{ "bcoid": "GLY_000035", "title": "Human Protein Citations (UniProtKB)", "description": "The Human Protein Citations dataset contains publication information for human [taxid:9606] UniProtKB ...", "filename": "human_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Homo Sapiens", "molecule": "Protein", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q5MIZ7-1...", "11230166..." ], [ "Q5MIZ7-1...", "16964243..." ] ], "headers": [ "uniprotkb_ca...", "pmid..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "pmid" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" } ], [ "Q5MIZ7-1", "11230166", "Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs.", "Genome Res.", "2001", "Ansorge W., Bauersachs S., Beyer A., Bloecker H., Blum H., Boecher M., Duesterhoeft A., Gassenhuber J., Glassl S., Heubner D., Klein M., Koehrer K., Korn B., Lauber J., Mewes H.-W., Obermaier B., Ottenwaelder B., Poustka A., Strack N., Tampe J., Wambutt R., Weil B., Wellenreuther R., Wiemann S." ], [ "Q5MIZ7-1", "16964243", "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "Nat. Biotechnol.", "2006", "Beausoleil S.A., Gerber S.A., Gygi S.P., Rush J., Villen J." ], [ "Q5MIZ7-1", "15616564", "An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division.", "Nature", "2004", "Korn B., Yaspo M.-L., Pisabarro M.T., Habermann B., Buchholz F., Poser I., Pelletier L., Drechsel D., Kittler R., Fischer S., Grabner H., Heninger A.-K., Himmelbauer H., Konstantinova I., Neugebauer K., Putz G." ], [ "Q5MIZ7-1", "16085932", "A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity.", "Mol. Cell. Proteomics", "2005", "Aebersold R., Sanchez A., Gingras A.-C., Raught B., Sonenberg N., Fields S., Hafen E., Caballero M., Hazbun T.R., Zarske M." ], [ "Q5MIZ7-1", "18487071", "Depletion of protein phosphatase 4 in human cells reveals essential roles in centrosome maturation, cell migration and the regulation of Rho GTPases.", "Int. J. Biochem. Cell Biol.", "2008", "Cohen P.T.W., Philp A., Prescott A.R., Martin-Granados C., Oxenham S.K." ], [ "Q5MIZ7-1", "18614045", "A PP4-phosphatase complex dephosphorylates gamma-H2AX generated during DNA replication.", "Mol. Cell", "2008", "Xu X., Lieberman J., Pfeifer G.P., Zhong J., Chowdhury D., Liao J., Zhong X., Weinstock D.M., Ahmed F., Dykxhoorn D.M." ], [ "P23919-1", "19608861", "Lysine acetylation targets protein complexes and co-regulates major cellular functions.", "Science", "2009", "Choudhary C., Gnad F., Kumar C., Mann M., Nielsen M.L., Olsen J.V., Rehman M., Walther T.C." ], [ "P23919-1", "12614151", "Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds.", "Biochemistry", "2003", "Konrad M., Meier C., Lavie A., Ostermann N., Monnerjahn C., Segura-Pena D., Veit T." ], [ "P23919-1", "2017365", "Molecular cloning and expression of the human deoxythymidylate kinase gene in yeast.", "Nucleic Acids Res.", "1991", "Sclafani R.A., Su J.Y." ], [ "P23919-1", "8024690", "Human dTMP kinase: gene expression and enzymatic activity coinciding with cell cycle progression and cell growth.", "DNA Cell Biol.", "1994", "Li C., Tang A., Zhang S.Q., Drisco B., Huang S.H., Jong A., Seeger R." ], [ "Q8NHX4-1", "12812072", "Molecular cloning for testis spermatogenesis cell apoptosis related gene TSARG1 and Mtsarg1 and expression analysis for Mtsarg1 gene.", "Yi Chuan Xue Bao", "2003", "Liu G., Li L.Y., Lu G.X., Xing X.W., Fu J.J., Liu S.F." ], [ "Q8NHX9-1", "18488028", "Two newly identified genetic determinants of pigmentation in Europeans.", "Nat. Genet.", "2008", "Gudbjartsson D.F., Jakobsdottir M., Kiemeney L.A., Kong A., Rafnar T., Stacey S.N., Stefansson K., Steinberg S., Sulem P., Thorleifsson G., Thorsteinsdottir U., Gudjonsson S.A., Tucker M.A., Palsson S., Goldstein A.M., Aben K.K., Benediktsdottir K.R., Vermeulen S.H., Helgason A., Gulcher J., Olafsson J.H., Palsson A., Ragnarsson R., Sigurgeirsson B., Thorisdottir K." ], [ "Q8NHX9-1", "19387438", "NAADP mobilizes calcium from acidic organelles through two-pore channels.", "Nature", "2009", "Lin Y., Ma J., Pan Z., Tang J., Wang C., Zhu Y., Cheng X., Hao X., Lin P., Xiao R., Rietdorf K., Zhu M.X., Ruas M., Evans A.M., Parrington J., Galione A., Arredouani A., Calcraft P.J., Chuang K.T., Teboul L., Wyatt C.N." ], [ "Q8NHX9-1", "19620632", "Essential requirement for two-pore channel 1 in NAADP-mediated calcium signaling.", "J. Cell Biol.", "2009", "Gao X., Cai X., Patel S., Brailoiu E., Brailoiu G.C., Dun N.J., Churamani D., Marchant J.S., Boulware M.J., Hooper R., Schrlau M.G." ], [ "Q8NHX9-1", "22012985", "Leucine-rich repeat kinase 2 regulates autophagy through a calcium-dependent pathway involving NAADP.", "Hum. Mol. Genet.", "2012", "Zhang L., Patel S., Woodman P.G., Churchill G.C., Bloor-Young D., Churamani D., Gomez-Suaga P., Hilfiker S., Luzon-Toro B." ], [ "Q8NHX9-1", "24188827", "Hax-1 identified as a two-pore channel (TPC)-binding protein.", "FEBS Lett.", "2013", "Lai F.A., Galione A., Lam A.K., Zissimopoulos S." ], [ "Q9NXR8-1", "12080476", "Allelic loss and reduced expression of the ING3, a candidate tumor suppressor gene at 7q31, in human head and neck cancers.", "Oncogene", "2002", "Ito S., Shimizu K., Fukushima K., Ouchida M., Nakashima T., Nagai N., Gunduz M., Jitsumori Y., Nishizaki K." ], [ "Q9NXR8-1", "12545155", "A novel PHD-finger motif protein, p47ING3, modulates p53-mediated transcription, cell cycle control, and apoptosis.", "Oncogene", "2003", "Yokota J., Miura K., Nagashima M., Okamura S., Harris C.C., Shiseki M., Kitahama-Shiseki M., Pedeux R.M." ], [ "Q9NXR8-1", "16728974", "ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression.", "Nature", "2006", "Cote J., Shi Y., Shi X., Ayer D.E., Hong T., Kutateladze T.G., Cairns B.R., Cayrou C., Michishita E., Lacoste N., Lan F., Hung T., Chua K.F., Gozani O., Saha A., Carney D., Davrazou F., Ewalt M., Kaadige M.R., Pena P., Walter K.L." ], [ "Q9NXR8-1", "19154204", "Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers.", "Plant J.", "2009", "Lee D., Lee W.Y., Chung W.I., Kwon C.S." ], [ "Q9NXR8-1", "12963728", "Identification of new subunits of the multiprotein mammalian TRRAP/TIP60-containing histone acetyltransferase complex.", "J. Biol. Chem.", "2003", "Cai Y., Conaway J.W., Conaway R.C., Jin J., Parmely T.J., Sato S., Sorokina I., Tomomori-Sato C." ], [ "Q9NXR8-1", "14966270", "Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans.", "Mol. Cell. Biol.", "2004", "Cote J., Doyon Y., Lane W.S., Selleck W., Tan S." ], [ "Q9NXR8-1", "15196461", "The highly conserved and multifunctional NuA4 HAT complex.", "Curr. Opin. Genet. Dev.", "2004", "Cote J., Doyon Y." ], [ "Q9C0H2-1", "17081983", "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "Cell", "2006", "Blagoev B., Gnad F., Kumar C., Macek B., Mann M., Mortensen P., Olsen J.V." ], [ "Q9C0H2-1", "18220336", "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis.", "J. Proteome Res.", "2008", "Cantin G.T., Lee J.-D., Lu B., Park S.K., Xu T., Yates J.R. 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Cell", "2008", "Bairlein M., Daub H., Gnad F., Greff Z., Keri G., Korner R., Mann M., Olsen J.V., Oppermann F.S., Stemmann O." ], [ "Q9C0H6-1", "11401425", "Identification and characterization of KLHL4, a novel human homologue of the Drosophila Kelch gene that maps within the X-linked cleft palate and ankyloglossia (CPX) critical region.", "Genomics", "2001", "Moore G.E., Ross M.T., Stanier P., Arnason A., Bjornsson A., Braybrook C., Howell G., Warry G." ], [ "Q9C0H9-5", "17525734", "p140Cap protein suppresses tumour cell properties, regulating Csk and Src kinase activity.", "EMBO J.", "2007", "Silengo L., Tarone G., Turco E., Aramu S., Cabodi S., Cavallo F., Damiano L., Defilippi P., Di Stefano P., Forni G., Piva R., Praduroux A., Tordella L." ], [ "Q9C0H9-5", "14657239", "p130Cas-associated protein (p140Cap) as a new tyrosine-phosphorylated protein involved in cell spreading.", "Mol. Biol. Cell", "2004", "Silengo L., Tarone G., Turco E., Cabodi S., Defilippi P., Di Stefano P., Giuffrida M.G., Bergatto E., Erba E.B., Margaria V." ], [ "Q9C0H9-5", "18475297", "SNIP/p140Cap mRNA expression is an unfavourable prognostic factor in breast cancer and is not expressed in normal breast tissue.", "Br. J. Cancer", "2008", "Kennedy S., Clynes M., Crown J., Doolan P., Mehta J.P., O'Driscoll L., Rani S." ], [ "Q9C0H9-5", "18662323", "Characterization of a multidomain adaptor protein, p140Cap, as part of a pre-synaptic complex.", "J. 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Biol.", "2011", "Wotton D., Bjerke G.A., Hyman-Walsh C." ], [ "P40424-1", "12609849", "Homeodomain proteins MEIS1 and PBXs regulate the lineage-specific transcription of the platelet factor 4 gene.", "Blood", "2003", "Doi T., Sato T., Matsuura E., Okada Y., Nagai R., Minami T., Morita I." ], [ "P40424-1", "19559479", "MEIS proteins as partners of the TLX1/HOX11 oncoprotein.", "Leuk. Res.", "2010", "Kees U.R., Ford J., Greene W.K., D'Souza D., Gottardo N.G., Milech N., Watt P.M." ], [ "P40424-1", "20553494", "An autoinhibitory effect of the homothorax domain of Meis2.", "FEBS J.", "2010", "Wotton D., Bjerke G.A., Hyman-Walsh C." ], [ "P40424-1", "15684392", "FOXC1 transcriptional regulatory activity is impaired by PBX1 in a filamin A-mediated manner.", "Mol. Cell. 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Biol.", "1994", "Lu Q., Kamps M.P., Wright D.D." ] ] }, "readme": "Name\n - Human Protein Citations (UniProtKB)\n\nVersion\n - 1.4.5\n\nCreated on\n - 2019-01-23T17:21:05.902655\n\nModified on\n - 2019-09-12T13:10:47.922761\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Human Protein Citations dataset contains publication information for human [taxid:9606] UniProtKB accessions that includes PMID, journal name, date and author and title. Publications of large scale studies, and high frequency publications pertaining to genome sequencing, cDNA, chromosomes have been filtered out as per https://data.glygen.org/ln2data/releases/data/v-1.4.5/compiled/human_protein_blacklisted_pmids_uniprotkb.csv. The dataset is derived from 2019-05 UniProt release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - publications\n - PMID\n - journal\n - citations\n - authors\n - UniProtKB\n - PubMed\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB publication data from the triplestore containing triples from nt file to retrieve the publication information associated with the UniProtKB accession and maps it to the UniProtKB canonical accessions. The script also filters out publications of large scale studies, and high frequency publications pertaining to DNA sequencing, cDNA, chromosomes using blacklisted PMIDs file.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-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: uniprot-proteome-9606-homo-sapiens-2019-05.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/source/uniprot-proteome-9606-homo-sapiens-2019-05.nt\n Name: human_protein_blacklisted_pmids_uniprotkb.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/compiled/human_protein_blacklisted_pmids_uniprotkb.csv\n Name: human_protein_idmapping.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/human_protein_idmapping.csv\n Output Subdomain\n Name: human_protein_citations_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/human_protein_citations_uniprotkb.csv\n Name: human_protein_citations_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/human_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"15944\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"65198\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"1518\"\n Name: \"authors\"\n Description: \"\"\n Unique Values: \"64284\"\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: \"60\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"65216\"", "downloadurl": "/ln2data/releases/data/v-1.4.5/reviewed/human_protein_citations_uniprotkb.csv" }