{ "bcoid": "GLY_000029", "title": "Gene Expression (Cancer)", "description": "Gene Expression (Cancer) dataset contains the gene expression information in cancers from BioXpress database. ...", "filename": "human_protein_expression_disease.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Cancer Gene Expression", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P04217-1...", "No..." ], [ "P04217-1...", "Yes..." ] ], "headers": [ "uniprotkb_ca...", "significance..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "significance" }, { "type": "string", "label": "direction" }, { "type": "string", "label": "do_id" }, { "type": "string", "label": "do_name" }, { "type": "string", "label": "parent_doid" }, { "type": "string", "label": "parent_doname" } ], [ "P04217-1", "No", "Up", "11054", "DOID:11054 / Urinary bladder cancer [UBC]", "11054", "DOID:11054 / urinary bladder cancer" ], [ "P04217-1", "Yes", "Down", "10283", "DOID:10283 / Prostate cancer [PCa]", "10283", "DOID:10283 / prostate cancer" ], [ "P04217-1", "No", "Up", "263", "DOID:263 / Kidney cancer [Kidca] & Kidney renal cl ...", "263", "DOID:263 / kidney cancer" ], [ "P04217-1", "No", "Down", "4471", "DOID:4471 / Chromophobe adenocarcinoma", "263", "DOID:263 / kidney cancer" ], [ "P04217-1", "No", "Up", "11934", "DOID:11934 / Head and neck cancer [H&NC]", "11934", "DOID:11934 / head and neck cancer" ], [ "P04217-1", "No", "Down", "3907", "DOID:3907 / Lung squamous cell carcinoma", "1324", "DOID:1324 / lung cancer" ], [ "P04217-1", "Yes", "Up", "1612", "DOID:1612 / Breast cancer [BRCA]", "1612", "DOID:1612 / breast cancer" ], [ "P04217-1", "No", "Down", "3910", "DOID:3910 / Lung adenocarcinoma", "1324", "DOID:1324 / lung cancer" ], [ "P04217-1", "No", "Up", "5041", "DOID:5041 / Esophageal cancer [EC]", "5041", "DOID:5041 / esophageal cancer" ], [ "P04217-1", "Yes", "Up", "1781", "DOID:1781 / Thyroid cancer [Thyca]", "3963", "DOID:3963 / thyroid carcinoma" ], [ "P04217-1", "No", "Down", "3571", "DOID:3571 / Liver cancer [Livca]", "0070003", "DOID:0070003 / blastoma" ], [ "P04217-1", "No", "Up", "4465", "DOID:4465 / Papillary renal cell carcinoma", "", "" ], [ "P04217-1", "No", "Up", "234", "DOID:234 / Colon adenocarcinoma", "9256", "DOID:9256 / colorectal cancer" ], [ "P04217-1", "No", "Up", "10534", "DOID:10534 / Stomach cancer [Stoca]", "10534", "DOID:10534 / stomach cancer" ], [ "Q9NQ94-1", "Yes", "Up", "5041", "DOID:5041 / Esophageal cancer [EC]", "5041", "DOID:5041 / esophageal cancer" ], [ "Q9NQ94-1", "No", "Up", "263", "DOID:263 / Kidney cancer [Kidca] & Kidney renal cl ...", "263", "DOID:263 / kidney cancer" ], [ "Q9NQ94-1", "No", "Down", "4465", "DOID:4465 / Papillary renal cell carcinoma", "", "" ], [ "Q9NQ94-1", "No", "Down", "4471", "DOID:4471 / Chromophobe adenocarcinoma", "263", "DOID:263 / kidney cancer" ], [ "Q9NQ94-1", "No", "Down", "3571", "DOID:3571 / Liver cancer [Livca]", "0070003", "DOID:0070003 / blastoma" ], [ "Q9NQ94-1", "No", "Up", "3910", "DOID:3910 / Lung adenocarcinoma", "1324", "DOID:1324 / lung cancer" ], [ "Q9NQ94-1", "No", "Down", "1612", "DOID:1612 / Breast cancer [BRCA]", "1612", "DOID:1612 / breast cancer" ], [ "Q9NQ94-1", "No", "Up", "11054", "DOID:11054 / Urinary bladder cancer [UBC]", "11054", "DOID:11054 / urinary bladder cancer" ], [ "Q9NQ94-1", "No", "Up", "3907", "DOID:3907 / Lung squamous cell carcinoma", "1324", "DOID:1324 / lung cancer" ], [ "Q9NQ94-1", "No", "Down", "234", "DOID:234 / Colon adenocarcinoma", "9256", "DOID:9256 / colorectal cancer" ], [ "Q9NQ94-1", "No", "Up", "10534", "DOID:10534 / Stomach cancer [Stoca]", "10534", "DOID:10534 / stomach cancer" ], [ "Q9NQ94-1", "No", "Up", "1781", "DOID:1781 / Thyroid cancer [Thyca]", "3963", "DOID:3963 / thyroid carcinoma" ], [ "Q9NQ94-1", "No", "Up", "11934", "DOID:11934 / Head and neck cancer [H&NC]", "11934", "DOID:11934 / head and neck cancer" ], [ "Q9NQ94-1", "No", "Up", "10283", "DOID:10283 / Prostate cancer [PCa]", "10283", "DOID:10283 / prostate cancer" ], [ "Q9BVM4-1", "No", "Down", "3571", "DOID:3571 / Liver cancer [Livca]", "0070003", "DOID:0070003 / blastoma" ], [ "Q9BVM4-1", "No", "Up", "10534", "DOID:10534 / Stomach cancer [Stoca]", "10534", "DOID:10534 / stomach cancer" ], [ "Q9BVM4-1", "No", "Down", "5041", "DOID:5041 / Esophageal cancer [EC]", "5041", "DOID:5041 / esophageal cancer" ], [ "Q9BVM4-1", "No", "Down", "11934", "DOID:11934 / Head and neck cancer [H&NC]", "11934", "DOID:11934 / head and neck cancer" ], [ "Q9BVM4-1", "Yes", "Up", "3907", "DOID:3907 / Lung squamous cell carcinoma", "1324", "DOID:1324 / lung cancer" ], [ "Q9BVM4-1", "Yes", "Down", "263", "DOID:263 / Kidney cancer [Kidca] & Kidney renal cl ...", "263", "DOID:263 / kidney cancer" ], [ "Q9BVM4-1", "No", "Up", "1781", "DOID:1781 / Thyroid cancer [Thyca]", "3963", "DOID:3963 / thyroid carcinoma" ], [ "Q9BVM4-1", "Yes", "Down", "4465", "DOID:4465 / Papillary renal cell carcinoma", "", "" ], [ "Q9BVM4-1", "No", "Down", "4471", "DOID:4471 / Chromophobe adenocarcinoma", "263", "DOID:263 / kidney cancer" ], [ "Q9BVM4-1", "No", "Down", "234", "DOID:234 / Colon adenocarcinoma", "9256", "DOID:9256 / colorectal cancer" ], [ "Q9BVM4-1", "Yes", "Up", "10283", "DOID:10283 / Prostate cancer [PCa]", "10283", "DOID:10283 / prostate cancer" ], [ "Q9BVM4-1", "No", "Down", "1612", "DOID:1612 / Breast cancer [BRCA]", "1612", "DOID:1612 / breast cancer" ], [ "Q9BVM4-1", "No", "Up", "3910", "DOID:3910 / Lung adenocarcinoma", "1324", "DOID:1324 / lung cancer" ], [ "Q9BVM4-1", "No", "Up", "11054", "DOID:11054 / Urinary bladder cancer [UBC]", "11054", "DOID:11054 / urinary bladder cancer" ], [ "P01023-1", "Yes", "Up", "263", "DOID:263 / Kidney cancer [Kidca] & Kidney renal cl ...", "263", "DOID:263 / kidney cancer" ], [ "P01023-1", "No", "Up", "234", "DOID:234 / Colon adenocarcinoma", "9256", "DOID:9256 / colorectal cancer" ], [ "P01023-1", "No", "Down", "3571", "DOID:3571 / Liver cancer [Livca]", "0070003", "DOID:0070003 / blastoma" ], [ "P01023-1", "No", "Down", "4471", "DOID:4471 / Chromophobe adenocarcinoma", "263", "DOID:263 / kidney cancer" ], [ "P01023-1", "No", "Down", "3910", "DOID:3910 / Lung adenocarcinoma", "1324", "DOID:1324 / lung cancer" ], [ "P01023-1", "No", "Down", "10534", "DOID:10534 / Stomach cancer [Stoca]", "10534", "DOID:10534 / stomach cancer" ], [ "P01023-1", "Yes", "Down", "11054", "DOID:11054 / Urinary bladder cancer [UBC]", "11054", "DOID:11054 / urinary bladder cancer" ], [ "P01023-1", "Yes", "Down", "10283", "DOID:10283 / Prostate cancer [PCa]", "10283", "DOID:10283 / prostate cancer" ], [ "P01023-1", "No", "Down", "11934", "DOID:11934 / Head and neck cancer [H&NC]", "11934", "DOID:11934 / head and neck cancer" ], [ "P01023-1", "No", "Down", "5041", "DOID:5041 / Esophageal cancer [EC]", "5041", "DOID:5041 / esophageal cancer" ], [ "P01023-1", "Yes", "Up", "1781", "DOID:1781 / Thyroid cancer [Thyca]", "3963", "DOID:3963 / thyroid carcinoma" ], [ "P01023-1", "Yes", "Down", "3907", "DOID:3907 / Lung squamous cell carcinoma", "1324", "DOID:1324 / lung cancer" ], [ "P01023-1", "No", "Down", "4465", "DOID:4465 / Papillary renal cell carcinoma", "", "" ], [ "P01023-1", "Yes", "Down", "1612", "DOID:1612 / Breast cancer [BRCA]", "1612", "DOID:1612 / breast cancer" ], [ "A8K2U0-1", "Yes", "Down", "10534", "DOID:10534 / Stomach cancer [Stoca]", "10534", "DOID:10534 / stomach cancer" ], [ "A8K2U0-1", "No", "Down", "10283", "DOID:10283 / Prostate cancer [PCa]", "10283", "DOID:10283 / prostate cancer" ], [ "A8K2U0-1", "No", "Down", "3910", "DOID:3910 / Lung adenocarcinoma", "1324", "DOID:1324 / lung cancer" ], [ "A8K2U0-1", "No", "Down", "4465", "DOID:4465 / Papillary renal cell carcinoma", "", "" ], [ "A8K2U0-1", "Yes", "Up", "11054", "DOID:11054 / Urinary bladder cancer [UBC]", "11054", "DOID:11054 / urinary bladder cancer" ], [ "A8K2U0-1", "Yes", "Up", "3907", "DOID:3907 / Lung squamous cell carcinoma", "1324", "DOID:1324 / lung cancer" ], [ "A8K2U0-1", "No", "Up", "1612", "DOID:1612 / Breast cancer [BRCA]", "1612", "DOID:1612 / breast cancer" ], [ "A8K2U0-1", "No", "Down", "5041", "DOID:5041 / Esophageal cancer [EC]", "5041", "DOID:5041 / esophageal cancer" ], [ "A8K2U0-1", "No", "Down", "263", "DOID:263 / Kidney cancer [Kidca] & Kidney renal cl ...", "263", "DOID:263 / kidney cancer" ], [ "A8K2U0-1", "No", "Down", "1781", "DOID:1781 / Thyroid cancer [Thyca]", "3963", "DOID:3963 / thyroid carcinoma" ], [ "A8K2U0-1", "Yes", "Down", "11934", "DOID:11934 / Head and neck cancer [H&NC]", "11934", "DOID:11934 / head and neck cancer" ], [ "A8K2U0-1", "No", "Down", "3571", "DOID:3571 / Liver cancer [Livca]", "0070003", "DOID:0070003 / blastoma" ], [ "A8K2U0-1", "No", "Up", "4471", "DOID:4471 / Chromophobe adenocarcinoma", "263", "DOID:263 / kidney cancer" ], [ "A8K2U0-1", "No", "Up", "234", "DOID:234 / Colon adenocarcinoma", "9256", "DOID:9256 / colorectal cancer" ], [ "Q9NPC4-1", "Yes", "Up", "1781", "DOID:1781 / Thyroid cancer [Thyca]", "3963", "DOID:3963 / thyroid carcinoma" ], [ "Q9NPC4-1", "Yes", "Down", "10283", "DOID:10283 / Prostate cancer [PCa]", "10283", "DOID:10283 / prostate cancer" ], [ "Q9NPC4-1", "Yes", "Down", "11054", "DOID:11054 / Urinary bladder cancer [UBC]", "11054", "DOID:11054 / urinary bladder cancer" ], [ "Q9NPC4-1", "No", "Down", "4471", "DOID:4471 / Chromophobe adenocarcinoma", "263", "DOID:263 / kidney cancer" ], [ "Q9NPC4-1", "No", "Up", "234", "DOID:234 / Colon adenocarcinoma", "9256", "DOID:9256 / colorectal cancer" ], [ "Q9NPC4-1", "Yes", "Up", "3907", "DOID:3907 / Lung squamous cell carcinoma", "1324", "DOID:1324 / lung cancer" ], [ "Q9NPC4-1", "No", "Down", "1612", "DOID:1612 / Breast cancer [BRCA]", "1612", "DOID:1612 / breast cancer" ], [ "Q9NPC4-1", "No", "Up", "11934", "DOID:11934 / Head and neck cancer [H&NC]", "11934", "DOID:11934 / head and neck cancer" ], [ "Q9NPC4-1", "No", "Down", "3910", "DOID:3910 / Lung adenocarcinoma", "1324", "DOID:1324 / lung cancer" ], [ "Q9NPC4-1", "No", "Down", "10534", "DOID:10534 / Stomach cancer [Stoca]", "10534", "DOID:10534 / stomach cancer" ], [ "Q9NPC4-1", "No", "Up", "4465", "DOID:4465 / Papillary renal cell carcinoma", "", "" ], [ "Q9NPC4-1", "Yes", "Up", "263", "DOID:263 / Kidney cancer [Kidca] & Kidney renal cl ...", "263", "DOID:263 / kidney cancer" ], [ "Q9NPC4-1", "No", "Up", "3571", "DOID:3571 / Liver cancer [Livca]", "0070003", "DOID:0070003 / blastoma" ], [ "Q9NPC4-1", "Yes", "Down", "5041", "DOID:5041 / Esophageal cancer [EC]", "5041", "DOID:5041 / esophageal cancer" ] ] }, "readme": "Name\n - Gene Expression (Cancer)\n\nVersion\n - 1.5.18\n\nCreated on\n - 2019-01-23T17:21:05.896478\n\nModified on\n - 2020-04-11T11:26:52.178903\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 - \n\nChecksum\n - \n\nUsability Domain\n - Gene Expression (Cancer) dataset contains the gene expression information in cancers from BioXpress database. The GlyGen interface shows the gene expression (cancer) information for select cancer types/DOIDs. For more cancer types/DOIDs please refer - https://hive.biochemistry.gwu.edu/bioxpress. If you use this dataset please give proper attribution to BioXpress and GlyGen.\n\nDescription Domain\n Keywords\n - gene expression (cancer)\n - Disease Ontology\n - differential expression\n - BioXpress\n\n Pipeline Steps\n - Step-1: The script extracts the expression information and maps the UniProtKB accession/ gene name to UniProtKB canonical accession\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: human_protein_expression_cancer.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.18/source/human_protein_expression_cancer.csv\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/human_protein_masterlist.csv\n Output Subdomain\n Name: human_protein_expression_disease.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/human_protein_expression_disease.csv\n Name: human_protein_expression_disease.stat.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/human_protein_expression_disease.stat.csv\n\nFields\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"14\"\n Name: \"parent_doid\"\n Description: \"Disease Ontology identifier of the parent disease\"\n Unique Values: \"12\"\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: \"18197\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"14\"\n Name: \"direction\"\n Description: \"Expression trend of the gene that can be either `Up` or `Down`\n Unique Values: \"2\"\n Name: \"parent_doname\"\n Description: \"Disease Ontology name of the parent disease\"\n Unique Values: \"12\"\n Name: \"significance\"\n Description: \"Significant differential expression of the gene that can be either `Yes` or `No`\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-1.5.18/reviewed/human_protein_expression_disease.csv" }