----------------------------------------------- Pentacon NSAID Project Curation Princeton University, NJ, USA University of Pennsylvania, PA, USA ----------------------------------------------- Readme file name: Orthologs_and_analogs_README_20131125_production.txt Readme for the following files: Orthologs_and_analogs_20131125_production.txt Orthologs_and_analogs_Evidence_Codes_20130710_production.txt Contents: Mouse (Mus musculus), zebrafish (Danio rerio), and yeast (Saccharomyces cerevisiae) orthologs/analogs of the 133 human genes PENTACON curators have identified as being involved in the arachidonic acid pathway. These non-human genes are suggested as good models of the corresponding human genes in their respective model organisms. Date: 11/25/2013 Curation Overview ----------------- PENTACON curators identified consensus orthologs/analogs using P-POD version 4 and IMP. Orthologs were identified using P-POD's OrthoMCL analysis when possible or, when the human gene was not assigned to an OrthoMCL family, on P-POD's MultiParanoid analysis. Functional analogs were obtained from IMP using a cutoff of p < 0.05. PENTACON curators reviewed the ortholog and analog calls and evidence and, using the following evidence codes, identified the consensus ortholog/analog: Evidence code Description 1 P-POD identifies a single ortholog, IMP identifies a single analog, and they agree. 1P P-POD identifies a single ortholog, IMP identifies a single analog, and they agree; P-POD ortholog is found in MultiParanoid family. 2 Call based on orthology (P-POD) only. P-POD identified 1 or more orthologs, but IMP did not identify an analog. 2P Call based on orthology (P-POD) only. P-POD identified 1 or more orthologs, but IMP did not identify an analog; P-POD ortholog is found in MultiParanoid family. 3 Call based on analogy (IMP) only. IMP identified 1 or more orthologs, but P-POD did not identify an ortholog. 4 Multiple or ambiguous orthologs resolved by referring to analogs. 5 Multiple or ambiguous orthologs resolved by referring to both IMP and P-POD. 6 P-POD and IMP disagree. Selection made by curator judgment. 7 IMP identifies no analog, and P-POD identifies no ortholog. 8 P-POD and IMP identify the same proteins, and curator selected a subset based on additional evidence. The P-POD and IMP web sites can be found here: http://ppod.princeton.edu/ http://imp.princeton.edu/ References: Heinicke S, Livstone MS, Lu C, Oughtred R, Kang F, Angiuoli SV, White O, Botstein D, Dolinski K. "The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists." PLoS One. 2007 Aug 22;2(8):e766. Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG. "IMP: A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks." Nucleic Acids Research. July 2012;40:W484-W490. -------------------------------------------------------------- Orthologs_and_analogs_20131125_production.txt File Information -------------------------------------------------------------- The file contains 12 columns as follows: Columns 1-3: The standard name, UniProt ID, and NCBI Gene ID for the 133 genes in the arachidonic acid pathway. Column 4: The name and NCBI Gene ID of the mouse gene identified as the consensus ortholog/analog of the human gene, separated by a pipe symbol. Example: "Abcc1|17250". When more than one ortholog/analog is listed, they are separated by semicolons. Example: "Acot1|26897; Acot2|171210". Column 5: The evidence code (see above) supporting the identification of the mouse gene(s) as the ortholog/analog. Column 6: Relevant free-text notes pertaining to the mouse gene(s). Columns 7-9: Similar to columns 4-6, but for zebrafish genes. Columns 10-12: Similar to columns 4-6, but for yeast genes. Also, the standard yeast ORF identifier (e.g.: "YDR135C") is used in place of the NCBI Gene ID. -------------------------------------------------------------- Updates and changes -------------------------------------------------------------- The initial production release (20130710) contained mouse, fish, and yeast ortholog/analogs of 112 human genes. The second production release (20131125) had the following changes: 1) Standard names were added as aliases to two human genes: C1ORF93 (UniProt ID Q8TBF2, NCBI GeneID 127281) became “FAM213B/C1ORF93,” and GPR44 (UniProt ID Q9Y5Y4, NCBI GeneID 11251) became "PTGDR2/GPR44." 2) The following 21 human genes were added, and orthologs/analogs were identified, in order to match the AAP gene list: ABCC1, ABCC4, ACOT1, ACOT11, ACOT13, ACOT2, ACOT4, ACOT7, ACOT8, ACSL6, BAAT, ELOVL2, ELOVL5, FADS1, FADS2, GPR17, MGST2, MGST3, OXER1, PLA2G16, and PNPLA2. 3) The capitalization of a number of mouse and zebrafish genes was standardized. 4) Standard names were added as aliases to the following mouse and zebrafish gene names (shown with both gene names): mouse: Alox15/Alox12l, Fam213b/2810405K02RIK|. zebrafish: acsl1b/Zgc:101071, dpep1/zgc:153024 ---------------------------------------------------------------------------- For questions please contact Mike Livstone (livstone at genomics.princeton.edu). ----------------------------------------------------------------------------