{ "bcoid": "GLY_000573", "title": "Mouse Proteoform Citations (Literature Mining)", "description": "The dataset provides citation details corresponding to the PubMed ID (PMID) from file https://data.glygen.org/GLYDS000481. ...", "filename": "mouse_proteoform_citations_glycosylation_sites_literature_mining.csv", "filetype": "csv", "categories": { "species": [ "Mus musculus" ], "molecule": [ "Proteoform" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q9JIP7-1...", "Glycans in t..." ], [ "Q9EQN9-1...", "Slc19a2: clo..." ] ], "headers": [ "uniprotkb_ca...", "title..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" }, { "type": "string", "label": "glytoucan_ac" } ], [ "Q9JIP7-1", "Glycans in the intestinal peptide transporter PEPT1 contribute to function and protect from proteolysis.", "American journal of physiology. Gastrointestinal and liver physiology", "2017 Jun 1", "Stelzl T, Geillinger-Kastle KE, Stolz J, Daniel H", "protein_xref_pubmed", "28336547", "protein_xref_automatic_literature_mining", "28336547", "" ], [ "Q9EQN9-1", "Slc19a2: cloning and characterization of the murine thiamin transporter cDNA and genomic sequence, the orthologue of the human TRMA gene.", "Molecular genetics and metabolism", "2001 Jun", "Oishi K, Hirai T, Gelb BD, Diaz GA", "protein_xref_pubmed", "11386850", "protein_xref_automatic_literature_mining", "11386850", "" ], [ "Q9CQS3-1", "Characterization of the expression, promoter activity and molecular architecture of fibin.", "BMC biochemistry", "2011 May 26", "Lakner J, Seyer C, Hermsdorf T, Schoneberg T", "protein_xref_pubmed", "21615908", "protein_xref_automatic_literature_mining", "21615908", "" ], [ "Q60715-1", "Ascorbate inducible N259 glycans on prolyl 4-hydroxylase subunit alpha1 promote hydroxylation and secretion of type I collagen.", "Cellular and molecular life sciences : CMLS", "2019 Sep", "Shi R, Hu W, Zhang Y, Gao S, Smith AH, Ye J, Cai L, Graham LM, Li C", "protein_xref_pubmed", "30919021", "protein_xref_automatic_literature_mining", "30919021", "" ], [ "P56677-1", "Addition of beta1-6 GlcNAc branching to the oligosaccharide attached to Asn 772 in the serine protease domain of matriptase plays a pivotal role in its stability and resistance against trypsin.", "Glycobiology", "2004-02", "Ihara Shinji, Miyoshi Eiji, Nakahara Susumu, Sakiyama Haruhiko, Ihara Hideyuki, Akinaga Ayumi, Honke Koichi, Dickson Robert B, Lin Chen-Yong, Taniguchi Naoyuki", "protein_xref_pubmed", "14551220", "protein_xref_automatic_literature_mining", "14551220", "" ], [ "Q9WVL3-1", "Glycosylation regulates the function and membrane localization of KCC4.", "Biochimica et biophysica acta", "2013 May", "Weng TY, Chiu WT, Liu HS, Cheng HC, Shen MR, Mount DB, Chou CY", "protein_xref_pubmed", "23376777", "protein_xref_automatic_literature_mining", "23376777", "" ], [ "P46096-1", "Vesicle-associated membrane protein-2/synaptobrevin binding to synaptotagmin I promotes O-glycosylation of synaptotagmin I.", "The Journal of biological chemistry", "2002 Aug 16", "Fukuda M", "protein_xref_pubmed", "12048209", "protein_xref_automatic_literature_mining", "12048209", "" ], [ "Q9D806-1", "Differential effects of N-linked glycosylation of Vstm5 at multiple sites on surface expression and filopodia formation.", "PloS one", "2017", "Lee AR, Kim S, Ko KW, Park CS", "protein_xref_pubmed", "28746350", "protein_xref_automatic_literature_mining", "28746350", "" ], [ "P21729-1", "Glycosylation of the gastrin-releasing peptide receptor and its effect on expression, G protein coupling, and receptor modulatory processes.", "Molecular pharmacology", "2000 Dec", "Benya RV, Kusui T, Katsuno T, Tsuda T, Mantey SA, Battey JF, Jensen RT", "protein_xref_pubmed", "11093789", "protein_xref_automatic_literature_mining", "11093789", "" ], [ "Q04519-1", "Functional analysis of the glycosylation of murine acid sphingomyelinase.", "The Journal of biological chemistry", "1996 Dec 13", "Newrzella D, Stoffel W", "protein_xref_pubmed", "8943261", "protein_xref_automatic_literature_mining", "8943261", "" ], [ "Q61009-1", "Identification of the N-linked glycosylation sites on the high density lipoprotein (HDL) receptor SR-BI and assessment of their effects on HDL binding and selective lipid uptake.", "The Journal of biological chemistry", "2003 Feb 14", "Vinals M, Xu S, Vasile E, Krieger M", "protein_xref_pubmed", "12429731", "protein_xref_automatic_literature_mining", "12429731", "" ], [ "Q9JL99-1", "Structural and functional conservation of CLEC-2 with the species-specific regulation of transcript expression in evolution.", "Glycoconjugate journal", "2012 Aug", "Wang L, Ren S, Zhu H, Zhang D, Hao Y, Ruan Y, Zhou L, Lee C, Qiu L, Yun X, Xie J", "protein_xref_pubmed", "22740230", "protein_xref_automatic_literature_mining", "22740230", "" ], [ "Q60994-1", "N-linked glycosylation of mouse adiponectin.", "Hormone and metabolic research = Hormon- und Stoffwechselforschung = Hormones et metabolisme", "2011 Jul", "Tanaka M, Fukuhara A, Shimomura I", "protein_xref_pubmed", "21769758", "protein_xref_automatic_literature_mining", "21769758", "" ], [ "P16388-1", "The brain Kv1.1 potassium channel: in vitro and in vivo studies on subunit assembly and posttranslational processing.", "The Journal of neuroscience : the official journal of the Society for Neuroscience", "1994 Mar", "Deal KK, Lovinger DM, Tamkun MM", "protein_xref_pubmed", "8126562", "protein_xref_automatic_literature_mining", "8126562", "" ], [ "P31648-1", "Effect of mutation of glycosylation sites on the Na+ dependence of steady-state and transient currents generated by the neuronal GABA transporter.", "Biochimica et biophysica acta", "1998 Dec 9", "Liu Y, Eckstein-Ludwig U, Fei J, Schwarz W", "protein_xref_pubmed", "9858742", "protein_xref_automatic_literature_mining", "9858742", "" ], [ "Q8CIZ8-1", "In vivo analysis of the role of O-glycosylations of von Willebrand factor.", "PloS one", "2012", "Badirou I, Kurdi M, Legendre P, Rayes J, Bryckaert M, Casari C, Lenting PJ, Christophe OD, Denis CV", "protein_xref_pubmed", "22616016", "protein_xref_automatic_literature_mining", "22616016", "" ], [ "Q9D1N2-1", "Glycosylation of Asn-76 in mouse GPIHBP1 is critical for its appearance on the cell surface and the binding of chylomicrons and lipoprotein lipase.", "Journal of lipid research", "2008 Jun", "Beigneux AP, Gin P, Davies BS, Weinstein MM, Bensadoun A, Ryan RO, Fong LG, Young SG", "protein_xref_pubmed", "18340083", "protein_xref_automatic_literature_mining", "18340083", "" ], [ "Q05769-1", "N-glycosylation of prostaglandin endoperoxide synthases-1 and -2 and their orientations in the endoplasmic reticulum.", "The Journal of biological chemistry", "1993 Aug 25", "Otto JC, DeWitt DL, Smith WL", "protein_xref_pubmed", "8349699", "protein_xref_automatic_literature_mining", "8349699", "" ], [ "P22723-1", "Co-expression of \u03b32 subunits hinders processing of N-linked glycans attached to the N104 glycosylation sites of GABAA receptor \u03b22 subunits.", "Neurochemical research", "2014-06", "Lo Wen-Yi, Lagrange Andre H, Hernandez Ciria C, Gurba Katharine N, Macdonald Robert L", "protein_xref_pubmed", "24213971", "protein_xref_automatic_literature_mining", "24213971", "" ], [ "Q60625-1", "Asn54-linked glycan is critical for functional folding of intercellular adhesion molecule-5.", "Glycoconjugate journal", "2012 Jan", "Ohgomori T, Nanao T, Morita A, Ikekita M", "protein_xref_pubmed", "22187327", "protein_xref_automatic_literature_mining", "22187327", "" ], [ "Q3TYD4-1", "Molecular characterization of arylsulfatase G: expression, processing, glycosylation, transport, and activity.", "The Journal of biological chemistry", "2014 Oct 3", "Kowalewski B, Lubke T, Kollmann K, Braulke T, Reinheckel T, Dierks T, Damme M", "protein_xref_pubmed", "25135642", "protein_xref_automatic_literature_mining", "25135642", "" ], [ "P06797-1", "Abnormal glycosylation of procathepsin L due to N-terminal point mutations correlates with failure to sort to lysosomes.", "The Journal of biological chemistry", "1997 Mar 28", "Chapman RL, Kane SE, Erickson AH", "protein_xref_pubmed", "9079717", "protein_xref_automatic_literature_mining", "9079717", "" ], [ "P10761-1", "Inactivation of the mouse sperm receptor, mZP3, by site-directed mutagenesis of individual serine residues located at the combining site for sperm.", "Proceedings of the National Academy of Sciences of the United States of America", "1998 May 26", "Chen J, Litscher ES, Wassarman PM", "protein_xref_pubmed", "9600940", "protein_xref_automatic_literature_mining", "9600940", "" ], [ "O88935-2", "Protonation states at different pH, conformational changes and impact of glycosylation in synapsin Ia.", "Physical chemistry chemical physics : PCCP", "2021-08-12", "Mir Sonia, Ashraf Sajda, Saeed Maria, Rahman Atta-Ur, Ul-Haq Zaheer", "protein_xref_pubmed", "34318818", "protein_xref_automatic_literature_mining", "34318818", "" ], [ "P43432-1", "Engineering N-glycosylation mutations in IL-12 enhances sustained cytotoxic T lymphocyte responses for DNA immunization.", "Nature biotechnology", "2002 Apr", "Ha SJ, Chang J, Song MK, Suh YS, Jin HT, Lee CH, Nam GH, Choi G, Choi KY, Lee SH, Kim WB, Sung YC", "protein_xref_pubmed", "11923845", "protein_xref_automatic_literature_mining", "11923845", "" ], [ "P56818-1", "Bisecting GlcNAc modification stabilizes BACE1 protein under oxidative stress conditions.", "The Biochemical journal", "2016 Jan 1", "Kizuka Y, Nakano M, Kitazume S, Saito T, Saido TC, Taniguchi N", "protein_xref_pubmed", "26467158", "protein_xref_automatic_literature_mining", "26467158", "" ], [ "O55188-1", "Glycosylation of Dentin Matrix Protein 1 is critical for osteogenesis.", "Scientific reports", "2015 Dec 4", "Sun Y, Weng Y, Zhang C, Liu Y, Kang C, Liu Z, Jing B, Zhang Q, Wang Z", "protein_xref_pubmed", "26634432", "protein_xref_automatic_literature_mining", "26634432", "" ], [ "P61290-1", "Site-specific O-GlcNAcylation of Psme3 maintains mouse stem cell pluripotency by impairing P-body homeostasis.", "Cell reports", "2021 Jul 13", "Pecori F, Kondo N, Ogura C, Miura T, Kume M, Minamijima Y, Yamamoto K, Nishihara S", "protein_xref_pubmed", "34260942", "protein_xref_automatic_literature_mining", "34260942", "" ], [ "O55188-1", "Glycosylation of dentin matrix protein 1 is a novel key element for astrocyte maturation and BBB integrity.", "Protein & cell", "2018 Mar", "Jing B, Zhang C, Liu X, Zhou L, Liu J, Yao Y, Yu J, Weng Y, Pan M, Liu J, Wang Z, Sun Y, Sun YE", "protein_xref_pubmed", "28822114", "protein_xref_automatic_literature_mining", "28822114", "" ], [ "Q6NXK8-1", "N-glycosylation of acid-sensing ion channel 1a regulates its trafficking and acidosis-induced spine remodeling.", "The Journal of neuroscience : the official journal of the Society for Neuroscience", "2012 Mar 21", "Jing L, Chu XP, Jiang YQ, Collier DM, Wang B, Jiang Q, Snyder PM, Zha XM", "protein_xref_pubmed", "22442073", "protein_xref_automatic_literature_mining", "22442073", "" ] ] }, "readme": "Name\n - Mouse Proteoform Citations (Literature Mining)\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2021-06-04T10:20:39.827303\n\nModified on\n - 2023-03-14T17:00:09.743Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The dataset provides citation details corresponding to the PubMed ID (PMID) from file https://data.glygen.org/GLYDS000481. The script accesses the NCBI ENTREZ infrastructure to retrieve the publication information of the given PMID.\n\nDescription Domain\n Keywords\n - PMID\n - journal\n - citations\n - authors\n - Literature\n - PubMed\n\n Pipeline Steps\n - Step-1: The script parses the input file for PMIDs and accesses the NCBI Entrez infrastructure to download the publication information of the corresponding PMIDs.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: mouse_proteoform_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/mouse_proteoform_glycosylation_sites_literature_mining.csv\n Output Subdomain\n Name: mouse_proteoform_citations_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/mouse_proteoform_citations_glycosylation_sites_literature_mining.csv\n Name: mouse_proteoform_citations_glycosylation_sites_literature_mining.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/mouse_proteoform_citations_glycosylation_sites_literature_mining.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"29\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"30\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"21\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"30\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"30\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"30\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"30\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/mouse_proteoform_citations_glycosylation_sites_literature_mining.csv" }