{ "bcoid": "GLY_000335", "title": "HCV1a Glycosylation Sites (literature)", "description": "The HCV1a [TaxID:1108] glycosylations sites dataset contains glycosylation sites experimentally reported ...", "filename": "hcv1a_proteoform_glycosylation_sites_literature.csv", "filetype": "csv", "categories": { "species": "Hepatitis C virus (genotype 1a, isolate H)", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "external" }, "minitable": { "content": [ [ "P27958-1...", "N-Linked..." ], [ "P27958-1...", "N-Linked..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "cell_line" }, { "type": "string", "label": "cellosaurus_id" }, { "type": "string", "label": "abundance_normalized" } ], [ "P27958-1", "N-Linked", "G92050GC", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "14.59" ], [ "P27958-1", "N-Linked", "G92050GC", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "14.59" ], [ "P27958-1", "N-Linked", "G02815KT", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "7.42" ], [ "P27958-1", "N-Linked", "G02815KT", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "7.42" ], [ "P27958-1", "N-Linked", "G41247ZX", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "23.92" ], [ "P27958-1", "N-Linked", "G41247ZX", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "23.92" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "13.64" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "13.64" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "12.92" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "12.92" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "10.05" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "10.05" ], [ "P27958-1", "N-Linked", "G83460ZZ", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "9.09" ], [ "P27958-1", "N-Linked", "G83460ZZ", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "9.09" ], [ "P27958-1", "N-Linked", "G58087IP", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "4.78" ], [ "P27958-1", "N-Linked", "G58087IP", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "4.78" ], [ "P27958-1", "N-Linked", "G59324HL", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "3.59" ], [ "P27958-1", "N-Linked", "G59324HL", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "3.59" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "576", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "29.41" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "576", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "29.41" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "576", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "49.02" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "576", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "49.02" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "576", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "21.57" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "576", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "21.57" ], [ "P27958-1", "N-Linked", "G02815KT", "Asn", "623", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "11.49" ], [ "P27958-1", "N-Linked", "G02815KT", "Asn", "623", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "11.49" ], [ "P27958-1", "N-Linked", "G41247ZX", "Asn", "623", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "21.28" ], [ "P27958-1", "N-Linked", "G41247ZX", "Asn", "623", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "21.28" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "623", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "13.83" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "623", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "13.83" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "623", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "8.09" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "623", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "8.09" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "623", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "11.06" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "623", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "11.06" ], [ "P27958-1", "N-Linked", "G83460ZZ", "Asn", "623", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "9.36" ], [ "P27958-1", "N-Linked", "G83460ZZ", "Asn", "623", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "9.36" ], [ "P27958-1", "N-Linked", "G58087IP", "Asn", "623", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "14.89" ], [ "P27958-1", "N-Linked", "G58087IP", "Asn", "623", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "14.89" ], [ "P27958-1", "N-Linked", "G59324HL", "Asn", "623", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "10" ], [ "P27958-1", "N-Linked", "G59324HL", "Asn", "623", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "10" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "645", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "7.46" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "645", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "7.46" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "645", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "8.96" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "645", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "8.96" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "645", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "20.9" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "645", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "20.9" ], [ "P27958-1", "N-Linked", "G83460ZZ", "Asn", "645", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "29.85" ], [ "P27958-1", "N-Linked", "G83460ZZ", "Asn", "645", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "29.85" ], [ "P27958-1", "N-Linked", "G58087IP", "Asn", "645", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "13.43" ], [ "P27958-1", "N-Linked", "G58087IP", "Asn", "645", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "13.43" ], [ "P27958-1", "N-Linked", "G59324HL", "Asn", "645", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "19.4" ], [ "P27958-1", "N-Linked", "G59324HL", "Asn", "645", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "19.4" ], [ "P27958-1", "N-Linked", "G28681TP", "Asn", "417", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "12.08" ], [ "P27958-1", "N-Linked", "G28681TP", "Asn", "417", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "12.08" ], [ "P27958-1", "N-Linked", "G92050GC", "Asn", "417", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "22.95" ], [ "P27958-1", "N-Linked", "G92050GC", "Asn", "417", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "22.95" ], [ "P27958-1", "N-Linked", "G02815KT", "Asn", "417", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "19.81" ], [ "P27958-1", "N-Linked", "G02815KT", "Asn", "417", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "19.81" ], [ "P27958-1", "N-Linked", "G41247ZX", "Asn", "417", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "24.15" ], [ "P27958-1", "N-Linked", "G41247ZX", "Asn", "417", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "24.15" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "417", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "8.94" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "417", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "8.94" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "417", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "6.04" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "417", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "6.04" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "417", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "6.04" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "417", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "6.04" ], [ "P27958-1", "N-Linked", "G92050GC", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "26.56" ], [ "P27958-1", "N-Linked", "G92050GC", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "26.56" ], [ "P27958-1", "N-Linked", "G02815KT", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "15.63" ], [ "P27958-1", "N-Linked", "G02815KT", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "15.63" ], [ "P27958-1", "N-Linked", "G41247ZX", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "31.25" ], [ "P27958-1", "N-Linked", "G41247ZX", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "31.25" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "11.56" ], [ "P27958-1", "N-Linked", "G31852PQ", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "11.56" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "11.25" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "11.25" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "448", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "3.75" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "448", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "3.75" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "476", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "7.94" ], [ "P27958-1", "N-Linked", "G62765YT", "Asn", "476", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "7.94" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "476", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "23.36" ], [ "P27958-1", "N-Linked", "G80920RR", "Asn", "476", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "23.36" ], [ "P27958-1", "N-Linked", "G83460ZZ", "Asn", "476", "18187336", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "46.73" ], [ "P27958-1", "N-Linked", "G83460ZZ", "Asn", "476", "GLYDS000335", "Chinese hamster ovary (CHO) cells", "CVCL_0213", "46.73" ] ] }, "readme": "Name\n - HCV1a Glycosylation Sites (literature)\n\nVersion\n - 1.5.23\n\nCreated on\n - 2020-02-10T14:13:38.047090\n\nModified on\n - 2020-04-09T17:48:45.549047\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - Rahi Navelkar [rsn13@gwu.edu], Matthew Campbell [m.campbell2@griffith.edu.au]\n\nChecksum\n - \n\nUsability Domain\n - The HCV1a [TaxID:1108] glycosylations sites dataset contains glycosylation sites experimentally reported on Hepatitis C Virus 1a protein. The data was extracted from publication PMID:18187336 (Iacob RE, Perdivara I, Przybylski M, Tomer KB. Mass spectrometric characterization of glycosylation of hepatitis C virus E2 envelope glycoprotein reveals extended microheterogeneity of N-glycans. J Am Soc Mass Spectrom. 2008;19(3):428\u2013444. doi:10.1016/j.jasms.2007.11.022).\n\nDescription Domain\n Keywords\n - reported glycosylation\n - HCV\n\n Pipeline Steps\n - Step-1: 1) The data was extracted from the publications using supplemental material (Table 1,2,3). 2) The GenBank accession number (AF009606) retrieved from the paper was matched to the best hit UniProtKB Ac. (P27958) using the NCBI BLAST. 3) The glycan compositions provided by the paper were mapped to GlyTouCan Accession manually. 4) The source cell-line and mass-spectrometry data such as analyzer, chromatography, etc. were also extracted from the paper. 5) QC checks mapped the UniProtKB accessions to UniProtKB canonical accessions and checked the validity of amino acid and glycosite position on the .fasta sequence of the 2019-09 UniProtKB release for that protein.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: hcv1a_proteoform_glycosylation_sites_literature.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/source/hcv1a_proteoform_glycosylation_sites_literature.csv\n Name: hcv1a_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/hcv1a_protein_masterlist.csv\n Name: hcv_protein_canonicalsequences.fasta\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/hcv_protein_canonicalsequences.fasta\n Output Subdomain\n Name: hcv1a_proteoform_glycosylation_sites_literature.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/hcv1a_proteoform_glycosylation_sites_literature.csv\n Name: hcv1a_proteoform_glycosylation_sites_literature.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/hcv1a_proteoform_glycosylation_sites_literature.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: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"11\"\n Name: \"abundance_normalized\"\n Description: \"Abundance ratio of the glycan from the total glycan pool.\"\n Unique Values: \"79\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"1\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"1\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n Unique Values: \"2\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"14\"\n Name: \"cell_line\"\n Description: \"Cell line name\"\n Unique Values: \"1\"\n Name: \"cellosaurus_id\"\n Description: \"Cell line Id from the Cellosaurus database\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/hcv1a_proteoform_glycosylation_sites_literature.csv" }