{ "bcoid": "GLY_000355", "title": "HCV1a Protein Citations (UniProtKB)", "description": "The Hepatitis C virus (genotype 1a, isolate H) Protein Citations dataset contains publication information ...", "filename": "hcv1a_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Hepatitis C virus (genotype 1a, isolate H)", "molecule": "Protein", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P27958-1...", "SPSB2 inhibi..." ], [ "P27958-1...", "Inhibition o..." ] ], "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" } ], [ "P27958-1", "SPSB2 inhibits hepatitis C virus replication by targeting NS5A for ubiquitination and degradation.", "PLoS ONE", "2019", "Li J., Liu Y., Shen C., Wang H., Wang Y., Wang M., Han L., Hao Y., Xin X., Yu F., Zheng C.", "protein_xref_pubmed", "31344133", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Inhibition of the interferon-inducible protein kinase PKR by HCV E2 protein.", "Science", "1999", "Barber G.N., Lai M.M.C., Romano P.R., Shi S.T., Taylor D.R.", "protein_xref_pubmed", "10390359", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Protein kinase C-related kinase 2 regulates hepatitis C virus RNA polymerase function by phosphorylation.", "J. Biol. Chem.", "2004", "Kim S.J., Kim J.H., Kim Y.G., Oh J.W., Lim H.S.", "protein_xref_pubmed", "15364941", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Hepatitis C virus protease NS3/4A cleaves mitochondrial antiviral signaling protein off the mitochondria to evade innate immunity.", "Proc. Natl. Acad. Sci. U.S.A.", "2005", "Sun L., Chen Z.J., Seth R.B., Pineda G., Li X.D.", "protein_xref_pubmed", "16301520", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Hepatitis C virus NS5A protein modulates transcription through a novel cellular transcription factor SRCAP.", "J. Biol. Chem.", "2000", "Ghosh A.K., Yaciuk P., Ray R., Chrivia J., Majumder M., Ray R.B., Steele R.", "protein_xref_pubmed", "10702287", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Identification of a novel protein binding to hepatitis C virus core protein.", "J. Gastroenterol. Hepatol.", "2009", "Liu M., Zhang X., Shi L., Chen T.Y., Chen Y.R., Dang S.S., Lin S.M., Ye F., Zhang S.L., Zhao Y.R.", "protein_xref_pubmed", "19486448", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Apolipoprotein E likely contributes to a maturation step of infectious hepatitis C virus particles and interacts with viral envelope glycoproteins.", "J. Virol.", "2014", "Lee J.Y., Fackler O.T., Mueller B., Bartenschlager R., Acosta E.G., Hiet M.S., Kallis S., Long G., Stoeck I.K.", "protein_xref_pubmed", "25122793", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus.", "Nature", "2005", "Hofmann K., Tschopp J., Bartenschlager R., Binder M., Curran J., Meylan E., Moradpour D.", "protein_xref_pubmed", "16177806", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "The human scavenger receptor class B type I is a novel candidate receptor for the hepatitis C virus.", "EMBO J.", "2002", "Cortese R., Traboni C., Nicosia A., Scarselli E., Vitelli A., Acali S., Ansuini H., Cerino R., Filocamo G., Roccasecca R.M.", "protein_xref_pubmed", "12356718", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Hepatitis C virus NS4B blocks the interaction of STING and TBK1 to evade host innate immunity.", "J. Hepatol.", "2013", "Kato N., Lu J., Cao X., Ding Q., Liu Y.J., Huang B., Shu H.B., Zhong J.", "protein_xref_pubmed", "23542348", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "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_pubmed", "17229681", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Interaction between complement receptor gC1qR and hepatitis C virus core protein inhibits T-lymphocyte proliferation.", "J. Clin. Invest.", "2000", "Yao Z.Q., Braciale T.J., Chianese-Bullock K.A., Hahn Y.S., Kittlesen D.J.", "protein_xref_pubmed", "11086025", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "The SH3 binding motif of HCV NS5A protein interacts with Bin1 and is important for apoptosis and infectivity.", "Gastroenterology", "2006", "Herion D., Liang T.J., Nanda S.K.", "protein_xref_pubmed", "16530520", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "HCV core protein interaction with gC1q receptor inhibits Th1 differentiation of CD4+ T cells via suppression of dendritic cell IL-12 production.", "J. Leukoc. Biol.", "2007", "Hahn Y.S., Hall C.H., Waggoner S.N.", "protein_xref_pubmed", "17881511", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "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_pubmed", "16227268", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Cell entry of hepatitis C virus requires a set of co-receptors that include the CD81 tetraspanin and the SR-B1 scavenger receptor.", "J. Biol. Chem.", "2003", "Cortese R., Cosset F.-L., Bartosch B., Dubuisson J., Goujon C., Granier C., Nicosia A., Pascale S., Scarselli E., Vitelli A.", "protein_xref_pubmed", "12913001", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "CD81-dependent binding of hepatitis C virus E1E2 heterodimers.", "J. Virol.", "2003", "Levy S., Cocquerel L., Dubuisson J., Kuo C.-C.", "protein_xref_pubmed", "12970454", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Claudin association with CD81 defines hepatitis C virus entry.", "J. Biol. Chem.", "2010", "Davis C., Hu K., Balfe P., Drummer H., Farquhar M.J., Goodall M., Harris H.J., McCaffrey K., McKeating J.A., Mee C.J., Mullins J.G., Young S.", "protein_xref_pubmed", "20375010", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "L-SIGN (CD209L) and DC-SIGN (CD209) mediate transinfection of liver cells by hepatitis C virus.", "Proc. Natl. Acad. Sci. U.S.A.", "2004", "Dragic T., Boussemart L., Cormier E.G., Durso R.J., Gardner J.P., Manix C., Olson W.C., Tsamis F.", "protein_xref_pubmed", "15371595", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "ISG12a Restricts Hepatitis C Virus Infection through the Ubiquitination-Dependent Degradation Pathway.", "J. Virol.", "2016", "Chen S., Wang J., Wang X., Zhu H., Tian R., Xu Y., Yang D., Qin Y., Xie Q., Liu N., Xue B.", "protein_xref_pubmed", "27194766", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Mass spectrometric characterization of glycosylation of hepatitis C virus E2 envelope glycoprotein reveals extended microheterogeneity of N-glycans.", "J. Am. Soc. Mass Spectrom.", "2008", "Tomer K.B., Przybylski M., Iacob R.E., Perdivara I.", "protein_xref_pubmed", "18187336", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Intrinsically unstructured domain 3 of hepatitis C Virus NS5A forms a 'fuzzy complex' with VAPB-MSP domain which carries ALS-causing mutations.", "PLoS ONE", "2012", "Song J., Qin H., Gupta G.", "protein_xref_pubmed", "22720086", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Hepatitis C Virus Modulates Solute carrier family 3 member 2 for Viral Propagation.", "Sci. Rep.", "2018", "Choi J.W., Pham H.T., Lim Y.S., Hwang S.B., Han S.S., Nguyen L.P., Nguyen T.T.T., Luong T.T.D., Mai H.N., Nguyen N.N.T., Tran S.C.", "protein_xref_pubmed", "30341327", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae.", "Nucleic Acids Res.", "2008", "Darlix J.L., Ficheux D., Gabus C., Ivanyi-Nagy R., Lavergne J.P.", "protein_xref_pubmed", "18033802", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Identification of the major phosphorylation site of the hepatitis C virus H strain NS5A protein as serine 2321.", "J. Biol. Chem.", "1999", "Rice C.M., Reed K.E.", "protein_xref_pubmed", "10488152", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Properties of the hepatitis C virus core protein: a structural protein that modulates cellular processes.", "J. Viral Hepat.", "2000", "McLauchlan J.", "protein_xref_pubmed", "10718937", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Charged residues in the transmembrane domains of hepatitis C virus glycoproteins play a major role in the processing, subcellular localization, and assembly of these envelope proteins.", "J. Virol.", "2000", "Cocquerel L., Dubuisson J., Minner F., Penin F., Wychowski C.", "protein_xref_pubmed", "10729138", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "The transmembrane domain of the hepatitis C virus E2 glycoprotein is required for correct folding of the E1 glycoprotein and native complex formation.", "Virology", "2001", "Patel A.H., Patel J., McLauchlan J.", "protein_xref_pubmed", "11145889", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Conservation of the conformation and positive charges of hepatitis C virus E2 envelope glycoprotein hypervariable region 1 points to a role in cell attachment.", "J. Virol.", "2001", "Deleage G., Combet C., Frainais P.-O., Germanidis G., Pawlotsky J.-M., Penin F.", "protein_xref_pubmed", "11356980", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Determinants for membrane association of the hepatitis C virus RNA-dependent RNA polymerase.", "J. Biol. Chem.", "2001", "Rice C.M., Moradpour D., Schmidt-Mende J., Blum H.E., Bieck E., Huegle T., Penin F.", "protein_xref_pubmed", "11557752", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "An amino-terminal amphipathic alpha-helix mediates membrane association of the hepatitis C virus nonstructural protein 5A.", "J. Biol. Chem.", "2002", "Moradpour D., Blum H.E., Bieck E., Brass V., Hellings J.A., Montserret R., Penin F., Woelk B.", "protein_xref_pubmed", "11744739", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Hepatitis C virus (HCV) NS5A binds RNA-dependent RNA polymerase (RdRP) NS5B and modulates RNA-dependent RNA polymerase activity.", "J. Biol. Chem.", "2002", "Kobayashi K., Qin W., Kaneko S., Luo H., Yamashita T., Murakami S., Shirota Y.", "protein_xref_pubmed", "11801599", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Solution structure and backbone dynamics of an engineered arginine-rich subdomain 2 of the hepatitis C virus NS3 RNA helicase.", "J. Mol. Biol.", "2001", "Liu D., Wyss D.F., Wang Y.-S., Gesell J.J.", "protein_xref_pubmed", "11846566", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Subcellular localization and topology of the p7 polypeptide of hepatitis C virus.", "J. Virol.", "2002", "Cocquerel L., Dubuisson J., Carrere-Kremer S., Montpellier-Pala C., Penin F., Wychowski C.", "protein_xref_pubmed", "11907211", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex.", "J. Virol.", "2002", "Bianchi L., Moradpour D., Blum H.E., Bienz K., Egger D., Gosert R., Woelk B.", "protein_xref_pubmed", "12021330", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Topological changes in the transmembrane domains of hepatitis C virus envelope glycoproteins.", "EMBO J.", "2002", "Cocquerel L., Dubuisson J., Roussel J., Delgrange D., Lambot M., Op de Beeck A., Penin F., Pillez A., Wychowski C.", "protein_xref_pubmed", "12065403", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Pyrrolidine-5,5-trans-lactams. 2. The use of X-ray crystal structure data in the optimization of P3 and P4 substituents.", "Org. Lett.", "2002", "Mills G., Johnson M.R., Jones P.S., Somers D.O., Andrews D.M., Chaignot H., Coomber B.A., Good A.C., Hind S.L., Robinson J.E., Skarzynski T., Slater M.J.", "protein_xref_pubmed", "12465917", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "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_pubmed", "12560074", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Protein-protein interactions between hepatitis C virus nonstructural proteins.", "J. Virol.", "2003", "Schuster C., Kieny M.P., Dimitrova M., Imbert I.", "protein_xref_pubmed", "12692242", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Topology of the membrane-associated hepatitis C virus protein NS4B.", "J. Virol.", "2003", "Monne M., Lundin M., Persson M.A.A., Von Heijne G., Widell A.", "protein_xref_pubmed", "12692244", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Identification of the hepatitis C virus RNA replication complex in Huh-7 cells harboring subgenomic replicons.", "J. Virol.", "2003", "Bartenschlager R., Moradpour D., Blum H.E., Lohmann V., Bienz K., Egger D., Gosert R.", "protein_xref_pubmed", "12692249", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "The hepatitis C virus p7 protein forms an ion channel that is inhibited by long-alkyl-chain iminosugar derivatives.", "Proc. Natl. Acad. Sci. U.S.A.", "2003", "Dwek R.A., Zitzmann N., Blumberg B., Pavlovic D., Argaud O., Fischer W.B., Neville D.C.", "protein_xref_pubmed", "12719519", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "The p7 polypeptide of hepatitis C virus is critical for infectivity and contains functionally important genotype-specific sequences.", "Proc. Natl. Acad. Sci. U.S.A.", "2003", "Purcell R.H., Sakai A., Bukh J., Claire M.S., Emerson S.U., Faulk K., Govindarajan S.", "protein_xref_pubmed", "14504405", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Induction of FAS ligand expression in a human hepatoblastoma cell line by HCV core protein.", "Virus Res.", "2003", "Ruggieri A., Murdolo M., Rapicetta M.", "protein_xref_pubmed", "14602201", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Structural biology of hepatitis C virus.", "Hepatology", "2004", "Dubuisson J., Rey F.A., Moradpour D., Pawlotsky J.-M., Penin F.", "protein_xref_pubmed", "14752815", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Characterization of functional hepatitis C virus envelope glycoproteins.", "J. Virol.", "2004", "Cosset F.-L., Bartosch B., Cocquerel L., Dubuisson J., Voisset C., Ciczora Y., Foung S., Keck Z., Op De Beeck A.", "protein_xref_pubmed", "14990718", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Regulation of hepatitis C virus polyprotein processing by signal peptidase involves structural determinants at the p7 sequence junctions.", "J. Biol. Chem.", "2004", "Cocquerel L., Dubuisson J., Lorenzo L., Belouzard S., Brulin B., Carrere-Kremer S., Montpellier C., Penin F.", "protein_xref_pubmed", "15247249", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Analysis of the processing and transmembrane topology of the E2p7 protein of hepatitis C virus.", "J. Gen. Virol.", "2005", "Patel A.H., Isherwood B.J.", "protein_xref_pubmed", "15722527", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "The membrane-active regions of the hepatitis C virus E1 and E2 envelope glycoproteins.", "Biochemistry", "2006", "Guillen J., Bernabeu A., Moreno M.R., Perez-Berna A.J., Villalain J.", "protein_xref_pubmed", "16533059", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Genomic structure of the human prototype strain H of hepatitis C virus: comparison with American and Japanese isolates.", "Proc. Natl. Acad. Sci. U.S.A.", "1991", "Inchauspe G., Lee D.H.H., Nasoff M., Prince A.M., Sugitani M., Zebedee S.", "protein_xref_pubmed", "1658800", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Palmitoylation and polymerization or in protein-protein interactions of hepatitis C virus NS4B protein.", "J. Virol.", "2006", "Gao L., Lai M.M.C., Lee K.-J., Yu G.-Y.", "protein_xref_pubmed", "16731940", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Structure of the catalytic domain of the hepatitis C virus NS2-3 protease.", "Nature", "2006", "Rice C.M., Marcotrigiano J., Dentzer T.G., Lorenz I.C.", "protein_xref_pubmed", "16862121", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Entry of hepatitis C virus pseudotypes into primary human hepatocytes by clathrin-dependent endocytosis.", "J. Gen. Virol.", "2006", "Baumert T.F., Royer C., Jaeck D., Kieny M.P., Bastien-Valle M., Codran A., Martin J.P., Pereira C.A.", "protein_xref_pubmed", "16894197", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Molecular and structural characterization of the domain 2 of hepatitis C virus non-structural protein 5A.", "Mol. Cells", "2006", "Liang Y., Kang C.B., Yoon H.S.", "protein_xref_pubmed", "16951545", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Dual topology of the processed hepatitis C virus protein NS4B is influenced by the NS5A protein.", "J. Gen. Virol.", "2006", "Lindstrom H., Groenwall C., Lundin M., Persson M.A.", "protein_xref_pubmed", "17030859", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Conserved determinants for membrane association of nonstructural protein 5A from hepatitis C virus and related viruses.", "J. Virol.", "2007", "Moradpour D., Deleage G., Blum H.E., Brass V., Pal Z., Penin F., Sapay N.", "protein_xref_pubmed", "17192310", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Intracellular proton conductance of the hepatitis C virus p7 protein and its contribution to infectious virus production.", "PLoS Pathog.", "2010", "Yi M., Lemon S.M., Weinman S.A., Harris M., Griffin S., Rowlands D., Wozniak A.L.", "protein_xref_pubmed", "20824094", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Mutations in the STAT1-interacting domain of the hepatitis C virus core protein modulate the response to antiviral therapy.", "Mol. Med. 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Virol.", "1996", "Selby M.J., Ou J.-H., Lo S.-Y.", "protein_xref_pubmed", "8764026", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide.", "Cell", "1996", "Lin C., Rice C.M., Morgenstern K.A., Caron P.R., Lepre C.A., Thomson J.A., Fox T., Chambers S.P., Markland W., Dwyer M.D., Kim J.L., Murcko M.A., Landro J.A., Harbeson S.L., O'Malley E.T.", "protein_xref_pubmed", "8861917", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Characterization of the nuclear localization signal and subcellular distribution of hepatitis C virus nonstructural protein NS5A.", "Gene", "1996", "Zhang L., Chen M., Sasaguri Y., Ide Y., Padmanabhan R., Bahl C., Inchauspe G.", "protein_xref_pubmed", "8982089", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Structure of the hepatitis C virus RNA helicase domain.", "Nat. Struct. Biol.", "1997", "Le H.V., Hong Z., Weber P.C., Yao N., Cable M.B., Hesson T., Kwong A.D.", "protein_xref_pubmed", "9187654", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA.", "Science", "1997", "Rice C.M., Feinstone S.M., Mihalik K., Blight K.J., Agapov E.V., Kolykhalov A.A.", "protein_xref_pubmed", "9228008", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Transcripts from a single full-length cDNA clone of hepatitis C virus are infectious when directly transfected into the liver of a chimpanzee.", "Proc. Natl. Acad. Sci. U.S.A.", "1997", "Purcell R.H., Yanagi M., Bukh J., Emerson S.U.", "protein_xref_pubmed", "9238047", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding.", "Structure", "1998", "Lin C., Morgenstern K.A., Caron P.R., Thomson J.A., Griffith J.P., Dwyer M.D., Kim J.L., Murcko M.A.", "protein_xref_pubmed", "9493270", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Critical interaction between E1 and E2 glycoproteins determines binding and fusion properties of hepatitis C virus during cell entry.", "Hepatology", "2014", "Lavillette D., Baumert T.F., Cosset F.L., Fresquet J., Zeisel M.B., Dao Thi V.L., Douam F., Maurin G., Mompelat D.", "protein_xref_pubmed", "24038151", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Analysis of the glycosylation sites of hepatitis C virus (HCV) glycoprotein E1 and the influence of E1 glycans on the formation of the HCV glycoprotein complex.", "J. Gen. Virol.", "1999", "Cocquerel L., Dubuisson J., Cahour A., Wychowski C., Choukhi A., Fournillier A., Meunier J.C.", "protein_xref_pubmed", "10211957", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Synthesis of a novel hepatitis C virus protein by ribosomal frameshift.", "EMBO J.", "2001", "Choi J., Xu Z., Chien D., Lu W., Selby M.J., Ou J.-H., Yen T.S.B., Govindarajan S., Strohecker A.", "protein_xref_pubmed", "11447125", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "The domains required to direct core proteins of hepatitis C virus and GB virus-B to lipid droplets share common features with plant oleosin proteins.", "J. Biol. Chem.", "2002", "McLauchlan J., Hope R.G., Murphy D.J.", "protein_xref_pubmed", "11706032", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Cation-selective ion channels formed by p7 of hepatitis C virus are blocked by hexamethylene amiloride.", "FEBS Lett.", "2004", "Wilson L., Gage P.W., Ewart G.D., Premkumar A.", "protein_xref_pubmed", "14741348", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Structure and function of the membrane anchor domain of hepatitis C virus nonstructural protein 5A.", "J. Biol. Chem.", "2004", "Bartenschlager R., Moradpour D., Blum H.E., Brass V., Montserret R., Penin F., Appel N., Ficheux D., Ramboarina S.", "protein_xref_pubmed", "15247283", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase.", "Nature", "2004", "Pyle A.M., Serebrov V.", "protein_xref_pubmed", "15269774", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP.", "Nature", "2006", "Cheng W., Pyle A.M., Beran R.K., Bustamante C., Dumont S., Serebrov V., Tinoco I. Jr.", "protein_xref_pubmed", "16397502", "protein_xref_uniprotkb", "P27958" ], [ "P27958-1", "Identification of a novel determinant for membrane association in hepatitis C virus nonstructural protein 4B.", "J. Virol.", "2009", "Moradpour D., Castet V., Blum H.E., Gouttenoire J., Arora N., Montserret R., Penin F., Diesis E., Raussens V., Ruysschaert J.M.", "protein_xref_pubmed", "19357161", "protein_xref_uniprotkb", "P27958" ] ] }, "readme": "Name\n - HCV1a Protein Citations (UniProtKB)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2020-03-13T11:25:59.634509\n\nModified on\n - 2020-04-09T17:33:53.624980\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@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 Hepatitis C virus (genotype 1a, isolate H) Protein Citations dataset contains publication information for hcv1a [taxid:11108] 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-1.11.2/compiled/hcv1a_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-hepatitis-c-virus-1a.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/source/uniprot-proteome-hepatitis-c-virus-1a.nt\n Name: hcv1a_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/hcv1a_protein_masterlist.csv\n Output Subdomain\n Name: hcv1a_protein_citations_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/hcv1a_protein_citations_uniprotkb.csv\n Name: hcv1a_protein_citations_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/hcv1a_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/hcv1a_protein_citations_uniprotkb.csv" }