{ "bcoid": "GLY_000507", "title": "Human Cancer Mutation LOG and GOG effect", "description": "", "filename_list": "human_protein_mutation_cancer_glycoeffect.csv", "filename": "human_protein_mutation_cancer_glycoeffect.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Protein" ], "tag": [ "Somatic Cancer Mutations LOG-GOG" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P42345-1...", "2215..." ], [ "P42345-1...", "2213..." ] ], "headers": [ "uniprotkb_ca...", "aa_pos..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "aa_pos" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "chr_id" }, { "type": "string", "label": "chr_start_pos" }, { "type": "string", "label": "chr_end_pos" }, { "type": "string", "label": "ref_nt" }, { "type": "string", "label": "alt_nt" }, { "type": "string", "label": "patients_positive" }, { "type": "string", "label": "patients_tested" }, { "type": "string", "label": "mut_freq" }, { "type": "string", "label": "data_source" }, { "type": "string", "label": "do_id" }, { "type": "string", "label": "do_name" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "filter_flags" }, { "type": "string", "label": "mim_id" }, { "type": "string", "label": "somatic_status" }, { "type": "string", "label": "minor_allelic_frequency" }, { "type": "string", "label": "is_known_glycoprotein" }, { "type": "string", "label": "motif_start" }, { "type": "string", "label": "ref_motif" }, { "type": "string", "label": "alt_motif" }, { "type": "string", "label": "effect" } ], [ "P42345-1", "2215", "S", "Y", "1", "11124516", "11124516", "G", "T", "0", "0", "0.0", "civic", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P42345", "Somatic mutation passed 1 out of 6 filters: num. of cancers (7).", "", "1", "", "yes", "2215", "S", "Y", "o-glyco-site-loss" ], [ "P42345-1", "2213", "P", "S", "1", "11124523", "11124523", "G", "A", "0", "0", "0.0", "civic", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "P42345", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NDP->NDS).", "", "1", "", "yes", "2211", "NDP", "NDS", "n-glyco-sequon-gain" ] ] }, "readme": "Name\n - Human Cancer Mutation LOG and GOG effect\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2020-06-25T13:28:50.371628\n\nModified on\n - 2024-05-17T11:24:02.862Z\n\nCreated by\n - [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nExecution Domain\n Scripts\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: glycan_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/glycan_masterlist.csv\n Name: human_protein_mutation_cancer.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_protein_mutation_cancer.csv\n Name: aadict.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/misc/aadict.csv\n Output Subdomain\n Name: human_protein_mutation_cancer_glycoeffect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_protein_mutation_cancer_glycoeffect.csv\n Name: human_protein_mutation_cancer_glycoeffect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_protein_mutation_cancer_glycoeffect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"12031\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"4386\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"18\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"20\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"24\"\n Name: \"chr_start_pos\"\n Description: \"\"\n Unique Values: \"61778\"\n Name: \"chr_end_pos\"\n Description: \"\"\n Unique Values: \"61778\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"4\"\n Name: \"patients_positive\"\n Description: \"The number of the patients having the cancer mutation\"\n Unique Values: \"54\"\n Name: \"patients_tested\"\n Description: \"The total number of patients tested for the given cancer mutation\"\n Unique Values: \"21\"\n Name: \"mut_freq\"\n Description: \"Frequency count of mutations across datasets\"\n Unique Values: \"40\"\n Name: \"data_source\"\n Description: \"The source database for the data\"\n Unique Values: \"2\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"19\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"19\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"12031\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"2442\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\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: \"minor_allelic_frequency\"\n Description: \"\"\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: \"2\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"4481\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"551\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"577\"\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\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/human_protein_mutation_cancer_glycoeffect.csv" }