----------------------------------------------- Pentacon NSAID Project Curation Princeton University, NJ, USA University of Pennsylvania, PA, USA ----------------------------------------------- Readme file name: BP_AAE_genelist_Readme_20130725_preliminary.txt Readme for the following files: BP_AAE_genelist_20130725_preliminary.txt Total Number of Genes: 63 Number of Gold Standard (Direct) Genes: to be determined Number of Likely (Indirect) Genes: to be determined Number of Predicted Genes: to be determined Version: Preliminary Date: 7/25/2013 Curation Overview ----------------- This list was started March 14, 2013, and the last gene (Q13018) was added on 07/02/2013. The curation process involved creating a list of genes from Reactome pathways (pathways annotated with experimental evidence) identified as related to the phenotype of blood pressure, experimentally-supported GO annotations for blood pressure, and the literature. The genes for the identified Reactome pathways were taken from "Reactome Pathways Gene Set." Genes obtained from GO were assembled from those directly annotated to "regulation of blood pressure" (GO:0008217), "regulation of blood vessel size" (GO:0050880), and manually-selected children of these two terms. Genes associated with arachidonic acid metabolsm (in a regulatory manner) found in literature by curators have also been added to this list. The search was restricted to experimental annotations. Currently, not all genes have a Gene Set Qualifier. Curators are reviewing associated publications to assign Gene Set Qualifiers for each gene. The GO annotations are available here: https://docs.google.com/spreadsheet/ccc?key=0Aq_I_6K-fUKqdGxpcFdqOS1zWC14NDlWSElCeFgxbVE#gid=2 The Reactome Pathways Gene Set was downloaded on 3/11/2013. This list, which may have been updated by Reactome, is available here: http://www.reactome.org/download/index.html The list of arachidonic acid metabolism genes are available here: https://docs.google.com/spreadsheet/ccc?key=0Avit99d8o9hWdDh0Q3dMeU5lbmV1ejlnQmF1YW9MWFE#gid=14 -------------------------------------------------------------- BP_AAE_genelist_20130725_preliminary.txt File Information -------------------------------------------------------------- Curation files: ---------------------- Public file(s): BP_AAE_genelist_20130725_preliminary.txt This file contains genes identified from the GO search and Reactome pathways that were not already present in the list of arachidonic acid metabolism genes (AAP_genelist_20130725_production.txt). GO:BP genes were compared to the list of arachidonic acid metabolism genes, and new genes are noted in this file. Then genes from the Reactome pathways were compared to the list of arachidonic acid metabolism genes and GO:BP genes. New genes are are noted in this file. List comparisons were made on gene symbol. Entrez gene IDs were identified using a Python script utilizing geneDocSum.pl. Reviewed UniProt entry IDs were identified manually for the Reactome genes. Columns for "BP_AAE_genelist_20130725_preliminary.txt" file: ---------------------------------------------------------------------------- (---Notes provided for specific columns where applicable.) Gene Set AAP is used for genes directly involved in the 'arachidonic acid pathway'. AAE is used for genes related to the arachidonic acid pathway. BP is used for genes related to the phenotype of blood pressure. Gene Set Qualifier Genes were assigned a qualifier (Gold Standard, Likely, or Predicted) based on the level of evidence supporting involvement in the pathway or phenotype captured by the column Gene Set. 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 When Reactome is the information source, the stable identifer is used. This looks like: REACT_147707.2. Genes identified from GO annotations have GO:BP. 'Literature' denotes that genes were added based on evidence present in literature reviews; this information source should be accompanied by entries in the Pubmed ID column. 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 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). ----------------------------------------------------------------------------