----------------------------------------------- Pentacon NSAID Project Curation Princeton University, NJ, USA University of Pennsylvania, PA, USA ----------------------------------------------- Readme file name: AAP_genelist_Readme_20141013_production.txt Readme for the following files: AAP_genelist_20141013_production.txt Content: Genes associated with the Arachidonic Acid Pathway (AAP) Total Number of Genes: 158 Number of Gold Standard (Direct) Genes: 118 Number of Likely (Indirect) Genes: 13 Number of Predicted Genes: 27 Version: Production Date: 10/13/2014 Curation Overview ----------------- This list of genes contains genes involved in arachidonic acid metabolism and remodeling. The curation process involved creating a list of genes involved in arachidonic acid metabolism and remodeling in humans supported with evidence. This list includes genes from the KEGG arachidonic acid metabolism pathway, Reactome pathways (arachidonic acid metabolism, eicosanoids, COX reactions, eicosanoid ligand-binding receptors), Rat Genome Database Pathways, relevant Gene Ontology (GO) annotations, investigator suggested genes and relevant genes found in literature. Genes were subdivided into a Gold Standard, Likely, or Predicted list based on the level of evidence supporting involvement in arachidonic acid metabolism and remodeling. The KEGG arachidonic acid metabolism reference pathway is available here: http://www.genome.jp/kegg/pathway/map/map00590.html Reactome 'arachidonic acid metabolism' pathway is available here: http://www.reactome.org/PathwayBrowser/#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=2142753&ID=2142753 Reactome 'eicosanoids' is available here: http://www.reactome.org/PathwayBrowser/#DIAGRAM=211945&ID=211979&PATH=1430728,211859,211945,211897 Reactome 'COX reactions' is available here: http://www.reactome.org/PathwayBrowser/#DIAGRAM=211945&ID=140180&PATH=1430728,211859, Reactome 'eicosanoid ligand binding receptors' is available here: http://www.reactome.org/PathwayBrowser/#DIAGRAM=500792&ID=391903&PATH=162582,372790,500792,373076 Rat Genome Database Pathways 'prostanoid biosynthetic pathway' is available here: http://rgd.mcw.edu/rgdweb/pathway/pathwayRecord.html?acc_id=PW:0001243&species=Human#annot MICROSOMAL GLUTATHIONE S-TRANSFERASE Family (PTHR10250) http://www.pantherdb.org/panther/family.do?clsAccession=PTHR10250 Arachidonic acid metabolism related GO annotations are available here: https://docs.google.com/a/itmat.upenn.edu/spreadsheets/d/1b9iPl_Jw8q1l53bvOY6B-1Z-TQHicMICM3U0UzHc6kg/edit#gid=259971399 -------------------------------------------------------------- AAP_genelist_20141013_production.txt File Information -------------------------------------------------------------- Curation files: ---------------------- Public file(s): AAP_genelist_20141013_production.txt All_genes is comprised of Gold Standard (Direct), Likely (Indirect), and Predicted genes. Internal Pentacon file(s): Deleted_Genes-AA_Gene_List These genes were once under consideration for inclusion in the arachidonic acid metabolism and arachidonic acid remodeling pathways, but have been removed from consideration after reviewing evidence. Columns for files: ---------------------------------------------------------------------------- (---Notes provided for specific columns where applicable.) Gene Set AAP is used for genes in the 'arachidonic acid pathway'. Gene Set Qualifier Genes were assigned a qualifier (Gold Standard, Likely, or Predicted) based on the level of evidence supporting involvement in arachidonic acid metabolism and remodeling. See notes below for details about the assignment of gene set qualifiers. Gene Name Alternative Names Recommended Name UniProt ID NCBI Gene ID EC Species Name Taxonomy ID Pathway This column denotes the name of a pathway in which the gene is listed as participating by the Information Source Information Source GO - Gene Ontology: http://www.geneontology.org Reactome: http://www.reactome.org PTHR - Panther: http://www.pantherdb.org KEGG: http://www.kegg.jp Rat Genome Database (RGD) pathways: http://rgd.mcw.edu Information source is provided followed by the information source's internal identifier. Evidence Type The evidence code C is used to denote review articles. The evidence code E is used for articles that present experimental evidence including, but not limited to, tissue distribution and enzyme characterization. The evidence code P is used for publications that (1) predict presence based on evidence in mice/rabbits (2) use bioinformatics tools to identify human genes and (3) contain non-traceable author statements. Bioinformatics approaches would include using conserved sequence motifs to identify candidate genes, using a known human gene to identify sequences with significant identity (and finding cDNA in EST database). If there are multiple Pubmed IDs in the PubMed ID column, but only one evidence code in the Evidence Type column, it means that all Pubmed IDs were assigned the same evidence code. If there are multiple reference codes, each evidence code correlates with each corresponding PMID in the PubMed ID column. PubMed ID Notes Internal Pentacon curator notes Notes/SubPathway Notes/SubPathway are assigned by Pentacon curators Gene Set Qualifiers ---------------------------------------------------------------------------- Gold Standard (Direct): The gene set qualifier "Gold Standard" is assigned when experimental evidence demonstrates involvement of the gene in the arachidonic acid metabolism and arachidonic acid remodeling pathways. Experimental evidence means that an enzyme has been assayed with substrates that are in these pathways, a receptor binds ligands in these pathways, or the protein interacts with another protein in the pathway. Genes assigned the "Gold Standard" gene set qualifier can be used for computational analyses. Likely (Indirect): The gene set qualifier "Likely" is assigned when genes ‘likely’ participate in the arachidonic acid metabolism and remodelling pathway. Genes are assigned "Likely" when there is experimental evidence for the predicted/expected activity for a relevant probe substrate, but not definitive experimental evidence for participation in the arachidonic acid metabolism and remodelling pathway. For example, an enzyme expected to be involved in AA remodelling for which activity was demonstrated using palmitic, oleic, or linoleic acid, but not arachidonic acid, would be assigned the gene set qualifier "Likely". These genes can be included in a computational analysis based on programmer discretion. Predicted: The gene set qualifier "Predicted" is assigned when genes have been inferred to be involved in the arachidonic acid metabolism and remodelling pathways based on (1) evidence from other organisms or (2) homology. "Predicted" is assigned to genes for which participation in the arachidonic acid pathway is purely predicted and/or gene products have not been characterized. These genes should not be used in a computational analysis. ---------------------------------------------------------------------------- For questions please contact Rose Oughtred (rose at genomics.princeton.edu). ----------------------------------------------------------------------------