "most somatic tissues", "tissues yet", "yet remains active", "remains active in", "active in renewable", "in renewable tissues", "tissues taylor", "taylor and delany", "and delany 2000", "delany 2000 .", "2000 . telomerase", ". telomerase activity", "telomerase activity is", "activity is also", "is also present", "also present in", "present in most", "in most transformed", "most transformed cells", "transformed cells examined", "cells examined thus", "examined thus far", "thus far in", "far in both", "in both human", "both human and", "chicken newbold", "2002 swanberg", "swanberg and delany", "and delany 2003", "2003 swanberg", "and delany 2005", "delany 2005 .", "2005 . telomerase", ". telomerase component", "telomerase component transcript", "component transcript analysis", "analysis gene", "expression was", "was examined and", "examined and cterc", "and cterc down", "cterc down regulation", "down regulation correlates", "regulation correlates with", "correlates with absence", "with absence of", "absence of telomerase", "of telomerase activity", "activity in telomerase", "in telomerase negative", "telomerase negative cells", "cells suggesting", "suggesting that cterc", "that cterc may", "cterc may be", "may be the", "be the rate", "the rate limiting", "rate limiting component", "limiting component in", "component in some", "in some cell", "some cell types", "types o'hare", "2005 swanberg", "2005 . telomere", ". telomere shortening", "telomere shortening occurs", "shortening occurs in", "occurs in somatic", "in somatic tissues", "somatic tissues in", "tissues in vivo", "in vivo and", "vivo and correlates", "and correlates with", "correlates with age", "age taylor", "2000 delany", "2003 . division", ". division dependent", "telomere shortening is", "shortening is observed", "is observed in", "observed in non", "in non immortalized", "immortalized non", "non transformed chicken", "transformed chicken cells", "chicken cells in", "cells in vitro", "vitro swanberg", "delany 2003 .

", "2003 .

in", ".

in human", "human proteins", "proteins involved in", "involved in the", "in the protection", "the protection of", "protection of telomeres", "of telomeres include", "telomeres include the", "include the shelterin", "the shelterin complex", "shelterin complex composed", "complex composed of", "composed of trf1", "trf1 trf2", "trf2 and pot1", "and pot1 all", "pot1 all of", "all of which", "of which recognize", "recognize ttaggg", "ttaggg n sequence", "n sequence repeats", "sequence repeats and", "repeats and tin2", "tin2 tpp1", "tpp1 and rap1", "and rap1 which", "rap1 which are", "which are thought", "are thought to", "thought to interconnect", "to interconnect with", "interconnect with trf1", "pot1 de", "de lange 2005", "2005 palm", "palm and de", "and de lange", "de lange 2008", "lange 2008 .", "2008 . known", ". known telomere", "known telomere related", "telomere related proteins", "related proteins found", "proteins found in", "found in chicken", "in chicken include:", "chicken include: trf1", "trf1 cooley", "cooley et al.", "et al. 2009", "trf2 konrad", "konrad et al.", "et al. 1999", "pot1 wei", "wei and price", "and price 2004", "the chicken homolog", "chicken homolog of", "homolog of rap1", "rap1 tan", "tan and price", "and price 2003", "2003 and", "and tankyrases 1", "tankyrases 1 and", "1 and 2", "2 de", "de rycker et", "rycker et al.", "al. 2003 .

the", "2003 .

the figure", ".

the figure shows", "figure shows mitotic", "shows mitotic metaphase", "mitotic metaphase chromosomes", "metaphase chromosomes from", "chromosomes from a", "from a ucd", "a ucd 001", "001 red", "red jungle fowl", "fowl female", "female 2n=78", "2n=78 zw", "zw illustrating", "illustrating the chicken", "the chicken telomeric", "chicken telomeric dna", "telomeric dna profile.", "dna profile. ucd", "profile. ucd 001", "ucd 001 is", "001 is the", "is the sequenced", "the sequenced chicken", "sequenced chicken genome", "genome international", ". a", "a dapi", "dapi stained mitotic", "stained mitotic metaphase", "chromosomes blue", "blue with", "with autosomes 1", "autosomes 1 4", "4 9", "and zw sex", "zw sex chromosomes", "sex chromosomes indicated.", "indicated. b", "b the", "the same metaphase", "same metaphase displaying", "metaphase displaying a", "displaying a fitc", "a fitc labeled", "fitc labeled telomeric", "labeled telomeric probe", "telomeric probe showing", "probe showing the", "showing the telomeric", "the telomeric dna", "telomeric dna locations", "locations including", "including interstitial arrays", "arrays e.g.", "e.g. gga", "gga 1 arrays", "1 arrays located", "arrays located within", "located within chromosome", "within chromosome arms", "chromosome arms and", "arms and near", "and near the", "near the centromere", "the typical terminal", "typical terminal arrays", "arrays and", "and mega telomeres", "mega telomeres on", "telomeres on gga", "on gga 9", "gga 9 and", "9 and w.", "chicken and human telomeres", "and human telomeres share", "human telomeres share many", "telomeres share many features", "share many features including", "many features including the", "features including the sequence", "including the sequence of", "the sequence of telomeric", "sequence of telomeric repeats", "repeats ttaggg", "n the", "the structure and function", "structure and function of", "and function of telomerase", "function of telomerase and", "of telomerase and its", "telomerase and its components", "its components differential", "components differential telomerase", "differential telomerase activity profiles", "telomerase activity profiles among", "activity profiles among cell", "profiles among cell types", "cell types age", "types age related", "age related and division", "related and division dependent", "and division dependent telomere", "division dependent telomere shortening", "telomere shortening the", "shortening the complement", "the complement of binding", "complement of binding proteins", "of binding proteins associated", "binding proteins associated with", "proteins associated with the", "associated with the telomere", "with the telomere and", "the telomere and the", "telomere and the role", "and the role of", "the role of telomerase", "role of telomerase in", "of telomerase in immortalization", "telomerase in immortalization and", "in immortalization and cellular", "immortalization and cellular transformation.

three", "and cellular transformation.

three to", "cellular transformation.

three to five", "transformation.

three to five percent", "to five percent of", "five percent of the", "percent of the chicken", "of the chicken genome", "the chicken genome is", "chicken genome is telomeric", "genome is telomeric dna", "is telomeric dna including", "telomeric dna including both", "dna including both terminal", "including both terminal and", "both terminal and interstitial", "terminal and interstitial telomeric", "and interstitial telomeric repeats", "telomeric repeats which", "repeats which is", "which is ten times", "is ten times that", "ten times that found", "times that found in", "that found in the", "found in the human", "in the human genome", "human genome delany", "genome delany et", "delany et al. 2000", "al. 2000 nanda", "2000 nanda et", "nanda et al. 2002", "al. 2002 o'hare", "2002 o'hare and", "o'hare and delany 2009", "and delany 2009 .", "delany 2009 . the", "2009 . the quantity", ". the quantity of", "the quantity of telomeric", "quantity of telomeric dna", "of telomeric dna is", "telomeric dna is striking", "dna is striking because", "is striking because the", "striking because the chicken", "because the chicken genome", "chicken genome is one", "genome is one third", "is one third the", "one third the size", "third the size of", "the size of human", "of human 1.25", "human 1.25 pg", "1.25 pg versus 3", "pg versus 3 pg", "versus 3 pg per", "3 pg per haploid", "pg per haploid genome", "haploid genome and", "genome and the", "and the sequencing and", "the sequencing and assembly", "sequencing and assembly of", "and assembly of the", "assembly of the chicken", "the chicken genome indicate", "chicken genome indicate an", "genome indicate an overall", "indicate an overall reduction", "an overall reduction of", "overall reduction of repetitive", "reduction of repetitive dna", "repetitive dna international", "dna international chicken", "international chicken genome sequencing", "chicken genome sequencing consortium", "genome sequencing consortium 2004", "sequencing consortium 2004 .", "2004 . there", ". there are", "there are three classes", "are three classes of", "three classes of telomeric", "classes of telomeric arrays", "of telomeric arrays in", "telomeric arrays in chicken:", "arrays in chicken: interstitial", "in chicken: interstitial arrays", "chicken: interstitial arrays of", "interstitial arrays of ~2", "arrays of ~2 to", "of ~2 to 10", "~2 to 10 kb", "10 kb terminal", "kb terminal arrays", "terminal arrays ranging from", "arrays ranging from 10", "ranging from 10 40", "from 10 40 kb", "40 kb and", "kb and a", "and a second class", "a second class of", "second class of terminal", "class of terminal arrays", "of terminal arrays called", "terminal arrays called mega", "arrays called mega telomeres", "mega telomeres also", "telomeres also known", "also known as ultra", "known as ultra long", "ultra long ranging", "long ranging from", "ranging from 50 kb", "from 50 kb to", "50 kb to several", "kb to several mb", "several mb delany", "mb delany et", "et al. 2000 .", "2000 . the", ". the mega", "the mega telomeres show", "mega telomeres show evidence", "telomeres show evidence of", "show evidence of a", "evidence of a high", "of a high meiotic", "a high meiotic recombination", "high meiotic recombination rate", "meiotic recombination rate and", "recombination rate and genotype", "rate and genotype specific", "and genotype specific variation", "specific variation delany", "variation delany et", "delany et al. 2003", "al. 2003 rodrigue", "2003 rodrigue et", "rodrigue et al. 2005", "al. 2005 o'hare", "2005 o'hare and", "2009 . despite", ". despite these", "despite these extremes in", "these extremes in size", "extremes in size and", "in size and abundance", "and abundance shown", "abundance shown in", "shown in the photomicrograph", "in the photomicrograph below", "photomicrograph below chicken", "below chicken telomeres", "chicken telomeres closely resemble", "telomeres closely resemble their", "closely resemble their human", "resemble their human counterparts", "their human counterparts in", "human counterparts in sequence", "counterparts in sequence and", "in sequence and organization", "and organization nanda", "organization nanda and", "nanda and schmid 1994", "schmid 1994 nikitina", "1994 nikitina and", "nikitina and woodcock 2004", "and woodcock 2004 .

telomerase", "woodcock 2004 .

telomerase genes", "2004 .

telomerase genes characterized", ".

telomerase genes characterized in", "genes characterized in chicken", "characterized in chicken include", "in chicken include telomerase", "chicken include telomerase rna", "telomerase rna cterc", "rna cterc also", "cterc also known as", "also known as ctr", "as ctr and", "ctr and telomerase", "and telomerase reverse transcriptase", "reverse transcriptase ctert", "ctert delany", "delany and daniels 2003", "daniels 2003 delany", "2003 delany and", "delany and daniels 2004", "and daniels 2004 .", "daniels 2004 . chicken", "2004 . chicken terc", ". chicken terc maps", "chicken terc maps to", "terc maps to gga", "maps to gga 9q", "to gga 9q and", "gga 9q and displays", "9q and displays conservation", "and displays conservation of", "displays conservation of sequence", "of sequence regulatory", "sequence regulatory elements", "regulatory elements and synteny", "elements and synteny among", "and synteny among viral", "among viral avian", "viral avian and", "avian and mammalian genomes", "mammalian genomes delany", "genomes delany and", "daniels 2003 fragnet", "2003 fragnet et", "fragnet et al. 2003", "et al. 2003 .", "al. 2003 . the", "2003 . the template", "the template cr1", "cr1 region of", "region of terc is", "of terc is conserved", "terc is conserved between", "is conserved between human", "conserved between human and", "between human and chicken", "and chicken chen", "chicken chen et", "chen et al. 2000", "al. 2000 . in", "2000 . in addition", ". in addition to", "in addition to its", "addition to its role", "to its role as", "its role as the", "role as the template", "as the template for", "the template for addition", "template for addition of", "for addition of telomeric", "addition of telomeric sequence", "telomeric sequence terc", "sequence terc may", "terc may be required", "may be required for", "be required for proliferation", "required for proliferation in", "for proliferation in dt40", "proliferation in dt40 cells", "in dt40 cells as", "dt40 cells as faure", "cells as faure et", "as faure et al.", "et al. 2008", "2008 were unable", "were unable to generate", "unable to generate terc", "to generate terc null", "generate terc null dt40", "terc null dt40 cells", "null dt40 cells by", "dt40 cells by gene", "cells by gene targeting.", "by gene targeting. the", "gene targeting. the chicken", "targeting. the chicken dt40", "the chicken dt40 cell", "chicken dt40 cell line", "dt40 cell line was", "cell line was derived", "line was derived from", "was derived from an", "derived from an alv", "from an alv transformed", "an alv transformed b", "alv transformed b cell", "transformed b cell lymphoma", "cell lymphoma baba", "lymphoma baba et", "et al.1985 and", "al.1985 and possesses", "and possesses a high", "possesses a high rate", "a high rate of", "high rate of homologous", "rate of homologous recombination.", "of homologous recombination. therefore", "recombination. therefore it", "therefore it is", "it is widely used", "is widely used for", "widely used for transfection", "used for transfection of", "for transfection of genes", "transfection of genes or", "of genes or knockdown", "genes or knockdown of", "or knockdown of expression", "knockdown of expression to", "of expression to explore", "expression to explore vertebrate", "to explore vertebrate gene", "explore vertebrate gene function", "gene function buerstedde", "function buerstedde et", "buerstedde et al. 1991", "al. 1991 winding", "1991 winding and", "winding and berchtold 2001", "berchtold 2001 arakawa", "2001 arakawa and", "arakawa and buerstedde 2006", "buerstedde 2006 bachl", "2006 bachl et", "bachl et al. 2007", "et al. 2007 .

the", "al. 2007 .

the sequence", "2007 .

the sequence and", ".

the sequence and structure", "sequence and structure of", "and structure of the", "structure of the catalytic", "of the catalytic subunit", "the catalytic subunit ctert", "subunit ctert which", "ctert which maps", "which maps to gga", "maps to gga 2q", "gga 2q is", "2q is highly", "is highly conserved with", "highly conserved with regions", "conserved with regions and", "with regions and motifs", "regions and motifs in", "and motifs in common", "motifs in common with", "in common with human", "with human xenopus", "mouse rat and", "rat and hamster terts", "hamster terts delany", "terts delany and", "2004 . chicken tert", "chicken tert 1346", "tert 1346 amino", "amino acids shares", "acids shares 45%", "shares 45% amino acid", "45% amino acid identity", "amino acid identity with", "acid identity with human", "identity with human tert", "human tert 1132", "tert 1132 amino", "acids delany", "daniels 2004 . interesting", "2004 . interesting differences", ". interesting differences include", "interesting differences include a", "differences include a substantially", "include a substantially larger", "a substantially larger region", "substantially larger region of", "larger region of the", "region of the protein", "of the protein termed", "the protein termed the", "protein termed the flexible", "termed the flexible linker", "the flexible linker which", "flexible linker which is", "linker which is located", "which is located near", "is located near the", "located near the n", "near the n terminus", "the n terminus and", "n terminus and includes", "terminus and includes 298", "and includes 298 amino", "includes 298 amino acids", "298 amino acids in", "amino acids in chicken", "acids in chicken and", "in chicken and only", "chicken and only 155", "and only 155 in", "only 155 in human.", "155 in human. comparisons", "in human. comparisons between", "human. comparisons between human", "comparisons between human and", "human and chicken 5'", "and chicken 5' regulatory", "chicken 5' regulatory motifs", "5' regulatory motifs are", "regulatory motifs are reviewed", "motifs are reviewed further", "are reviewed further in", "reviewed further in delany", "further in delany and", "in delany and daniels", "2004 . both full", ". both full length", "both full length ctert", "full length ctert mrna", "length ctert mrna and", "ctert mrna and numerous", "mrna and numerous shorter", "and numerous shorter mrnas", "numerous shorter mrnas generated", "shorter mrnas generated by", "mrnas generated by alternative", "generated by alternative splicing", "by alternative splicing have", "alternative splicing have been", "splicing have been described", "have been described although", "been described although the", "described although the function", "although the function of", "the function of these", "function of these splice", "of these splice variants", "these splice variants remains", "splice variants remains to", "variants remains to be", "remains to be clarified", "be clarified chang", "clarified chang and", "chang and delany 2006", "delany 2006 hrdlickova", "2006 hrdlickova et", "hrdlickova et al. 2006", "et al. 2006 .

in", "al. 2006 .

in both", "2006 .

in both chicken", ".

in both chicken and", "both chicken and human", "and human telomerase", "human telomerase activity", "telomerase activity in vivo", "activity in vivo is", "in vivo is robust", "vivo is robust early", "is robust early in", "robust early in development", "in development declines", "development declines thereafter", "declines thereafter in most", "thereafter in most somatic", "in most somatic tissues", "somatic tissues yet", "tissues yet remains", "yet remains active in", "remains active in renewable", "active in renewable tissues", "renewable tissues taylor", "tissues taylor and", "taylor and delany 2000", "and delany 2000 .", "delany 2000 . telomerase", "2000 . telomerase activity", ". telomerase activity is", "telomerase activity is also", "activity is also present", "is also present in", "also present in most", "present in most transformed", "in most transformed cells", "most transformed cells examined", "transformed cells examined thus", "cells examined thus far", "examined thus far in", "thus far in both", "far in both human", "in both human and", "both human and chicken", "and chicken newbold", "chicken newbold 2002", "newbold 2002 swanberg", "2002 swanberg and", "swanberg and delany 2003", "delany 2003 swanberg", "2003 swanberg and", "swanberg and delany 2005", "and delany 2005 .", "delany 2005 . telomerase", "2005 . telomerase component", ". telomerase component transcript", "telomerase component transcript analysis", "transcript analysis gene", "analysis gene expression", "gene expression was", "expression was examined", "was examined and cterc", "examined and cterc down", "and cterc down regulation", "cterc down regulation correlates", "down regulation correlates with", "regulation correlates with absence", "correlates with absence of", "with absence of telomerase", "absence of telomerase activity", "of telomerase activity in", "telomerase activity in telomerase", "activity in telomerase negative", "in telomerase negative cells", "negative cells suggesting", "cells suggesting that", "suggesting that cterc may", "that cterc may be", "cterc may be the", "may be the rate", "be the rate limiting", "the rate limiting component", "rate limiting component in", "limiting component in some", "component in some cell", "in some cell types", "cell types o'hare", "types o'hare and", "o'hare and delany 2005", "delany 2005 swanberg", "2005 swanberg and", "delany 2005 . telomere", "2005 . telomere shortening", ". telomere shortening occurs", "telomere shortening occurs in", "shortening occurs in somatic", "occurs in somatic tissues", "in somatic tissues in", "somatic tissues in vivo", "tissues in vivo and", "in vivo and correlates", "vivo and correlates with", "and correlates with age", "with age taylor", "age taylor and", "delany 2000 delany", "2000 delany et", "al. 2003 . division", "2003 . division dependent", ". division dependent telomere", "dependent telomere shortening is", "telomere shortening is observed", "shortening is observed in", "is observed in non", "observed in non immortalized", "non immortalized non", "immortalized non transformed", "non transformed chicken cells", "transformed chicken cells in", "chicken cells in vitro", "in vitro swanberg", "vitro swanberg and", "and delany 2003 .

", "delany 2003 .

in", "2003 .

in human", "in human proteins", "human proteins involved", "proteins involved in the", "involved in the protection", "in the protection of", "the protection of telomeres", "protection of telomeres include", "of telomeres include the", "telomeres include the shelterin", "include the shelterin complex", "the shelterin complex composed", "shelterin complex composed of", "complex composed of trf1", "of trf1 trf2", "trf1 trf2 and", "trf2 and pot1 all", "and pot1 all of", "pot1 all of which", "all of which recognize", "which recognize ttaggg", "recognize ttaggg n", "ttaggg n sequence repeats", "n sequence repeats and", "sequence repeats and tin2", "and tin2 tpp1", "tin2 tpp1 and", "tpp1 and rap1 which", "and rap1 which are", "rap1 which are thought", "which are thought to", "are thought to interconnect", "thought to interconnect with", "to interconnect with trf1", "with trf1 trf2", "and pot1 de", "pot1 de lange", "lange 2005 palm", "2005 palm and", "palm and de lange", "and de lange 2008", "de lange 2008 .", "lange 2008 . known", "2008 . known telomere", ". known telomere related", "known telomere related proteins", "telomere related proteins found", "related proteins found in", "proteins found in chicken", "found in chicken include:", "in chicken include: trf1", "include: trf1 cooley", "trf1 cooley et", "cooley et al. 2009", "2009 trf2", "trf2 konrad et", "konrad et al. 1999", "1999 pot1", "pot1 wei and", "wei and price 2004", "2004 the", "the chicken homolog of", "chicken homolog of rap1", "of rap1 tan", "rap1 tan and", "tan and price 2003", "price 2003 and", "2003 and tankyrases", "and tankyrases 1 and", "tankyrases 1 and 2", "and 2 de", "2 de rycker", "de rycker et al.", "rycker et al. 2003", "et al. 2003 .

the", "al. 2003 .

the figure", "2003 .

the figure shows", ".

the figure shows mitotic", "figure shows mitotic metaphase", "shows mitotic metaphase chromosomes", "mitotic metaphase chromosomes from", "metaphase chromosomes from a", "chromosomes from a ucd", "from a ucd 001", "ucd 001 red", "001 red jungle", "jungle fowl female", "zw illustrating the", "illustrating the chicken telomeric", "the chicken telomeric dna", "chicken telomeric dna profile.", "telomeric dna profile. ucd", "dna profile. ucd 001", "profile. ucd 001 is", "ucd 001 is the", "001 is the sequenced", "is the sequenced chicken", "the sequenced chicken genome", "chicken genome international", "genome international chicken", "2004 . a", "a dapi stained", "dapi stained mitotic metaphase", "stained mitotic metaphase chromosomes", "metaphase chromosomes blue", "blue with autosomes", "with autosomes 1 4", "1 4 9", "9 and zw", "and zw sex chromosomes", "zw sex chromosomes indicated.", "chromosomes indicated. b", "b the same", "the same metaphase displaying", "same metaphase displaying a", "metaphase displaying a fitc", "displaying a fitc labeled", "a fitc labeled telomeric", "fitc labeled telomeric probe", "labeled telomeric probe showing", "telomeric probe showing the", "probe showing the telomeric", "showing the telomeric dna", "the telomeric dna locations", "dna locations including", "locations including interstitial", "interstitial arrays e.g.", "e.g. gga 1", "gga 1 arrays located", "1 arrays located within", "arrays located within chromosome", "located within chromosome arms", "within chromosome arms and", "chromosome arms and near", "arms and near the", "and near the centromere", "centromere the", "the typical terminal arrays", "terminal arrays and", "arrays and mega", "and mega telomeres on", "mega telomeres on gga", "telomeres on gga 9", "on gga 9 and", "gga 9 and w.", "chicken and human telomeres share", "and human telomeres share many", "human telomeres share many features", "telomeres share many features including", "share many features including the", "many features including the sequence", "features including the sequence of", "including the sequence of telomeric", "the sequence of telomeric repeats", "telomeric repeats ttaggg", "repeats ttaggg n", "ttaggg n the", "n the structure", "the structure and function of", "structure and function of telomerase", "and function of telomerase and", "function of telomerase and its", "of telomerase and its components", "and its components differential", "its components differential telomerase", "components differential telomerase activity", "differential telomerase activity profiles among", "telomerase activity profiles among cell", "activity profiles among cell types", "among cell types age", "cell types age related", "types age related and", "age related and division dependent", "related and division dependent telomere", "and division dependent telomere shortening", "dependent telomere shortening the", "telomere shortening the complement", "shortening the complement of", "the complement of binding proteins", "complement of binding proteins associated", "of binding proteins associated with", "binding proteins associated with the", "proteins associated with the telomere", "associated with the telomere and", "with the telomere and the", "the telomere and the role", "telomere and the role of", "and the role of telomerase", "the role of telomerase in", "role of telomerase in immortalization", "of telomerase in immortalization and", "telomerase in immortalization and cellular", "in immortalization and cellular transformation.

three", "immortalization and cellular transformation.

three to", "and cellular transformation.

three to five", "cellular transformation.

three to five percent", "transformation.

three to five percent of", "to five percent of the", "five percent of the chicken", "percent of the chicken genome", "of the chicken genome is", "the chicken genome is telomeric", "chicken genome is telomeric dna", "genome is telomeric dna including", "is telomeric dna including both", "telomeric dna including both terminal", "dna including both terminal and", "including both terminal and interstitial", "both terminal and interstitial telomeric", "terminal and interstitial telomeric repeats", "interstitial telomeric repeats which", "telomeric repeats which is", "repeats which is ten", "which is ten times that", "is ten times that found", "ten times that found in", "times that found in the", "that found in the human", "found in the human genome", "the human genome delany", "human genome delany et", "genome delany et al.", "et al. 2000 nanda", "al. 2000 nanda et", "2000 nanda et al.", "et al. 2002 o'hare", "al. 2002 o'hare and", "2002 o'hare and delany", "o'hare and delany 2009 .", "and delany 2009 . the", "delany 2009 . the quantity", "2009 . the quantity of", ". the quantity of telomeric", "the quantity of telomeric dna", "quantity of telomeric dna is", "of telomeric dna is striking", "telomeric dna is striking because", "dna is striking because the", "is striking because the chicken", "striking because the chicken genome", "because the chicken genome is", "the chicken genome is one", "chicken genome is one third", "genome is one third the", "is one third the size", "one third the size of", "third the size of human", "size of human 1.25", "of human 1.25 pg", "human 1.25 pg versus", "1.25 pg versus 3 pg", "pg versus 3 pg per", "versus 3 pg per haploid", "3 pg per haploid genome", "per haploid genome and", "haploid genome and the", "genome and the sequencing", "and the sequencing and assembly", "the sequencing and assembly of", "sequencing and assembly of the", "and assembly of the chicken", "assembly of the chicken genome", "of the chicken genome indicate", "the chicken genome indicate an", "chicken genome indicate an overall", "genome indicate an overall reduction", "indicate an overall reduction of", "an overall reduction of repetitive", "overall reduction of repetitive dna", "of repetitive dna international", "repetitive dna international chicken", "dna international chicken genome", "international chicken genome sequencing consortium", "chicken genome sequencing consortium 2004", "genome sequencing consortium 2004 .", "consortium 2004 . there", "2004 . there are", ". there are three", "there are three classes of", "are three classes of telomeric", "three classes of telomeric arrays", "classes of telomeric arrays in", "of telomeric arrays in chicken:", "telomeric arrays in chicken: interstitial", "arrays in chicken: interstitial arrays", "in chicken: interstitial arrays of", "chicken: interstitial arrays of ~2", "interstitial arrays of ~2 to", "arrays of ~2 to 10", "of ~2 to 10 kb", "to 10 kb terminal", "10 kb terminal arrays", "kb terminal arrays ranging", "terminal arrays ranging from 10", "arrays ranging from 10 40", "ranging from 10 40 kb", "10 40 kb and", "40 kb and a", "kb and a second", "and a second class of", "a second class of terminal", "second class of terminal arrays", "class of terminal arrays called", "of terminal arrays called mega", "terminal arrays called mega telomeres", "called mega telomeres also", "mega telomeres also known", "telomeres also known as", "also known as ultra long", "as ultra long ranging", "ultra long ranging from", "long ranging from 50", "ranging from 50 kb to", "from 50 kb to several", "50 kb to several mb", "to several mb delany", "several mb delany et", "mb delany et al.", "delany et al. 2000 .", "al. 2000 . the", "2000 . the mega", ". the mega telomeres", "the mega telomeres show evidence", "mega telomeres show evidence of", "telomeres show evidence of a", "show evidence of a high", "evidence of a high meiotic", "of a high meiotic recombination", "a high meiotic recombination rate", "high meiotic recombination rate and", "meiotic recombination rate and genotype", "recombination rate and genotype specific", "rate and genotype specific variation", "genotype specific variation delany", "specific variation delany et", "variation delany et al.", "et al. 2003 rodrigue", "al. 2003 rodrigue et", "2003 rodrigue et al.", "et al. 2005 o'hare", "al. 2005 o'hare and", "2005 o'hare and delany", "delany 2009 . despite", "2009 . despite these", ". despite these extremes", "despite these extremes in size", "these extremes in size and", "extremes in size and abundance", "size and abundance shown", "and abundance shown in", "abundance shown in the", "shown in the photomicrograph below", "the photomicrograph below chicken", "photomicrograph below chicken telomeres", "below chicken telomeres closely", "chicken telomeres closely resemble their", "telomeres closely resemble their human", "closely resemble their human counterparts", "resemble their human counterparts in", "their human counterparts in sequence", "human counterparts in sequence and", "counterparts in sequence and organization", "sequence and organization nanda", "and organization nanda and", "organization nanda and schmid", "and schmid 1994 nikitina", "schmid 1994 nikitina and", "1994 nikitina and woodcock", "nikitina and woodcock 2004 .

telomerase", "and woodcock 2004 .

telomerase genes", "woodcock 2004 .

telomerase genes characterized", "2004 .

telomerase genes characterized in", ".

telomerase genes characterized in chicken", "genes characterized in chicken include", "characterized in chicken include telomerase", "in chicken include telomerase rna", "include telomerase rna cterc", "telomerase rna cterc also", "rna cterc also known", "cterc also known as ctr", "known as ctr and", "as ctr and telomerase", "ctr and telomerase reverse", "telomerase reverse transcriptase ctert", "ctert delany and", "and daniels 2003 delany", "daniels 2003 delany and", "2003 delany and daniels", "delany and daniels 2004 .", "and daniels 2004 . chicken", "daniels 2004 . chicken terc", "2004 . chicken terc maps", ". chicken terc maps to", "chicken terc maps to gga", "terc maps to gga 9q", "maps to gga 9q and", "to gga 9q and displays", "gga 9q and displays conservation", "9q and displays conservation of", "and displays conservation of sequence", "conservation of sequence regulatory", "of sequence regulatory elements", "sequence regulatory elements and", "regulatory elements and synteny among", "elements and synteny among viral", "synteny among viral avian", "among viral avian and", "viral avian and mammalian", "and mammalian genomes delany", "mammalian genomes delany and", "genomes delany and daniels", "and daniels 2003 fragnet", "daniels 2003 fragnet et", "2003 fragnet et al.", "fragnet et al. 2003 .", "et al. 2003 . the", "al. 2003 . the template", ". the template cr1", "template cr1 region", "cr1 region of terc", "region of terc is conserved", "of terc is conserved between", "terc is conserved between human", "is conserved between human and", "conserved between human and chicken", "human and chicken chen", "and chicken chen et", "chicken chen et al.", "chen et al. 2000 .", "et al. 2000 . in", "al. 2000 . in addition", "2000 . in addition to", ". in addition to its", "in addition to its role", "addition to its role as", "to its role as the", "its role as the template", "role as the template for", "as the template for addition", "the template for addition of", "template for addition of telomeric", "for addition of telomeric sequence", "of telomeric sequence terc", "telomeric sequence terc may", "sequence terc may be", "terc may be required for", "may be required for proliferation", "be required for proliferation in", "required for proliferation in dt40", "for proliferation in dt40 cells", "proliferation in dt40 cells as", "in dt40 cells as faure", "dt40 cells as faure et", "cells as faure et al.", "faure et al. 2008", "al. 2008 were", "2008 were unable to", "were unable to generate terc", "unable to generate terc null", "to generate terc null dt40", "generate terc null dt40 cells", "terc null dt40 cells by", "null dt40 cells by gene", "dt40 cells by gene targeting.", "cells by gene targeting. the", "by gene targeting. the chicken", "gene targeting. the chicken dt40", "targeting. the chicken dt40 cell", "the chicken dt40 cell line", "chicken dt40 cell line was", "dt40 cell line was derived", "cell line was derived from", "line was derived from an", "was derived from an alv", "derived from an alv transformed", "from an alv transformed b", "an alv transformed b cell", "alv transformed b cell lymphoma", "b cell lymphoma baba", "cell lymphoma baba et", "lymphoma baba et al.1985", "baba et al.1985 and", "et al.1985 and possesses", "al.1985 and possesses a", "and possesses a high rate", "possesses a high rate of", "a high rate of homologous", "high rate of homologous recombination.", "rate of homologous recombination. therefore", "homologous recombination. therefore it", "recombination. therefore it is", "therefore it is widely", "it is widely used for", "is widely used for transfection", "widely used for transfection of", "used for transfection of genes", "for transfection of genes or", "transfection of genes or knockdown", "of genes or knockdown of", "genes or knockdown of expression", "or knockdown of expression to", "knockdown of expression to explore", "of expression to explore vertebrate", "expression to explore vertebrate gene", "to explore vertebrate gene function", "vertebrate gene function buerstedde", "gene function buerstedde et", "function buerstedde et al.", "et al. 1991 winding", "al. 1991 winding and", "1991 winding and berchtold", "and berchtold 2001 arakawa", "berchtold 2001 arakawa and", "2001 arakawa and buerstedde", "and buerstedde 2006 bachl", "buerstedde 2006 bachl et", "2006 bachl et al.", "bachl et al. 2007 .

the", "et al. 2007 .

the sequence", "al. 2007 .

the sequence and", "2007 .

the sequence and structure", ".

the sequence and structure of", "sequence and structure of the", "and structure of the catalytic", "structure of the catalytic subunit", "of the catalytic subunit ctert", "catalytic subunit ctert which", "subunit ctert which maps", "ctert which maps to", "which maps to gga 2q", "to gga 2q is", "gga 2q is highly", "2q is highly conserved", "is highly conserved with regions", "highly conserved with regions and", "conserved with regions and motifs", "with regions and motifs in", "regions and motifs in common", "and motifs in common with", "motifs in common with human", "common with human xenopus", "human xenopus mouse", "xenopus mouse rat", "mouse rat and hamster", "and hamster terts delany", "hamster terts delany and", "terts delany and daniels", "daniels 2004 . chicken tert", ". chicken tert 1346", "chicken tert 1346 amino", "tert 1346 amino acids", "1346 amino acids shares", "amino acids shares 45%", "acids shares 45% amino", "shares 45% amino acid identity", "45% amino acid identity with", "amino acid identity with human", "acid identity with human tert", "with human tert 1132", "human tert 1132 amino", "tert 1132 amino acids", "amino acids delany", "acids delany and", "and daniels 2004 . interesting", "daniels 2004 . interesting differences", "2004 . interesting differences include", ". interesting differences include a", "interesting differences include a substantially", "differences include a substantially larger", "include a substantially larger region", "a substantially larger region of", "substantially larger region of the", "larger region of the protein", "region of the protein termed", "of the protein termed the", "the protein termed the flexible", "protein termed the flexible linker", "termed the flexible linker which", "the flexible linker which is", "flexible linker which is located", "linker which is located near", "which is located near the", "is located near the n", "located near the n terminus", "near the n terminus and", "the n terminus and includes", "n terminus and includes 298", "terminus and includes 298 amino", "and includes 298 amino acids", "includes 298 amino acids in", "298 amino acids in chicken", "amino acids in chicken and", "acids in chicken and only", "in chicken and only 155", "chicken and only 155 in", "and only 155 in human.", "only 155 in human. comparisons", "155 in human. comparisons between", "in human. comparisons between human", "human. comparisons between human and", "comparisons between human and chicken", "between human and chicken 5'", "human and chicken 5' regulatory", "and chicken 5' regulatory motifs", "chicken 5' regulatory motifs are", "5' regulatory motifs are reviewed", "regulatory motifs are reviewed further", "motifs are reviewed further in", "are reviewed further in delany", "reviewed further in delany and", "further in delany and daniels", "daniels 2004 . both", "2004 . both full length", ". both full length ctert", "both full length ctert mrna", "full length ctert mrna and", "length ctert mrna and numerous", "ctert mrna and numerous shorter", "mrna and numerous shorter mrnas", "and numerous shorter mrnas generated", "numerous shorter mrnas generated by", "shorter mrnas generated by alternative", "mrnas generated by alternative splicing", "generated by alternative splicing have", "by alternative splicing have been", "alternative splicing have been described", "splicing have been described although", "have been described although the", "been described although the function", "described although the function of", "although the function of these", "the function of these splice", "function of these splice variants", "of these splice variants remains", "these splice variants remains to", "splice variants remains to be", "variants remains to be clarified", "to be clarified chang", "be clarified chang and", "clarified chang and delany", "and delany 2006 hrdlickova", "delany 2006 hrdlickova et", "2006 hrdlickova et al.", "hrdlickova et al. 2006 .

in", "et al. 2006 .

in both", "al. 2006 .

in both chicken", "2006 .

in both chicken and", ".

in both chicken and human", "chicken and human telomerase", "and human telomerase activity", "human telomerase activity in", "telomerase activity in vivo is", "activity in vivo is robust", "in vivo is robust early", "vivo is robust early in", "is robust early in development", "early in development declines", "in development declines thereafter", "development declines thereafter in", "declines thereafter in most somatic", "thereafter in most somatic tissues", "most somatic tissues yet", "somatic tissues yet remains", "tissues yet remains active", "yet remains active in renewable", "remains active in renewable tissues", "in renewable tissues taylor", "renewable tissues taylor and", "tissues taylor and delany", "taylor and delany 2000 .", "and delany 2000 . telomerase", "delany 2000 . telomerase activity", "2000 . telomerase activity is", ". telomerase activity is also", "telomerase activity is also present", "activity is also present in", "is also present in most", "also present in most transformed", "present in most transformed cells", "in most transformed cells examined", "most transformed cells examined thus", "transformed cells examined thus far", "cells examined thus far in", "examined thus far in both", "thus far in both human", "far in both human and", "in both human and chicken", "human and chicken newbold", "and chicken newbold 2002", "newbold 2002 swanberg and", "2002 swanberg and delany", "and delany 2003 swanberg", "delany 2003 swanberg and", "2003 swanberg and delany", "swanberg and delany 2005 .", "and delany 2005 . telomerase", "delany 2005 . telomerase component", "2005 . telomerase component transcript", ". telomerase component transcript analysis", "component transcript analysis gene", "transcript analysis gene expression", "gene expression was examined", "expression was examined and", "was examined and cterc down", "examined and cterc down regulation", "and cterc down regulation correlates", "cterc down regulation correlates with", "down regulation correlates with absence", "regulation correlates with absence of", "correlates with absence of telomerase", "with absence of telomerase activity", "absence of telomerase activity in", "of telomerase activity in telomerase", "telomerase activity in telomerase negative", "activity in telomerase negative cells", "telomerase negative cells suggesting", "negative cells suggesting that", "cells suggesting that cterc", "suggesting that cterc may be", "that cterc may be the", "cterc may be the rate", "may be the rate limiting", "be the rate limiting component", "the rate limiting component in", "rate limiting component in some", "limiting component in some cell", "component in some cell types", "some cell types o'hare", "cell types o'hare and", "types o'hare and delany", "and delany 2005 swanberg", "delany 2005 swanberg and", "2005 swanberg and delany", "and delany 2005 . telomere", "delany 2005 . telomere shortening", "2005 . telomere shortening occurs", ". telomere shortening occurs in", "telomere shortening occurs in somatic", "shortening occurs in somatic tissues", "occurs in somatic tissues in", "in somatic tissues in vivo", "somatic tissues in vivo and", "tissues in vivo and correlates", "in vivo and correlates with", "vivo and correlates with age", "correlates with age taylor", "with age taylor and", "age taylor and delany", "and delany 2000 delany", "delany 2000 delany et", "2000 delany et al.", "delany et al. 2003 .", "et al. 2003 . division", "al. 2003 . division dependent", "2003 . division dependent telomere", ". division dependent telomere shortening", "division dependent telomere shortening is", "dependent telomere shortening is observed", "telomere shortening is observed in", "shortening is observed in non", "is observed in non immortalized", "in non immortalized non", "non immortalized non transformed", "immortalized non transformed chicken", "non transformed chicken cells in", "transformed chicken cells in vitro", "cells in vitro swanberg", "in vitro swanberg and", "vitro swanberg and delany", "swanberg and delany 2003 .

", "and delany 2003 .

in", "delany 2003 .

in human", ".

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chicken", "response in mammals.

chicken tlr4", "in mammals.

chicken tlr4 encodes", "mammals.

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"lack of myd88 independent", "of myd88 independent ifn", "myd88 independent ifn beta", "independent ifn beta production", "ifn beta production in", "beta production in chicken", "production in chicken after", "in chicken after tlr4", "chicken after tlr4 activation", "tlr4 activation keestra", "activation keestra et", "keestra et al. 2008", "al. 2008 zoete", "2008 zoete et", "zoete et al. 2009", "et al. 2009 .", "al. 2009 . unlike", "2009 . unlike its", ". unlike its human", "unlike its human counterpart", "its human counterpart activated", "human counterpart activated chicken", "counterpart activated chicken tlr4", "activated chicken tlr4 exclusively", "chicken tlr4 exclusively induces", "tlr4 exclusively induces the", "exclusively induces the myd88/tirap", "induces the myd88/tirap dependent", "myd88/tirap dependent but", "dependent but not", "but not the tram/trif", "not the tram/trif mediated", "the tram/trif mediated signaling", "tram/trif mediated signaling pathway.", "mediated signaling pathway. at", "signaling pathway. at present", "at present inspection", "present inspection of", "inspection of the chicken", "of the chicken genome", "the chicken genome indicated", "chicken genome indicated no", "genome indicated no orthologs", "indicated no orthologs for", "no orthologs for intracellular", "orthologs for intracellular human", "for intracellular human adaptor", "intracellular human adaptor tram", "adaptor tram keestra", "tram keestra et", "2008 which", "which acts as a", "acts as a bridge", "as a bridge to", "a bridge to recruit", "bridge to recruit trif", "to recruit trif to", "recruit trif to activated", "trif to activated tlr4.", "toll like receptor 4 is", "like receptor 4 is an", "receptor 4 is an evolutionarily", "4 is an evolutionarily conserved", "is an evolutionarily conserved microbe", "an evolutionarily conserved microbe associated", "evolutionarily conserved microbe associated molecular", "conserved microbe associated molecular pattern", "microbe associated molecular pattern receptor", "associated molecular pattern receptor well", "molecular pattern receptor well known", "pattern receptor well known for", "receptor well known for its", "well known for its sensitivity", "known for its sensitivity to", "for its sensitivity to bacterial", "its sensitivity to bacterial lipopolysaccharides", "to bacterial lipopolysaccharides lps", "bacterial lipopolysaccharides lps .", "lipopolysaccharides lps . lps", "lps . lps is a", ". lps is a major", "lps is a major cell", "is a major cell wall", "a major cell wall component", "major cell wall component in", "cell wall component in all", "wall component in all gram", "component in all gram negative", "in all gram negative bacteria", "all gram negative bacteria and", "gram negative bacteria and a", "negative bacteria and a potent", "bacteria and a potent activator", "and a potent activator of", "a potent activator of the", "potent activator of the innate", "activator of the innate immune", "of the innate immune response", "the innate immune response in", "innate immune response in mammals.

chicken", "immune response in mammals.

chicken tlr4", "response in mammals.

chicken tlr4 encodes", "in mammals.

chicken tlr4 encodes a", "mammals.

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. the major difference", ". the major difference between", "the major difference between mammalian", "major difference between mammalian and", "difference between mammalian and chicken", "between mammalian and chicken tlr", "mammalian and chicken tlr signaling", "and chicken tlr signaling is", "chicken tlr signaling is the", "tlr signaling is the lack", "signaling is the lack of", "is the lack of myd88", "the lack of myd88 independent", "lack of myd88 independent ifn", "of myd88 independent ifn beta", "myd88 independent ifn beta production", "independent ifn beta production in", "ifn beta production in chicken", "beta production in chicken after", "production in chicken after tlr4", "in chicken after tlr4 activation", "after tlr4 activation keestra", "tlr4 activation keestra et", "activation keestra et al.", "et al. 2008 zoete", "al. 2008 zoete et", "2008 zoete et al.", "zoete et al. 2009 .", "et al. 2009 . unlike", "al. 2009 . unlike its", "2009 . unlike its human", ". unlike its human counterpart", "unlike its human counterpart activated", "its human counterpart activated chicken", "human counterpart activated chicken tlr4", "counterpart activated chicken tlr4 exclusively", "activated chicken tlr4 exclusively induces", "chicken tlr4 exclusively induces the", "tlr4 exclusively induces the myd88/tirap", "exclusively induces the myd88/tirap dependent", "the myd88/tirap dependent but", "myd88/tirap dependent but not", "dependent but not the", "but not the tram/trif mediated", "not the tram/trif mediated signaling", "the tram/trif mediated signaling pathway.", "tram/trif mediated signaling pathway. at", "mediated signaling pathway. at present", "pathway. at present inspection", "at present inspection of", "present inspection of the", "inspection of the chicken genome", "of the chicken genome indicated", "the chicken genome indicated no", "chicken genome indicated no orthologs", "genome indicated no orthologs for", "indicated no orthologs for intracellular", "no orthologs for intracellular human", "orthologs for intracellular human adaptor", "for intracellular human adaptor tram", "human adaptor tram keestra", "adaptor tram keestra et", "tram keestra et al.", "al. 2008 which", "2008 which acts", "which acts as a bridge", "acts as a bridge to", "as a bridge to recruit", "a bridge to recruit trif", "bridge to recruit trif to", "to recruit trif to activated", "recruit trif to activated tlr4." ] }, { "record_id": "GLY_000968_1_442", "filename": "chicken_protein_pathways_reactome", "fieldtype": "id", "phraselist": [ "gly_000968", "gga", "433819", "r gga", "gga 433819", "r gga 433819" ] }, { "record_id": "GLY_000968_1_442", "filename": "chicken_protein_pathways_reactome", "fieldtype": "text", "phraselist": [ "viral dsrna:tlr3:ticam1", "dsrna:tlr3:ticam1 complex", "complex activates", "activates ikbke_chick", "viral dsrna:tlr3:ticam1 complex", "dsrna:tlr3:ticam1 complex activates", "complex activates ikbke_chick", "viral dsrna:tlr3:ticam1 complex 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", "

it", "it was", "was also", "also reported", "reported that", "that ikki", "ikki directly", "directly phophorylates", "phophorylates signal", "signal transducer", "transducer and", "and activator", "activator of", "of transcription", "transcription 1", "tenoever et", "al 2007", "2007 .

chicken", ".

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", ".

it", "

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chicken", "2007 .

chicken ikki", ".

chicken ikki shows", "ikki shows 68%", "68% and", "and 62% identity", "62% identity to", "identity to the", "to the human", "the human ikki", "human ikki and", "ikki and human", "and human tbk1", "human tbk1 respectively.", "embryonic fibroblast cells from", "fibroblast cells from tbk1", "cells from tbk1 deficient", "from tbk1 deficient mice", "tbk1 deficient mice show", "deficient mice show decreased", "mice show decreased irf3", "show decreased irf3 activation", "decreased irf3 activation and", "irf3 activation and ifn", "activation and ifn induction", "and ifn induction by", "ifn induction by poly", "induction by poly ic", "poly ic while", "ic while ikki", "while ikki deficient cells", "ikki deficient cells show", "deficient cells show normal", "cells show normal irf3", "show normal irf3 activation.", "normal irf3 activation. however", "activation. however residual", "however residual activation", "residual activation of irf3", "activation of irf3 in", "of irf3 in tbk1", "irf3 in tbk1 deficient", "in tbk1 deficient cells", "tbk1 deficient cells is", "deficient cells is totally", "cells is totally abolished", "is totally abolished in", "totally abolished in tbk1", "abolished in tbk1 and", "in tbk1 and ikki", "tbk1 and ikki double", "and ikki double deficient", "ikki double deficient cells", "deficient cells indicating", "cells indicating that", "indicating that the functions", "that the functions of", "the functions of tbk1", "functions of tbk1 and", "of tbk1 and ikki", "tbk1 and ikki are", "and ikki are redundant", "ikki are redundant in", "are redundant in fibroblast", "redundant in fibroblast cells.", "in fibroblast cells. hemmi", "fibroblast cells. hemmi et", "cells. hemmi et al", "hemmi et al 2004", "et al 2004 .", "al 2004 .

", "2004 .

it", ".

it was", "

it was also", "it was also reported", "was also reported that", "also reported that ikki", "reported that ikki directly", "that ikki directly phophorylates", "ikki directly phophorylates signal", "directly phophorylates signal transducer", "phophorylates signal transducer and", "signal transducer and activator", "transducer and activator of", "and activator of transcription", "activator of transcription 1", "transcription 1 stat1", "stat1 tenoever", "tenoever et al 2007", "et al 2007 .

chicken", "al 2007 .

chicken ikki", "2007 .

chicken ikki shows", ".

chicken ikki shows 68%", "shows 68% and", "68% and 62%", "and 62% identity to", "62% identity to the", "identity to the human", "to the human ikki", "the human ikki and", "human ikki and human", "ikki and human tbk1", "and human tbk1 respectively.", "embryonic fibroblast cells from tbk1", "fibroblast cells from tbk1 deficient", "cells from tbk1 deficient mice", "from tbk1 deficient mice show", "tbk1 deficient mice show decreased", "deficient mice show decreased irf3", "mice show decreased irf3 activation", "show decreased irf3 activation and", "decreased irf3 activation and ifn", "irf3 activation and ifn induction", "activation and ifn induction by", "and ifn induction by poly", "ifn induction by poly ic", "by poly ic while", "poly ic while ikki", "ic while ikki deficient", "while ikki deficient cells show", "ikki deficient cells show normal", "deficient cells show normal irf3", "cells show normal irf3 activation.", "show normal irf3 activation. however", "irf3 activation. however residual", "activation. however residual activation", "however residual activation of", "residual activation of irf3 in", "activation of irf3 in tbk1", "of irf3 in tbk1 deficient", "irf3 in tbk1 deficient cells", "in tbk1 deficient cells is", "tbk1 deficient cells is totally", "deficient cells is totally abolished", "cells is totally abolished in", "is totally abolished in tbk1", "totally abolished in tbk1 and", "abolished in tbk1 and ikki", "in tbk1 and ikki double", "tbk1 and ikki double deficient", "and ikki double deficient cells", "double deficient cells indicating", "deficient cells indicating that", "cells indicating that the", "indicating that the functions of", "that the functions of tbk1", "the functions of tbk1 and", "functions of tbk1 and ikki", "of tbk1 and ikki are", "tbk1 and ikki are redundant", "and ikki are redundant in", "ikki are redundant in fibroblast", "are redundant in fibroblast cells.", "redundant in fibroblast cells. hemmi", "in fibroblast cells. hemmi et", "fibroblast cells. hemmi et al", "cells. hemmi et al 2004", "hemmi et al 2004 .", "et al 2004 .

", "al 2004 .

it", "2004 .

it was", ".

it was also", "

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chicken", "et al 2007 .

chicken ikki", "al 2007 .

chicken ikki shows", "2007 .

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"cxcli2 through activation of", "through activation of transcription factors", "activation of transcription factors nfkb", "of transcription factors nfkb and", "transcription factors nfkb and ap", "factors nfkb and ap 1." ] }, { "record_id": "GLY_000968_1_444", "filename": "chicken_protein_pathways_reactome", "fieldtype": "id", "phraselist": [ "gly_000968", "gga", "433871", "r gga", "gga 433871", "r gga 433871" ] }, { "record_id": "GLY_000968_1_444", "filename": "chicken_protein_pathways_reactome", "fieldtype": "text", "phraselist": [ "traf6 mediated", "mediated induction", "induction of", "of proinflammatory", "proinflammatory cytokines", "traf6 mediated induction", "mediated induction of", "induction of proinflammatory", "of proinflammatory cytokines", "traf6 mediated induction of", "mediated induction of proinflammatory", "induction of proinflammatory cytokines", "traf6 mediated induction of proinflammatory", "mediated induction of proinflammatory cytokines", "together with", "with 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tak1", ".

tak1 phosphorylates", "phosphorylates ikk", "ikk alpha", "alpha and", "and ikk", "ikk beta", "which in", "in turn", "turn phosphorylate", "phosphorylate nf", "nf kb", "kb inhibitors", "and eventually", "eventually results", "results in", "in ikb", "ikb degradation", "degradation and", "and nf", "kb translocation", "translocation to", "to the", "the nucleus.", "nucleus. also", "also tak1", "tak1 mediates", "mediates jnk", "jnk and", "and p38", "p38 map", "map kinases", "kinases activation", "activation by", "by phosphorylating", "phosphorylating mkk4/7", "mkk4/7 and", "and mkk3/6", "mkk3/6 respectively", "respectively resulting", "resulting in", "in the", "the activation", "of many", "many transcription", "transcription factors.", "factors.

the", "

the role", "role of", "is somewhat", "somewhat controversial", "controversial and", "and probably", "probably cell", "cell type", "type specific.", "specific. traf6", "traf6 autoubiquitination", "autoubiquitination was", "was found", "found to", "to be", "be dispensable", "dispensable for", "for traf6", "traf6 function", "function to", "to activate", "activate the", "the tak1", "tak1 pathway.", "pathway. these", "these findings", "findings are", "are consistent", "consistent with", "with the", "the new", "new mechanism", "mechanism of", "mediated nf", "kb activation", "activation that", "that was", "was suggested", "suggested by", "by xia", "xia et", "et al.", "2009 .", ". traf6", "traf6 generates", "generates unanchored", "unanchored lys63", "linked polyubiquitin", "polyubiquitin chains", "chains that", "that bind", "bind to", "the regulatory", "regulatory subunits", "subunits of", "of the", "leading to", "the kinases.

", "kinases.

xia", "demonstrated in", "in vitro", "vitro that", "that unlike", "unlike polyubiquitin", "chains covalently", "covalently attached", "attached to", "to traf6", "traf6 or", "or irak", "tab2 and", "and nemo", "nemo associated", "associated ubiquitin", "ubiquitin chains", "chains were", "were unanchored", "unanchored and", "and susceptible", "susceptible to", "to n", "n terminal", "terminal ubiquitin", "ubiquitin cleavage.", "cleavage. only", "only k63", "k63 linked", "but not", "not monomeric", "monomeric ubiquitin", "activated tak1", "tak1 in", "in a", "a dose", "dose dependent", "dependent manner.", "manner. optimal", "optimal activation", "the ikk", "ikk complex", "complex was", "was achieved", "achieved using", "using ubiquitin", "ubiquitin polymers", "polymers containing", "containing both", "both k48", "k48 and", "and k63", "k63 linkages.

furthermore", "the authors", "authors proposed", "proposed that", "that the", "tak1 complexes", "complexes might", "might be", "be brougt", "brougt in", "in close", "close proximity", "proximity by", "binding several", "several tab2/3", "tab2/3 to", "to a", "a single", "single polyubiquitin", "polyubiquitin chain", "chain to", "to facilitate", "facilitate tak1", "tak1 kinases", "kinases trans", "trans phosphorylation.", "phosphorylation. alternatively", "the possibility", "possibility that", "that polyub", "polyub binding", "binding promotes", "promotes allosteric", "allosteric activation", "of tak1", "tak1 complex", "complex should", "be considered.", "together with ubiquitin", "with ubiquitin conjugating", "ubiquitin conjugating e2", "conjugating e2 type", "e2 type enzymes", "type enzymes ubc13", "enzymes ubc13 and", "ubc13 and uev1a", "uev1a also", "also known as", "known as ube2v1", "traf6 catalyzes lys63", "catalyzes lys63 linked", "lys63 linked ubiquitination.", "linked ubiquitination. it", "ubiquitination. it is", "it is believed", "is believed that", "believed that auto", "that auto polyubiquitination", "auto polyubiquitination and", "polyubiquitination and oligomerization", "and oligomerization of", "oligomerization of traf6", "of traf6 is", "traf6 is followed", "is followed by", "followed by binding", "by binding the", "binding the ubiquitin", "the ubiquitin receptors", "ubiquitin receptors of", "receptors of tab2", "of tab2 or", "tab2 or tab3", "tab3 tak1", "tak1 binding protein", "binding protein 2", "protein 2 and", "2 and 3", "which stimulates phosphorylation", "stimulates phosphorylation and", "phosphorylation and activation", "and activation of", "activation of tgf", "of tgf beta", "tgf beta activated", "beta activated kinase", "activated kinase 1", "kinase 1 tak1", "1 tak1 .

tak1", "tak1 .

tak1 phosphorylates", ".

tak1 phosphorylates ikk", "phosphorylates ikk alpha", "ikk alpha and", "alpha and ikk", "and ikk beta", "beta which", "which in turn", "in turn phosphorylate", "turn phosphorylate nf", "phosphorylate nf kb", "nf kb inhibitors", "ikb and", "and eventually results", "eventually results in", "results in ikb", "in ikb degradation", "ikb degradation and", "degradation and nf", "and nf kb", "nf kb translocation", "kb translocation to", "translocation to the", "to the nucleus.", "the nucleus. also", "nucleus. also tak1", "also tak1 mediates", "tak1 mediates jnk", "mediates jnk and", "jnk and p38", "and p38 map", "p38 map kinases", "map kinases activation", "kinases activation by", "activation by phosphorylating", "by phosphorylating mkk4/7", "phosphorylating mkk4/7 and", "mkk4/7 and mkk3/6", "and mkk3/6 respectively", "mkk3/6 respectively resulting", "respectively resulting in", "resulting in the", "in the activation", "the activation of", "activation of many", "of many transcription", "many transcription factors.", "transcription factors.

the", "factors.

the role", "

the role of", "role of traf6", "traf6 is somewhat", "is somewhat controversial", "somewhat controversial and", "controversial and probably", "and probably cell", "probably cell type", "cell type specific.", "type specific. traf6", "specific. traf6 autoubiquitination", "traf6 autoubiquitination was", "autoubiquitination was found", "was found to", "found to be", "to be dispensable", "be dispensable for", "dispensable for traf6", "for traf6 function", "traf6 function to", "function to activate", "to activate the", "activate the tak1", "the tak1 pathway.", "tak1 pathway. these", "pathway. these findings", "these findings are", "findings are consistent", "are consistent with", "consistent with the", "with the new", "the new mechanism", "new mechanism of", "mechanism of traf6", "of traf6 mediated", "traf6 mediated nf", "mediated nf kb", "nf kb activation", "kb activation that", "activation that was", "that was suggested", "was suggested by", "suggested by xia", "by xia et", "xia et al.", "al. 2009", "2009 . traf6", ". traf6 generates", "traf6 generates unanchored", "generates unanchored lys63", "unanchored lys63 linked", "lys63 linked polyubiquitin", "linked polyubiquitin chains", "polyubiquitin chains that", "chains that bind", "that bind to", "bind to the", "to the regulatory", "the regulatory subunits", "regulatory subunits of", "subunits of the", "of the tak1", "tak1 tab2", "tab3 and", "ikk nemo", "leading to the", "to the activation", "activation of the", "of the kinases.

", "the kinases.

xia", "kinases.

xia et", "2009 demonstrated", "demonstrated in vitro", "in vitro that", "vitro that unlike", "that unlike polyubiquitin", "unlike polyubiquitin chains", "polyubiquitin chains covalently", "chains covalently attached", "covalently attached to", "attached to traf6", "to traf6 or", "traf6 or irak", "irak tab2", "tab2 and nemo", "and nemo associated", "nemo associated ubiquitin", "associated ubiquitin chains", "ubiquitin chains were", "chains were unanchored", "were unanchored and", "unanchored and susceptible", "and susceptible to", "susceptible to n", "to n terminal", "n terminal ubiquitin", "terminal ubiquitin cleavage.", "ubiquitin cleavage. only", "cleavage. only k63", "only k63 linked", "k63 linked polyubiquitin", "chains but", "but not monomeric", "not monomeric ubiquitin", "ubiquitin activated", "activated tak1 in", "tak1 in a", "in a dose", "a dose dependent", "dose dependent manner.", "dependent manner. optimal", "manner. optimal activation", "optimal activation of", "of the ikk", "the ikk complex", "ikk complex was", "complex was achieved", "was achieved using", "achieved using ubiquitin", "using ubiquitin polymers", "ubiquitin polymers containing", "polymers containing both", "containing both k48", "both k48 and", "k48 and k63", "and k63 linkages.

furthermore", "linkages.

furthermore the", "the authors proposed", "authors proposed that", "proposed that the", "that the tak1", "the tak1 complexes", "tak1 complexes might", "complexes might be", "might be brougt", "be brougt in", "brougt in close", "in close proximity", "close proximity by", "proximity by binding", "by binding several", "binding several tab2/3", "several tab2/3 to", "tab2/3 to a", "to a single", "a single polyubiquitin", "single polyubiquitin chain", "polyubiquitin chain to", "chain to facilitate", "to facilitate tak1", "facilitate tak1 kinases", "tak1 kinases trans", "kinases trans phosphorylation.", "trans phosphorylation. alternatively", "alternatively the", "the possibility that", "possibility that polyub", "that polyub binding", "polyub binding promotes", "binding promotes allosteric", "promotes allosteric activation", "allosteric activation of", "activation of tak1", "of tak1 complex", "tak1 complex should", "should be", "together with ubiquitin conjugating", "with ubiquitin conjugating e2", "ubiquitin conjugating e2 type", "conjugating e2 type enzymes", "e2 type enzymes ubc13", "type enzymes ubc13 and", "enzymes ubc13 and uev1a", "and uev1a also", "uev1a also known", "also known as ube2v1", "ube2v1 traf6", "traf6 catalyzes lys63 linked", "catalyzes lys63 linked ubiquitination.", "lys63 linked ubiquitination. it", "linked ubiquitination. it is", "ubiquitination. it is believed", "it is believed that", "is believed that auto", "believed that auto polyubiquitination", "that auto polyubiquitination and", "auto polyubiquitination and oligomerization", "polyubiquitination and oligomerization of", "and oligomerization of traf6", "oligomerization of traf6 is", "of traf6 is followed", "traf6 is followed by", "is followed by binding", "followed by binding the", "by binding the ubiquitin", "binding the ubiquitin receptors", "the ubiquitin receptors of", "ubiquitin receptors of tab2", "receptors of tab2 or", "of tab2 or tab3", "or tab3 tak1", "tab3 tak1 binding", "tak1 binding protein 2", "binding protein 2 and", "protein 2 and 3", "3 which", "which stimulates phosphorylation and", "stimulates phosphorylation and activation", "phosphorylation and activation of", "and activation of tgf", "activation of tgf beta", "of tgf beta activated", "tgf beta activated kinase", "beta activated kinase 1", "activated kinase 1 tak1", "kinase 1 tak1 .

tak1", "1 tak1 .

tak1 phosphorylates", "tak1 .

tak1 phosphorylates ikk", ".

tak1 phosphorylates ikk alpha", "phosphorylates ikk alpha and", "ikk alpha and ikk", "alpha and ikk beta", "ikk beta which", "beta which in", "which in turn phosphorylate", "in turn phosphorylate nf", "turn phosphorylate nf kb", "phosphorylate nf kb inhibitors", "inhibitors ikb", "ikb and eventually", "and eventually results in", "eventually results in ikb", "results in ikb degradation", "in ikb degradation and", "ikb degradation and nf", "degradation and nf kb", "and nf kb translocation", "nf kb translocation to", "kb translocation to the", "translocation to the nucleus.", "to the nucleus. also", "the nucleus. also tak1", "nucleus. also tak1 mediates", "also tak1 mediates jnk", "tak1 mediates jnk and", "mediates jnk and p38", "jnk and p38 map", "and p38 map kinases", "p38 map kinases activation", "map kinases activation by", "kinases activation by phosphorylating", "activation by phosphorylating mkk4/7", "by phosphorylating mkk4/7 and", "phosphorylating mkk4/7 and mkk3/6", "mkk4/7 and mkk3/6 respectively", "and mkk3/6 respectively resulting", "mkk3/6 respectively resulting in", "respectively resulting in the", "resulting in the activation", "in the activation of", "the activation of many", "activation of many transcription", "of many transcription factors.", "many transcription factors.

the", "transcription factors.

the role", "factors.

the role of", "

the role of traf6", "role of traf6 is", "of traf6 is somewhat", "traf6 is somewhat controversial", "is somewhat controversial and", "somewhat controversial and probably", "controversial and probably cell", "and probably cell type", "probably cell type specific.", "cell type specific. traf6", "type specific. traf6 autoubiquitination", "specific. traf6 autoubiquitination was", "traf6 autoubiquitination was found", "autoubiquitination was found to", "was found to be", "found to be dispensable", "to be dispensable for", "be dispensable for traf6", "dispensable for traf6 function", "for traf6 function to", "traf6 function to activate", "function to activate the", "to activate the tak1", "activate the tak1 pathway.", "the tak1 pathway. these", "tak1 pathway. these findings", "pathway. these findings are", "these findings are consistent", "findings are consistent with", "are consistent with the", "consistent with the new", "with the new mechanism", "the new mechanism of", "new mechanism of traf6", "mechanism of traf6 mediated", "of traf6 mediated nf", "traf6 mediated nf kb", "mediated nf kb activation", "nf kb activation that", "kb activation that was", "activation that was suggested", "that was suggested by", "was suggested by xia", "suggested by xia et", "by xia et al.", "et al. 2009", "al. 2009 .", "2009 . traf6 generates", ". traf6 generates unanchored", "traf6 generates unanchored lys63", "generates unanchored lys63 linked", "unanchored lys63 linked polyubiquitin", "lys63 linked polyubiquitin chains", "linked polyubiquitin chains that", "polyubiquitin chains that bind", "chains that bind to", "that bind to the", "bind to the regulatory", "to the regulatory subunits", "the regulatory subunits of", "regulatory subunits of the", "subunits of the tak1", "the tak1 tab2", "tak1 tab2 or", "or tab3 and", "tab3 and ikk", "and ikk nemo", "nemo leading", "leading to the activation", "to the activation of", "the activation of the", "activation of the kinases.

", "of the kinases.

xia", "the kinases.

xia et", "kinases.

xia et al.", "2009 demonstrated in", "demonstrated in vitro that", "in vitro that unlike", "vitro that unlike polyubiquitin", "that unlike polyubiquitin chains", "unlike polyubiquitin chains covalently", "polyubiquitin chains covalently attached", "chains covalently attached to", "covalently attached to traf6", "attached to traf6 or", "to traf6 or irak", "or irak tab2", "irak tab2 and", "tab2 and nemo associated", "and nemo associated ubiquitin", "nemo associated ubiquitin chains", "associated ubiquitin chains were", "ubiquitin chains were unanchored", "chains were unanchored and", "were unanchored and susceptible", "unanchored and susceptible to", "and susceptible to n", "susceptible to n terminal", "to n terminal ubiquitin", "n terminal ubiquitin cleavage.", "terminal ubiquitin cleavage. only", "ubiquitin cleavage. only k63", "cleavage. only k63 linked", "only k63 linked polyubiquitin", "k63 linked polyubiquitin chains", "polyubiquitin chains but", "chains but not", "but not monomeric ubiquitin", "monomeric ubiquitin activated", "ubiquitin activated tak1", "activated tak1 in a", "tak1 in a dose", "in a dose dependent", "a dose dependent manner.", "dose dependent manner. optimal", "dependent manner. optimal activation", "manner. optimal activation of", "optimal activation of the", "activation of the ikk", "of the ikk complex", "the ikk complex was", "ikk complex was achieved", "complex was achieved using", "was achieved using ubiquitin", "achieved using ubiquitin polymers", "using ubiquitin polymers containing", "ubiquitin polymers containing both", "polymers containing both k48", "containing both k48 and", "both k48 and k63", "k48 and k63 linkages.

furthermore", "k63 linkages.

furthermore the", "linkages.

furthermore the authors", "the authors proposed that", "authors proposed that the", "proposed that the tak1", "that the tak1 complexes", "the tak1 complexes might", "tak1 complexes might be", "complexes might be brougt", "might be brougt in", "be brougt in close", "brougt in close proximity", "in close proximity by", "close proximity by binding", "proximity by binding several", "by binding several tab2/3", "binding several tab2/3 to", "several tab2/3 to a", "tab2/3 to a single", "to a single polyubiquitin", "a single polyubiquitin chain", "single polyubiquitin chain to", "polyubiquitin chain to facilitate", "chain to facilitate tak1", "to facilitate tak1 kinases", "facilitate tak1 kinases trans", "tak1 kinases trans phosphorylation.", "kinases trans phosphorylation. alternatively", "phosphorylation. alternatively the", "alternatively the possibility", "the possibility that polyub", "possibility that polyub binding", "that polyub binding promotes", "polyub binding promotes allosteric", "binding promotes allosteric activation", "promotes allosteric activation of", "allosteric activation of tak1", "activation of tak1 complex", "of tak1 complex should", "complex should be", "should be considered.", "together with ubiquitin conjugating e2", "with ubiquitin conjugating e2 type", "ubiquitin conjugating e2 type enzymes", "conjugating e2 type enzymes ubc13", "e2 type enzymes ubc13 and", "type enzymes ubc13 and uev1a", "ubc13 and uev1a also", "and uev1a also known", "uev1a also known as", "as ube2v1 traf6", "ube2v1 traf6 catalyzes", "traf6 catalyzes lys63 linked ubiquitination.", "catalyzes lys63 linked ubiquitination. it", "lys63 linked ubiquitination. it is", "linked ubiquitination. it is believed", "ubiquitination. it is believed that", "it is believed that auto", "is believed that auto polyubiquitination", "believed that auto polyubiquitination and", "that auto polyubiquitination and oligomerization", "auto polyubiquitination and oligomerization of", "polyubiquitination and oligomerization of traf6", "and oligomerization of traf6 is", "oligomerization of traf6 is followed", "of traf6 is followed by", "traf6 is followed by binding", "is followed by binding the", "followed by binding the ubiquitin", "by binding the ubiquitin receptors", "binding the ubiquitin receptors of", "the ubiquitin receptors of tab2", "ubiquitin receptors of tab2 or", "receptors of tab2 or tab3", "tab2 or tab3 tak1", "or tab3 tak1 binding", "tab3 tak1 binding protein", "tak1 binding protein 2 and", "binding protein 2 and 3", "and 3 which", "3 which stimulates", "which stimulates phosphorylation and activation", "stimulates phosphorylation and activation of", "phosphorylation and activation of tgf", "and activation of tgf beta", "activation of tgf beta activated", "of tgf beta activated kinase", "tgf beta activated kinase 1", "beta activated kinase 1 tak1", "activated kinase 1 tak1 .

tak1", "kinase 1 tak1 .

tak1 phosphorylates", "1 tak1 .

tak1 phosphorylates ikk", "tak1 .

tak1 phosphorylates ikk alpha", ".

tak1 phosphorylates ikk alpha and", "phosphorylates ikk alpha and ikk", "ikk alpha and ikk beta", "and ikk beta which", "ikk beta which in", "beta which in turn", "which in turn phosphorylate nf", "in turn phosphorylate nf kb", "turn phosphorylate nf kb inhibitors", "kb inhibitors ikb", "ikb and eventually results", "and eventually results in ikb", "eventually results in ikb degradation", "results in ikb degradation and", "in ikb degradation and nf", "ikb degradation and nf kb", "degradation and nf kb translocation", "and nf kb translocation to", "nf kb translocation to the", "kb translocation to the nucleus.", "translocation to the nucleus. also", "to the nucleus. also tak1", "the nucleus. also tak1 mediates", "nucleus. also tak1 mediates jnk", "also tak1 mediates jnk and", "tak1 mediates jnk and p38", "mediates jnk and p38 map", "jnk and p38 map kinases", "and p38 map kinases activation", "p38 map kinases activation by", "map kinases activation by phosphorylating", "kinases activation by phosphorylating mkk4/7", "activation by phosphorylating mkk4/7 and", "by phosphorylating mkk4/7 and mkk3/6", "phosphorylating mkk4/7 and mkk3/6 respectively", "mkk4/7 and mkk3/6 respectively resulting", "and mkk3/6 respectively resulting in", "mkk3/6 respectively resulting in the", "respectively resulting in the activation", "resulting in the activation of", "in the activation of many", "the activation of many transcription", "activation of many transcription factors.", "of many transcription factors.

the", "many transcription factors.

the role", "transcription factors.

the role of", "factors.

the role of traf6", "

the role of traf6 is", "role of traf6 is somewhat", "of traf6 is somewhat controversial", "traf6 is somewhat controversial and", "is somewhat controversial and probably", "somewhat controversial and probably cell", "controversial and probably cell type", "and probably cell type specific.", "probably cell type specific. traf6", "cell type specific. traf6 autoubiquitination", "type specific. traf6 autoubiquitination was", "specific. traf6 autoubiquitination was found", "traf6 autoubiquitination was found to", "autoubiquitination was found to be", "was found to be dispensable", "found to be dispensable for", "to be dispensable for traf6", "be dispensable for traf6 function", "dispensable for traf6 function to", "for traf6 function to activate", "traf6 function to activate the", "function to activate the tak1", "to activate the tak1 pathway.", "activate the tak1 pathway. these", "the tak1 pathway. these findings", "tak1 pathway. these findings are", "pathway. these findings are consistent", "these findings are consistent with", "findings are consistent with the", "are consistent with the new", "consistent with the new mechanism", "with the new mechanism of", "the new mechanism of traf6", "new mechanism of traf6 mediated", "mechanism of traf6 mediated nf", "of traf6 mediated nf kb", "traf6 mediated nf kb activation", "mediated nf kb activation that", "nf kb activation that was", "kb activation that was suggested", "activation that was suggested by", "that was suggested by xia", "was suggested by xia et", "suggested by xia et al.", "xia et al. 2009", "et al. 2009 .", "al. 2009 . traf6", "2009 . traf6 generates unanchored", ". traf6 generates unanchored lys63", "traf6 generates unanchored lys63 linked", "generates unanchored lys63 linked polyubiquitin", "unanchored lys63 linked polyubiquitin chains", "lys63 linked polyubiquitin chains that", "linked polyubiquitin chains that bind", "polyubiquitin chains that bind to", "chains that bind to the", "that bind to the regulatory", "bind to the regulatory subunits", "to the regulatory subunits of", "the regulatory subunits of the", "regulatory subunits of the tak1", "of the tak1 tab2", "the tak1 tab2 or", "tak1 tab2 or tab3", "tab2 or tab3 and", "or tab3 and ikk", "nemo leading to", "leading to the activation of", "to the activation of the", "the activation of the kinases.

", "activation of the kinases.

xia", "of the kinases.

xia et", "the kinases.

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activation", "for trif dependent activation of", "trif dependent activation of irf3", "activation of irf3 which", "of irf3 which occurs", "irf3 which occurs in", "which occurs in a trif/tbk1/ikki", "occurs in a trif/tbk1/ikki dependent", "in a trif/tbk1/ikki dependent manner", "trif/tbk1/ikki dependent manner cusson", "dependent manner cusson hermance", "manner cusson hermance et", "et al. 2005 sato", "al. 2005 sato et", "2005 sato et al." ] }, { "record_id": "GLY_000968_1_448", "filename": "chicken_protein_pathways_reactome", "fieldtype": "id", "phraselist": [ "gly_000968", "gga", "434136", "r gga", "gga 434136", "r gga 434136" ] }, { "record_id": "GLY_000968_1_448", "filename": "chicken_protein_pathways_reactome", "fieldtype": "text", "phraselist": [ "viral dsrna:tlr3:ticam1", "dsrna:tlr3:ticam1 complex", "complex activates", "activates tbk1", "viral dsrna:tlr3:ticam1 complex", "dsrna:tlr3:ticam1 complex activates", "complex activates tbk1", "viral dsrna:tlr3:ticam1 complex 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embryonic fibroblast", "fibroblast cells", "cells from", "from tbk1", "tbk1 deficient", "deficient mice", "mice show", "show decreased", "decreased irf3", "irf3 activation", "activation and", "and ifn", "ifn induction", "induction by", "by poly", "poly ic", "while ikki", "ikki deficient", "deficient cells", "cells show", "show normal", "normal irf3", "irf3 activation.", "activation. however", "the activation", "activation of", "of irf3", "irf3 is", "is totally", "totally abolished", "abolished in", "in tbk1", "and ikki", "ikki double", "double deficient", "indicating that", "that the", "the functions", "functions of", "of tbk1", "ikki are", "are redundant", "redundant in", "in mouse", "mouse embryo", "embryo fibroblast", "fibroblast cells.", "cells. hemmi", "hemmi et", "et al", "al 2004", "2004 .

tbk1/ikki", ".

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embryonic", "regulatory factors.

embryonic fibroblast", "factors.

embryonic fibroblast cells", "fibroblast cells from", "cells from tbk1", "from tbk1 deficient", "tbk1 deficient mice", "deficient mice show", "mice show decreased", "show decreased irf3", "decreased irf3 activation", "irf3 activation and", "activation and ifn", "and ifn induction", "ifn induction by", "induction by poly", "by poly ic", "ic while", "while ikki deficient", "ikki deficient cells", "deficient cells show", "cells show normal", "show normal irf3", "normal irf3 activation.", "irf3 activation. however", "however the", "the activation of", "activation of irf3", "of irf3 is", "irf3 is totally", "is totally abolished", "totally abolished in", "abolished in tbk1", "in tbk1 and", "tbk1 and ikki", "and ikki double", "ikki double deficient", "double deficient cells", "cells indicating", "indicating that the", "that the functions", "the functions of", "functions of tbk1", "of tbk1 and", "and ikki are", "ikki are redundant", "are redundant in", "redundant in mouse", "in mouse embryo", "mouse embryo fibroblast", "embryo fibroblast cells.", "fibroblast cells. hemmi", "cells. hemmi et", "hemmi et al", "et al 2004", "al 2004 .

tbk1/ikki", "2004 .

tbk1/ikki interact", ".

tbk1/ikki interact with", "interact with sike", "sike suppressor", "suppressor of ikk", "of ikk epsilon", "which was shown", "was shown to", "shown to act", "to act as", "act as an", "as an inhibitor", "an inhibitor of", "inhibitor of tbk1/ikki", "of tbk1/ikki mediated", "tbk1/ikki mediated type", "mediated type i", "type i ifn", "i ifn production", "production but", "but not nf", "not nf kb", "nf kb activation", "kb activation signaling", "activation signaling huang", "signaling huang j", "huang j et", "j et al", "et al 2005", "al 2005 .", "tbk1 and ikk epsilon", "and ikk epsilon ikki", "epsilon ikki are", "ikki are described", "are described as essential", "described as essential regulators", "as essential regulators of", "essential regulators of pathogen", "regulators of pathogen triggered", "of pathogen triggered ifn", "pathogen triggered ifn gene", "triggered ifn gene activation", "ifn gene activation through", "gene activation through the", "activation through the direct", "through the direct phosphorylation", "the direct phosphorylation of", "direct phosphorylation of ifn", "phosphorylation of ifn regulatory", "of ifn regulatory factors.

embryonic", "ifn regulatory factors.

embryonic fibroblast", "regulatory factors.

embryonic fibroblast cells", "factors.

embryonic fibroblast cells from", "fibroblast cells from tbk1", "cells from tbk1 deficient", "from tbk1 deficient mice", "tbk1 deficient mice show", "deficient mice show decreased", "mice show decreased irf3", "show decreased irf3 activation", "decreased irf3 activation and", "irf3 activation and ifn", "activation and ifn induction", "and ifn induction by", "ifn induction by poly", "induction by poly ic", "poly ic while", "ic while ikki", "while ikki deficient cells", "ikki deficient cells show", "deficient cells show normal", "cells show normal irf3", "show normal irf3 activation.", "normal irf3 activation. however", "activation. however the", "however the activation", "the activation of irf3", "activation of irf3 is", "of irf3 is totally", "irf3 is totally abolished", "is totally abolished in", "totally abolished in tbk1", "abolished in tbk1 and", "in tbk1 and ikki", "tbk1 and ikki double", "and ikki double deficient", "ikki double deficient cells", "deficient cells indicating", "cells indicating that", "indicating that the functions", "that the functions of", "the functions of tbk1", "functions of tbk1 and", "of tbk1 and ikki", "tbk1 and ikki are", "and ikki are redundant", "ikki are redundant in", "are redundant in mouse", "redundant in mouse embryo", "in mouse embryo fibroblast", "mouse embryo fibroblast cells.", "embryo fibroblast cells. hemmi", "fibroblast cells. hemmi et", "cells. hemmi et al", "hemmi et al 2004", "et al 2004 .

tbk1/ikki", "al 2004 .

tbk1/ikki interact", "2004 .

tbk1/ikki interact with", ".

tbk1/ikki interact with sike", "with sike suppressor", "sike suppressor of", "suppressor of ikk epsilon", "epsilon which", "which was shown to", "was shown to act", "shown to act as", "to act as an", "act as an inhibitor", "as an inhibitor of", "an inhibitor of tbk1/ikki", "inhibitor of tbk1/ikki mediated", "of tbk1/ikki mediated type", "tbk1/ikki mediated type i", "mediated type i ifn", "type i ifn production", "ifn production but", "production but not", "but not nf kb", "not nf kb activation", "nf kb activation signaling", "kb activation signaling huang", "activation signaling huang j", "signaling huang j et", "huang j et al", "j et al 2005", "et al 2005 .", "tbk1 and ikk epsilon ikki", "ikk epsilon ikki are", "epsilon ikki are described", "ikki are described as", "are described as essential regulators", "described as essential regulators of", "as essential regulators of pathogen", "essential regulators of pathogen triggered", "regulators of pathogen triggered ifn", "of pathogen triggered ifn gene", "pathogen triggered ifn gene activation", "triggered ifn gene activation through", "ifn gene activation through the", "gene activation through the direct", "activation through the direct phosphorylation", "through the direct phosphorylation of", "the direct phosphorylation of ifn", "direct phosphorylation of ifn regulatory", "phosphorylation of ifn regulatory factors.

embryonic", "of ifn regulatory factors.

embryonic fibroblast", "ifn regulatory factors.

embryonic fibroblast cells", "regulatory factors.

embryonic fibroblast cells from", "factors.

embryonic fibroblast cells from tbk1", "fibroblast cells from tbk1 deficient", "cells from tbk1 deficient mice", "from tbk1 deficient mice show", "tbk1 deficient mice show decreased", "deficient mice show decreased irf3", "mice show decreased irf3 activation", "show decreased irf3 activation and", "decreased irf3 activation and ifn", "irf3 activation and ifn induction", "activation and ifn induction by", "and ifn induction by poly", "ifn induction by poly ic", "by poly ic while", "poly ic while ikki", "ic while ikki deficient", "while ikki deficient cells show", "ikki deficient cells show normal", "deficient cells show normal irf3", "cells show normal irf3 activation.", "show normal irf3 activation. however", "irf3 activation. however the", "activation. however the activation", "however the activation of", "the activation of irf3 is", "activation of irf3 is totally", "of irf3 is totally abolished", "irf3 is totally abolished in", "is totally abolished in tbk1", "totally abolished in tbk1 and", "abolished in tbk1 and ikki", "in tbk1 and ikki double", "tbk1 and ikki double deficient", "and ikki double deficient cells", "double deficient cells indicating", "deficient cells indicating that", "cells indicating that the", "indicating that the functions of", "that the functions of tbk1", "the functions of tbk1 and", "functions of tbk1 and ikki", "of tbk1 and ikki are", "tbk1 and ikki are redundant", "and ikki are redundant in", "ikki are redundant in mouse", "are redundant in mouse embryo", "redundant in mouse embryo fibroblast", "in mouse embryo fibroblast cells.", "mouse embryo fibroblast cells. hemmi", "embryo fibroblast cells. hemmi et", "fibroblast cells. hemmi et al", "cells. hemmi et al 2004", "hemmi et al 2004 .

tbk1/ikki", "et al 2004 .

tbk1/ikki interact", "al 2004 .

tbk1/ikki interact with", "2004 .

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