analysis of chemicals, diseases, or genes ctd.pl $input $numerical_column $inType.inputType #if $inType.inputType == "disease" $inType.report ANY #else if $inType.reportType.report == "cgixns" $inType.reportType.report $inType.reportType.actType #else $inType.reportType.report ANY #end if $out_file1 Chemicals (MeSH names, synonyms or accession IDs, or CAS RNs) Diseases (MeSH or OMIM names, synonyms or accession IDs) Genes (NCBI official symbols or accession IDs) Curated chemical-gene interactions Curated gene associations Pathway associations All disease relationships Direct disease relationships only Inferred disease relationships only All GO associations GO biological Processes only GO molecular Functions only GO cellular Components only ANY abundance activity binding cotreatment expression folding localization metabolic processing - acetylation - acylation - alkylation - amination - carbamoylation - carboxylation - chemical synthesis - degradation - cleavage - hydrolysis - ethylation - glutathionylation - glycation - glycosylation - N-linked glycosylation - O-linked glycosylation - glucuronidation - hydroxylation - lipidation - farnesylation - geranolyation - myristolylation - palmitoylation - prenylation - methylation - nitrosation - nucleotidylation - oxidation - phosphorylation - reduction - ribosylation - ADP-ribosylation - sulfation - sumoylation - ubiquitination mutagenesis reaction response to chemical splicing stability transport - secretion - export - uptake - import Chemical associations Chemical associations direct relationships only Chemical associations inferred relationships only Curated gene associations Pathway associations Curated chemical-gene interactions Curated chemical associations Pathway associations All disease relationships Direct disease relationships only Inferred disease relationships only All GO associations GO biological Processes only GO molecular Functions only GO cellular Components only ANY abundance activity binding cotreatment expression folding localization metabolic processing - acetylation - acylation - alkylation - amination - carbamoylation - carboxylation - chemical synthesis - degradation - cleavage - hydrolysis - ethylation - glutathionylation - glycation - glycosylation - N-linked glycosylation - O-linked glycosylation - glucuronidation - hydroxylation - lipidation - farnesylation - geranolyation - myristolylation - palmitoylation - prenylation - methylation - nitrosation - nucleotidylation - oxidation - phosphorylation - reduction - ribosylation - ADP-ribosylation - sulfation - sumoylation - ubiquitination mutagenesis reaction response to chemical splicing stability transport - secretion - export - uptake - import **Dataset formats** The input and output datasets are tabular_. (`Dataset missing?`_) .. _tabular: ./static/formatHelp.html#tab .. _Dataset missing?: ./static/formatHelp.html ----- **What it does** This tool extracts data related to the provided list of identifiers from the Comparative Toxicogenomics Database (CTD). The fields extracted vary with the type of data requested; the first row of the output identifies the columns. For the curated chemical-gene interactions, you can also choose the interaction type from the search-and-select box. The choices that start with '-' are a subset of a choice above them; you can chose either the general interaction type or a more specific one. Website: http://ctd.mdibl.org/ ----- **Examples** - input data file: HBB - select Column = c1, Identifier type = Genes, and Data to extract = All disease relationships - output file:: #Input GeneSymbol GeneName GeneID DiseaseName DiseaseID GeneDiseaseRelation OmimIDs PubMedIDs hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Ethanol 17676605|18926900 hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Valproic Acid 8875741 etc. Another example: - same input file: HBB - select Column = c1, Identifier type = Genes, Data to extract = Curated chemical-gene interactions, and Interaction type = ANY - output file:: #Input GeneSymbol GeneName GeneID ChemicalName ChemicalID CasRN Organism OrganismID Interaction InteractionTypes PubMedIDs hbb HBB hemoglobin, beta 3043 1-nitronaphthalene C016614 86-57-7 Macaca mulatta 9544 1-nitronaphthalene metabolite binds to HBB protein binding 16453347 hbb HBB hemoglobin, beta 3043 2,6-diisocyanatotoluene C026942 91-08-7 Cavia porcellus 10141 2,6-diisocyanatotoluene binds to HBB protein binding 8728499 etc. ----- **Reference** Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. (2009) Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. Nucleic Acids Res. 37(Database issue):D786-92. Epub 2008 Sep 9.