{ "bcoid": "GLY_000028", "title": "Gene Expression (Normal)", "description": "The Gene Expression (Normal) dataset contains the normal expression information of human [taxid:9606] ...", "filename": "human_protein_expression_normal.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Normal Gene Expression", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q9H306-1...", "0.0504879951..." ], [ "Q9H306-1...", "0.0228621177..." ] ], "headers": [ "uniprotkb_ca...", "score..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "score" }, { "type": "string", "label": "uberon_dev_id" }, { "type": "string", "label": "sex" }, { "type": "string", "label": "uberon_anatomy_id" }, { "type": "string", "label": "expression_call" }, { "type": "string", "label": "uberon_name" } ], [ "Q9H306-1", 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"absent", "heart" ], [ "Q9H306-1", "0.0", "HsapDv:0000092", "female", "UBERON:0000948", "absent", "heart" ], [ "Q9H306-1", "0.0", "HsapDv:0000095", "male", "UBERON:0000473", "absent", "testis" ], [ "Q9H306-1", "0.0", "HsapDv:0000089", "male", "UBERON:0000473", "absent", "testis" ], [ "Q9H306-1", "0.0", "HsapDv:0000090", "male", "UBERON:0000473", "absent", "testis" ], [ "Q9H306-1", "0.00604768935591", "HsapDv:0000092", "male", "UBERON:0000473", "absent", "testis" ], [ "Q9H306-1", "0.00324610015377", "HsapDv:0000092", "male", "UBERON:0002369", "absent", "adrenal gland" ], [ "Q9H306-1", "0.00799152534455", "HsapDv:0000092", "female", "UBERON:0000992", "absent", "ovary" ], [ "Q9H306-1", "0.191976442933", "HsapDv:0000090", "female", "UBERON:0000996", "present", "vagina" ], [ "Q9H306-1", "0.223324611783", "HsapDv:0000087", "female", "UBERON:0000996", "present", "vagina" ], [ "Q9H306-1", "0.160430043936", "HsapDv:0000091", "female", "UBERON:0000996", "present", "vagina" ], [ "Q9H306-1", "0.229308143258", "HsapDv:0000092", "female", "UBERON:0000996", "present", "vagina" ], [ "Q9H306-1", "0.205209076405", "HsapDv:0000088", "female", "UBERON:0000996", "present", "vagina" ], [ "Q9H306-1", "0.0965099111199", "HsapDv:0000094", "female", "UBERON:0001155", "present", "colon" ], [ "Q9H306-1", "0.0252454783767", "HsapDv:0000087", "male", "UBERON:0001987", "absent", "placenta" ], [ "Q9H306-1", "0.0", "HsapDv:0000087", "female", "UBERON:0001987", "absent", "placenta" ], [ "Q9H306-1", "0.0", "HsapDv:0000087", "male", "UBERON:0000955", "absent", "brain" ], [ "Q9H306-1", "0.0", "HsapDv:0000094", "female", "UBERON:0000955", "absent", "brain" ], [ "Q9H306-1", "0.139979213476", "HsapDv:0000087", "male", "UBERON:0001160", "present", "fundus of stomach" ], [ "Q9H306-1", "0.0386858433485", "HsapDv:0000091", "male", "UBERON:0001160", "absent", "fundus of stomach" ], [ "Q9H306-1", "0.0247308351099", "HsapDv:0000092", "male", "UBERON:0001160", "absent", "fundus of stomach" ], [ "Q9H306-1", "0.0219416506588", "HsapDv:0000088", "female", "UBERON:0001160", "absent", "fundus of stomach" ], [ "Q9H306-1", "0.0", "HsapDv:0000090", "male", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.00130614615046", "HsapDv:0000087", "male", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.00185310072266", "HsapDv:0000087", "female", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.00252406229265", "HsapDv:0000091", "male", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.0", "HsapDv:0000091", "female", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.0", "HsapDv:0000094", "male", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.00287625775673", "HsapDv:0000092", "male", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.00134707044344", "HsapDv:0000092", "female", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.003868854139", "HsapDv:0000088", "male", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.0109474761412", "HsapDv:0000088", "female", "UBERON:0001150", "absent", "body of pancreas" ], [ "Q9H306-1", "0.0176728982478", "HsapDv:0000094", "male", "UBERON:0002048", "absent", "lung" ], [ "Q9H306-1", "0.0", "HsapDv:0000090", "male", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.0", "HsapDv:0000087", "male", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.0", "HsapDv:0000087", "female", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.0012814628426", "HsapDv:0000091", "male", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.0", "HsapDv:0000091", "female", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.0251853000373", "HsapDv:0000094", "male", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.000612650590483", "HsapDv:0000092", "male", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.0", "HsapDv:0000092", "female", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.0", "HsapDv:0000088", "male", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.0112835969776", "HsapDv:0000088", "female", "UBERON:0000007", "absent", "pituitary gland" ], [ "Q9H306-1", "0.0", "HsapDv:0000089", "male", "UBERON:0002107", "absent", "liver" ], [ "Q9H306-1", "0.0", "HsapDv:0000090", "male", "UBERON:0002107", "absent", "liver" ], [ "Q9H306-1", "0.00475245853886", "HsapDv:0000092", "male", "UBERON:0002107", "absent", "liver" ], [ "Q9H306-1", "0.0", "HsapDv:0000090", "male", "UBERON:0002046", "absent", "thyroid gland" ], [ "Q9H306-1", "0.0385929718614", "HsapDv:0000087", "male", "UBERON:0002046", "absent", "thyroid gland" ], [ "Q9H306-1", "0.0210947338492", "HsapDv:0000087", "female", "UBERON:0002046", "absent", "thyroid gland" ], [ "Q9H306-1", "0.256255179644", "HsapDv:0000091", "male", "UBERON:0002046", "present", "thyroid gland" ], [ "Q9H306-1", "0.0", "HsapDv:0000091", "female", "UBERON:0002046", "absent", "thyroid gland" ], [ "Q9H306-1", "0.0109700998291", "HsapDv:0000094", "male", "UBERON:0002046", "absent", "thyroid gland" ], [ "Q9H306-1", "0.0627906918526", "HsapDv:0000092", "male", "UBERON:0002046", "absent", "thyroid gland" ], [ "Q9H306-1", "0.0320259965956", "HsapDv:0000092", "female", "UBERON:0002046", "absent", "thyroid gland" ], [ "Q9H306-1", "0.0278340186924", "HsapDv:0000088", "male", "UBERON:0002046", "absent", "thyroid gland" ], [ "Q9H306-1", "0.00620215525851", "HsapDv:0000088", "female", "UBERON:0002046", "absent", "thyroid gland" ], [ "Q9H306-1", "0.123054653406", "HsapDv:0000090", "male", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.0027742786333", "HsapDv:0000090", "female", "UBERON:0000178", "absent", "blood" ], [ "Q9H306-1", "0.113111980259", "HsapDv:0000087", "male", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.14796423912", "HsapDv:0000087", "female", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.0571885704994", "HsapDv:0000091", "male", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.0342097990215", "HsapDv:0000091", "female", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.0756295993924", "HsapDv:0000094", "male", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.00133733998518", "HsapDv:0000094", "female", "UBERON:0000178", "absent", "blood" ], [ "Q9H306-1", "0.0510715506971", "HsapDv:0000092", "male", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.0251757018268", "HsapDv:0000092", "female", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.0724468454719", "HsapDv:0000088", "male", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.0371706485748", "HsapDv:0000088", "female", "UBERON:0000178", "present", "blood" ], [ "Q9H306-1", "0.312280148268", "HsapDv:0000087", "female", "UBERON:0001043", "present", "esophagus" ], [ "Q9H306-1", "0.0610108114779", "HsapDv:0000092", "male", "UBERON:0001043", "absent", "esophagus" ], [ "Q9H306-1", "0.00728583196178", "HsapDv:0000090", "male", "UBERON:0002367", "absent", "prostate gland" ], [ "Q9H306-1", "0.0121264792979", "HsapDv:0000087", "male", "UBERON:0002367", "absent", "prostate gland" ], [ "Q9H306-1", "0.00740570435301", "HsapDv:0000091", "male", "UBERON:0002367", "absent", "prostate gland" ], [ "Q9H306-1", "0.0272845942527", "HsapDv:0000094", "male", "UBERON:0002367", "absent", "prostate gland" ], [ "Q9H306-1", "0.114427566528", "HsapDv:0000092", "male", "UBERON:0002367", "present", "prostate gland" ] ] }, "readme": "Name\n - Gene Expression (Normal)\n\nVersion\n - 1.5.23\n\nCreated on\n - 2019-01-23T17:21:05.895453\n\nModified on\n - 2020-04-11T11:24:57.144309\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 - The Gene Expression (Normal) dataset contains the normal expression information of human [taxid:9606] genes from BioXpress database. The GlyGen Interface shows the normal gene expression information for select UBERON ids only which are mapped to corresponding DOIDs and have gene expression in cancer information for those DOID. For more gene expression information of other UBERON IDs (tissues) for a given gene, please refer to BioXpress - https://hive.biochemistry.gwu.edu/bioxpress. BioXpress is a gene/miRNA expression and disease association database with expression levels mapped to genes or miRNAs. The current version of BioXpress contains only genes associated with cancer. If you are using this dataset please give proper attribution to GlyGen and BioXpress\n\nDescription Domain\n Keywords\n - normal gene expression\n - BioXpress\n - UBERON\n - tissue\n - Bgee\n\n Pipeline Steps\n - Step-1: The script extracts the expression information and maps the UniProtKB accession/gene symbol to UniProtKB canonical expression\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_normal.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/source/human_protein_expression_normal.csv\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/human_protein_masterlist.csv\n Output Subdomain\n Name: human_protein_expression_normal.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/human_protein_expression_normal.csv\n Name: human_protein_expression_normal.stat.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/reviewed/human_protein_expression_normal.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: \"18608\"\n Name: \"sex\"\n Description: \"Biological and physiological characteristics that define a person\"\n Unique Values: \"2\"\n Name: \"expression_call\"\n Description: \"Presence or absence of gene expression\"\n Unique Values: \"2\"\n Name: \"score\"\n Description: \"The gene expression score based on the combined expression and tissue specificity that can be between 0 and 10\"\n Unique Values: \"1725466\"\n Name: \"uberon_name\"\n Description: \"Uberon anatomical entity term\"\n Unique Values: \"21\"\n Name: \"uberon_anatomy_id\"\n Description: \"Uberon anatomical entity identifier\"\n Unique Values: \"21\"\n Name: \"uberon_dev_id\"\n Description: \"Uberon Human Developmental Stages (HsapDv) identifier\"\n Unique Values: \"8\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/human_protein_expression_normal.csv" }