{ "bcoid": "GLY_000036", "title": "Mouse Protein Citations (UniProtKB)", "description": "The Mouse Protein Citations dataset contains publication information for mouse [taxid:10090] UniProtKB ...", "filename": "mouse_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Protein", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q9JHR7-1...", "Anti-diabeti..." ], [ "Q9JHR7-1...", "Insulin-degr..." ] ], "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" } ], [ "Q9JHR7-1", "Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones.", "Nature", "2014", "Saghatelian A., Seeliger M.A., Liu D.R., Leissring M.A., Charron M.J., Du X.Q., Tang W.J., Foda Z.H., Kleiner R.E., Maianti J.P., McFedries A.", "protein_xref_pubmed", "24847884", "protein_xref_uniprotkb", "Q9JHR7" ], [ "Q9JHR7-1", "Insulin-degrading enzyme regulates extracellular levels of amyloid beta-protein by degradation.", "J. Biol. Chem.", "1998", "Rosner M.R., Selkoe D.J., Walsh D.M., Zhang J., Ye Z., Hersh L.B., Qiu W.Q., Vekrellis K., Podlisny M.B., Safavi A.", "protein_xref_pubmed", "9830016", "protein_xref_uniprotkb", "Q9JHR7" ], [ "Q9JHR7-1", "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways.", "Mol. Cell", "2013", "Chen Y., Park J., Zhang Y., Zhao Y., Peng C., Tan M., Xie Z., Zwaans B.M., Lombard D.B., Dai L., Tishkoff D.X., Skinner M.E.", "protein_xref_pubmed", "23806337", "protein_xref_uniprotkb", "Q9JHR7" ], [ "Q9JHR7-1", "Functional relevance of a novel SlyX motif in non-conventional secretion of insulin-degrading enzyme.", "J. Biol. Chem.", "2011", "Walter J., Glebov K., Schutze S.", "protein_xref_pubmed", "21576244", "protein_xref_uniprotkb", "Q9JHR7" ], [ "Q9JHR7-1", "Loss of mPer2 increases plasma insulin levels by enhanced glucose-stimulated insulin secretion and impaired insulin clearance in mice.", "FEBS Lett.", "2012", "Wang S., Zhang J., Zhang Y., Zhao Y., Zhou M., Hua Z.", "protein_xref_pubmed", "22504074", "protein_xref_uniprotkb", "Q9JHR7" ], [ "Q9JHR7-1", "Insulin-degrading enzyme regulates the levels of insulin, amyloid beta-protein, and the beta-amyloid precursor protein intracellular domain in vivo.", "Proc. Natl. Acad. Sci. U.S.A.", "2003", "Eckman C.B., Selkoe D.J., Tanzi R.E., Chang Y., Frosch M.P., Eckman E.A., Farris W., Guenette S., Lindsley L., Mansourian S.", "protein_xref_pubmed", "12634421", "protein_xref_uniprotkb", "Q9JHR7" ], [ "Q9JHR7-1", "Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice.", "Nat. Commun.", "2015", "Deprez B., Dumont J., Leroux F., Paquet C., Herledan A., Lippens G., Liang W.G., Hermant P., Staels B., Cantrelle F.X., Tang W.J., Berte G., Bosc D., Charton J., Culot M., Dassonneville S., Deprez-Poulain R., Duplan I., Enee E., Gauriot M., Hennuyer N., Jahklal J., Landry V., Marechal X., Piveteau C., Sevin E., Totobenazara J., Verdelet T., Woitrain E., van Endert P.", "protein_xref_pubmed", "26394692", "protein_xref_uniprotkb", "Q9JHR7" ], [ "Q9JHR7-1", "Amyloid-beta peptide levels in brain are inversely correlated with insulysin activity levels in vivo.", "Proc. Natl. Acad. Sci. U.S.A.", "2003", "Eckman C.B., Sambamurti K., Thiele D.L., Hersh L.B., Chow K.M., Miller B.C., Eckman E.A., Dobbs N.", "protein_xref_pubmed", "12732730", "protein_xref_uniprotkb", "Q9JHR7" ], [ "B2RXV4-1", "A heme export protein is required for red blood cell differentiation and iron homeostasis.", "Science", "2008", "Chen J., Kaplan J., Yang Z., De Domenico I., Vaughn M.B., Abkowitz J.L., Keel S.B., Doty R.T., Quigley J.G., Palis J., Kingsley P.D., Knoblaugh S.", "protein_xref_pubmed", "18258918", "protein_xref_uniprotkb", "B2RXV4" ], [ "B2RXV4-1", "The mitochondrial heme exporter FLVCR1b mediates erythroid differentiation.", "J. Clin. Invest.", "2012", "Silengo L., Turco E., Altruda F., Tolosano E., Giorgi C., Pinton P., Camporeale A., Chiabrando D., Fagoonee S., Fiorito V., Marro S., Mercurio S., Merlo G.R., Petrillo S., Vinchi F.", "protein_xref_pubmed", "23187127", "protein_xref_uniprotkb", "B2RXV4" ], [ "Q9CXG9-1", "Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation.", "Nat. Struct. Mol. Biol.", "2012", "Loftus B.J., Shi X., Bracken A.P., Cagney G., Egan C.M., O'Connell D.J., Piao L., Brien G.L., Dunne E.J., Ferguson N., Gambero G., Jerman E., Jurgens M.C., Lohan A.J., Sinha K.M., Turner S.A., Wynne K.", "protein_xref_pubmed", "23160351", "protein_xref_uniprotkb", "Q9CXG9" ], [ "Q9CXG9-1", "Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.", "PLoS Genet.", "2012", "Diaz A., Shen Y., Cagney G., Reiter J.F., Krogan N., Song J.S., Ren B., Hunkapiller J., Ramalho-Santos M., McCleary D.", "protein_xref_pubmed", "22438827", "protein_xref_uniprotkb", "Q9CXG9" ], [ "Q9CXG9-1", "Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity.", "Nat. Struct. Mol. Biol.", "2012", "Lange M., Martin G.M., Shi Y., Simon B., Di Croce L., Morey L., Gozani O., Carlomagno T., Pascual G., Ballare C., Benitah S.A., Lapinaite A., Liefke R.", "protein_xref_pubmed", "23104054", "protein_xref_uniprotkb", "Q9CXG9" ], [ "Q9CXG9-1", "An H3K36 methylation-engaging Tudor motif of Polycomb-like proteins mediates PRC2 complex targeting.", "Mol. Cell", "2013", "Zheng D., Allis C.D., Strahl B.D., Cai L., Song J., Patel D.J., Xu B., Lu R., Tripathy A., Chen W.Y., Rothbart S.B., Wang G.G., Rockowitz S.", "protein_xref_pubmed", "23273982", "protein_xref_uniprotkb", "Q9CXG9" ], [ "Q07968-1", "Molecular cloning of the b subunit of mouse coagulation factor XIII and assignment of the gene to chromosome 1: close evolutionary relationship to complement factor H.", "Genomics", "1993", "Matsuda Y., Shiroishi T., Nonaka M., Moriwaki K., Natsuume-Sakai S., Nonaka M.'", "protein_xref_pubmed", "8468048", "protein_xref_uniprotkb", "Q07968" ], [ "Q07968-1", "Proteome-wide characterization of N-glycosylation events by diagonal chromatography.", "J. Proteome Res.", "2006", "Gevaert K., Martens L., Van Damme J., Vandekerckhove J., Ghesquiere B.", "protein_xref_pubmed", "16944957", "protein_xref_uniprotkb", "Q07968" ], [ "Q07968-1", "Enhanced analysis of the mouse plasma proteome using cysteine-containing tryptic glycopeptides.", "J. Proteome Res.", "2007", "Simpson R.J., Bernhard O.K., Kapp E.A.", "protein_xref_pubmed", "17330941", "protein_xref_uniprotkb", "Q07968" ], [ "A5H0M4-1", "Two novel transcripts encoding two Ankyrin repeat containing proteins have preponderant expression during the mouse spermatogenesis.", "Mol. Biol. Rep.", "2007", "Gong W., Wang F., Hu J., Song P.", "protein_xref_pubmed", "17171436", "protein_xref_uniprotkb", "A5H0M4" ], [ "Q9CXG3-1", "Comprehensive identification of phosphorylation sites in postsynaptic density preparations.", "Mol. Cell. Proteomics", "2006", "Schoepfer R., Burlingame A.L., Thalhammer A., Specht C.G., Trinidad J.C.", "protein_xref_pubmed", "16452087", "protein_xref_uniprotkb", "Q9CXG3" ], [ "Q9CXG3-1", "The phagosomal proteome in interferon-gamma-activated macrophages.", "Immunity", "2009", "Thibault P., Trost M., Desjardins M., Courcelles M., English L., Lemieux S.", "protein_xref_pubmed", "19144319", "protein_xref_uniprotkb", "Q9CXG3" ], [ "P01942-1", "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways.", "Mol. Cell", "2013", "Chen Y., Park J., Zhang Y., Zhao Y., Peng C., Tan M., Xie Z., Zwaans B.M., Lombard D.B., Dai L., Tishkoff D.X., Skinner M.E.", "protein_xref_pubmed", "23806337", "protein_xref_uniprotkb", "P01942" ], [ "P01942-1", "Characterization and kinetics of synthesis of 15S beta-globin RNA, a putative precursor of beta-globin mRNA.", "Cold Spring Harb. Symp. Quant. 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Cell", "2011", "Min J., Shi Y., Zhang H., Zheng L., Xu Y., Chen T., Zhang K., Tan L., Xu G., Wu F., Huang S., Kong L., Xiong L., Deng J., Barbera A.J., Shi Y.G., Nicholson T.", "protein_xref_pubmed", "21514197", "protein_xref_uniprotkb", "Q3URK3" ] ] }, "readme": "Name\n - Mouse Protein Citations (UniProtKB)\n\nVersion\n - 1.7.10\n\nCreated on\n - 2019-01-23T17:21:05.903678\n\nModified on\n - 2020-04-10T12:34:26.812397\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 Mouse Protein Citations dataset contains publication information for mouse [taxid:10090] 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/ln2wwwdata/compiled/mouse_protein_blacklisted_pmids_uniprotkb.csv. The dataset is derived from 2019-09 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\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-mus-musculus.nt\n URI: https://data.glygen.org/ln2wwwdata/source/uuniprot-proteome-mus-musculus.nt\n Name: mouse_protein_blacklisted_pmids_uniprotkb.csv\n URI: https://data.glygen.org/ln2wwwdata/compiled/mouse_protein_blacklisted_pmids_uniprotkb.csv\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_masterlist.csv\n Output Subdomain\n Name: mouse_protein_citations_uniprotkb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_citations_uniprotkb.csv\n Name: mouse_protein_citations_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"13822\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"30670\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"30663\"\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: \"13822\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"898\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"30264\"\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: \"53\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.7.10/reviewed/mouse_protein_citations_uniprotkb.csv" }