{ "bcoid": "GLY_000356", "title": "HCV1b Protein Citations (UniProtKB)", "description": "The Hepatitis C virus (genotype 1b, isolate Japanese) Protein Citations dataset contains publication ...", "filename": "hcv1b_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Hepatitis C virus (genotype 1b, isolate Japanese)", "molecule": "Protein", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P26662-1...", "15825084..." ], [ "P26662-1...", "16844119..." ] ], "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" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" } ], [ "P26662-1", "15825084", "Hepatitis C virus expression suppresses interferon signaling by degrading STAT1.", "Gastroenterology", "2005", "Lin W., Chung R.T., Blackard J.T., Choe W.H., Hiasa Y., Kamegaya Y., Schmidt E.V.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "16844119", "Hepatitis C virus non-structural protein NS5A interacts with FKBP38 and inhibits apoptosis in Huh7 hepatoma cells.", "FEBS Lett.", "2006", "Chen L., Hu Y., Wang J., Zhang X., Pan T., Yuan Z., Yi Z., Xiang L., Tong W.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "14559998", "Modulation of retinoid signaling by a cytoplasmic viral protein via sequestration of Sp110b, a potent transcriptional corepressor of retinoic acid receptor, from the nucleus.", "Mol. Cell. Biol.", "2003", "Doi T., Shimotohno K., Hijikata M., Marusawa H., Tagawa A., Watashi K.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "17229681", "An RNA-binding protein, hnRNP A1, and a scaffold protein, septin 6, facilitate hepatitis C virus replication.", "J. Virol.", "2007", "Kim C.S., Park J.H., Jang S.K., Seol S.K., Song O.-K.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "16227268", "Human VAP-B is involved in hepatitis C virus replication through interaction with NS5A and NS5B.", "J. Virol.", "2005", "Liu M., Matsuura Y., Okamoto T., Suzuki T., Abe T., Mori Y., Nishimura Y., Moriishi K., Miyamura T., Lai M.M., Aizaki H., Hamamoto I.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "10702283", "Inhibition of the hepatitis C virus NS3/4A protease. The crystal structures of two protease-inhibitor complexes.", "J. Biol. Chem.", "2000", "Rizzi M., Walsh M.A., Di Marco S., De Francesco R., Volpari C., Colarusso S., Matassa V.G., Narjes F., Sollazzo M.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "10793006", "Cleavage of hepatitis C virus nonstructural protein 5A by a caspase-like protease(s) in mammalian cells.", "Virology", "2000", "Shimotohno K., Hijikata M., Noguchi T., Handa H., Satoh S., Hirota M.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "11907226", "Oligomerization and cooperative RNA synthesis activity of hepatitis C virus RNA-dependent RNA polymerase.", "J. Virol.", "2002", "Lu J., Zhang F., Rathnachalam R., Kirkegaard K., Staschke K., Parsons S., Wang Q.M., Case K.A., Colacino J.M., Hockman M.A., Johnson R.B.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "15163730", "Intramembrane proteolysis and endoplasmic reticulum retention of hepatitis C virus core protein.", "J. Virol.", "2004", "Matsuura Y., Moriishi K., Okamoto K., Miyamura T.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "15588076", "The design and enzyme-bound crystal structure of indoline based peptidomimetic inhibitors of hepatitis C virus NS3 protease.", "J. Med. Chem.", "2004", "Di Marco S., Conte I., Steinkuehler C., Volpari C., Harper S., Koch U., Di Francesco M.E., Gardelli C., Matassa V.G., Ontoria J.M., Poma M.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "15613354", "Molecular determinants for subcellular localization of hepatitis C virus core protein.", "J. Virol.", "2005", "Matsuura Y., Suzuki T., Tanaka K., Mizumoto K., Suzuki R., Moriishi K., Sakamoto S., Iwasaki T., Tsutsumi T., Miyamura T., Shimoike T., Rikimaru A.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "15760888", "Hepatitis C virus core protein acts as a trans-modulating factor on internal translation initiation of the viral RNA.", "J. Biol. Chem.", "2005", "Boulant S., Cahour A., Boni S., Lavergne J.-P.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "16126720", "Hepatitis C virus nonstructural protein 5A (NS5A) is an RNA-binding protein.", "J. Biol. Chem.", "2005", "Chen Y., Huang L., Hwang J., Sharma S.D., Arnold J.J., Cameron C.E., Hargittai M.R., Raney K.D.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "16940534", "Hepatitis C virus core protein blocks interferon signaling by interaction with the STAT1 SH2 domain.", "J. Virol.", "2006", "Lin W., Kim S.S., Holtzman M.J., Kim K.A., Chung R.T., Blackard J.T., Kamegaya Y., Yeung E.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "1849488", "Molecular structure of the Japanese hepatitis C viral genome.", "FEBS Lett.", "1991", "Kato N., Shimotohno K., Hijikata M., Nakagawa M., Muraiso K., Ohkoshi S., Ootsuyama Y.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "2175903", "Molecular cloning of the human hepatitis C virus genome from Japanese patients with non-A, non-B hepatitis.", "Proc. Natl. Acad. Sci. U.S.A.", "1990", "Kato N., Shimotohno K., Hijikata M., Sugimura T., Nakagawa M., Ohkoshi S., Ootsuyama Y.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "23242014", "Mass spectrometric analysis of hepatitis C viral envelope protein E2 reveals extended microheterogeneity of mucin-type O-linked glycosylation.", "Glycobiology", "2013", "Scheidig A.J., Egge-Jacobsen W., Braeutigam J.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "7769656", "Phosphorylation of hepatitis C virus-encoded nonstructural protein NS5A.", "J. Virol.", "1995", "Shimotohno K., Kaneko T., Satoh S., Tanji Y.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "7999043", "Production of two phosphoproteins from the NS5A region of the hepatitis C viral genome.", "Biochem. Biophys. Res. Commun.", "1994", "Kimura K., Shimotohno K., Kaneko T., Hijikata M., Satoh S., Asabe S., Tanji Y.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "8389908", "Nonstructural protein 3 of the hepatitis C virus encodes a serine-type proteinase required for cleavage at the NS3/4 and NS4/5 junctions.", "J. Virol.", "1993", "Jacobsen H., Bartenschlager R., Mous J., Ahlborn-Laake L.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "8392606", "Two distinct proteinase activities required for the processing of a putative nonstructural precursor protein of hepatitis C virus.", "J. Virol.", "1993", "Kato N., Kimura K., Shimotohno K., Tanaka T., Hijikata M., Mori S., Mizushima H., Akagi T., Kakiuchi N.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "8396658", "Suppression of hepatitis B virus expression and replication by hepatitis C virus core protein in HuH-7 cells.", "J. Virol.", "1993", "Chen S.-Y., Miyamura T., Lee Y.-H.W., Lo S.J., Shih C.-M.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "8531962", "Mutations in the nonstructural protein 5A gene and response to interferon in patients with chronic hepatitis C virus 1b infection.", "N. Engl. J. Med.", "1996", "Murakami T., Kurosaki M., Marumo F., Ogura Y., Sato C., Izumi N., Enomoto N., Asahina Y., Sakuma I., Yamamoto C.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "9060645", "The NS3 proteinase domain of hepatitis C virus is a zinc-containing enzyme.", "J. Virol.", "1997", "Hostomska Z., Hostomsky Z., Nodes B.R., Stempniak M.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "9343247", "Hepatitis C virus nonstructural region 5A protein is a potent transcriptional activator.", "J. Virol.", "1997", "Kato N., Omata M., Shiratori Y., Lan K.H., Ono-Nita S.K.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "9525599", "Interferon resistance of hepatitis C virus genotype 1b: relationship to nonstructural 5A gene quasispecies mutations.", "J. Virol.", "1998", "Frainais P.-O., Germanidis G., Pawlotsky J.-M., Dhumeaux D., Neumann A.U., Pellerin M.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "9621068", "The native form and maturation process of hepatitis C virus core protein.", "J. Virol.", "1998", "Wands J.R., Ichikawa M., Funahashi S., Yasui K., Wakita T., Moradpour D., Kohara M., Kajita T., Tsukiyama-Kohara K.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "10718937", "Properties of the hepatitis C virus core protein: a structural protein that modulates cellular processes.", "J. Viral Hepat.", "2000", "McLauchlan J.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "12560074", "The p7 protein of hepatitis C virus forms an ion channel that is blocked by the antiviral drug, Amantadine.", "FEBS Lett.", "2003", "Jaeger J., Harris M.P., Beales L.P., Clarke D.S., Evans S.D., Griffin S.D., Rowlands D.J., Worsfold O.", "protein_xref_uniprotkb", "P26662" ], [ "P26662-1", "14752815", "Structural biology of hepatitis C virus.", "Hepatology", "2004", "Dubuisson J., Rey F.A., Moradpour D., Pawlotsky J.-M., Penin F.", "protein_xref_uniprotkb", "P26662" ] ] }, "readme": "Name\n - HCV1b Protein Citations (UniProtKB)\n\nVersion\n - 1.5.27\n\nCreated on\n - 2020-03-13T14:12:07.407873\n\nModified on\n - 2020-04-09T18:03:43.664394\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@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 Hepatitis C virus (genotype 1b, isolate Japanese) Protein Citations dataset contains publication information for hcv1b [taxid:11116] UniProtKB accessions that includes PMID, journal name, date and author and title. The dataset is derived from 2019-09 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.\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-hepatitis-c-virus-1b.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.27/source/uniprot-proteome-hepatitis-c-virus-1b.nt\n Name: hcv1b_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.27/reviewed/hcv1b_protein_masterlist.csv\n Output Subdomain\n Name: hcv1b_protein_citations_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.27/reviewed/hcv1b_protein_citations_uniprotkb.csv\n Name: hcv1b_protein_citations_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.27/reviewed/hcv1b_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: \"1\"\n Name: \"xref_id\"\n Description: \"\"\n Unique Values: \"1\"\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: \"13\"\n Name: \"authors\"\n Description: \"Authors of the associated publications\"\n Unique Values: \"30\"\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: \"16\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"30\"\n Name: \"xref_key\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.5.27/reviewed/hcv1b_protein_citations_uniprotkb.csv" }