* GeneMerge Gene-Association Files * For use with GeneMerge-- genomic analysis and hypothesis testing software Castillo-Davis, C.I. and D.L. Hartl 2003. Bioinformatics 19(7):891-892 For more information please see: http://genemerge.net This file describes packaged 'gene association' and 'description' files for use with GeneMerge. To make your own gene-association files, please visit the website or consult the GeneMerge Manual. ________________________________________________________________________________ Naming of Gene Association and Description Files 1. Gene-association files are named after organism Genus + species (G_species) and the type of gene-association. For example, the human chromosome location association file is called: H_sapiens.CHR 2. Corresponding 'description files' are labeled with ".use": H_sapiens.CHR.use In the case of Gene Ontology (GO) annotations, every species uses one of 3 corresponding description files: GO.MF.use, GO.BP.use, and GO.CC.use. GO files are prefixed with the date provided by GO inside each .gaf file and the name of the gaf file from which it was derived. For example: 2019-07-01-fb-D_melanogaster.MF ________________________________________________________________________________ --- Gene Ontology (GO) Files --- Each species has two sets of three gene-association files. One set includes the most specific GO annotations only for molecular function (MF), biological process (BP), and cellular component (CC). The other set includes the full GO hierarchy of annotation for each gene (hMF, hBP, hCC). Generically, the files are named as follows: * G_species.MF - molecular function * G_species.BP - biological process * G_species.CC - cellular component * G_species.hMF - molecular function (full GO hierarchy) * G_species.hBP - biological process (full GO hierarchy) * G_species.hCC - cellular component (full GO hierarchy) For multi-species gene-association data, an X is used to indicate it is a 'cross-species' gene-association file (X_Genus.MF etc.) All GO species use the correpsonding description files named: * GO.MF.use, GO.BP.use, and GO.CC.use. _______________________________________________________________________________ --- Chromosome Location Files --- Drosophila melanogaster * D_melanogaster.CHARM - chromosome arm location * D_melanogaster.CHR - chromosome location * D_melanogaster.CYTO - cytogenetic map location Drosophila species (12 genomes+) * X_Drosophila.CHARM - chromosome arm location * X_Drosophila.CHR - chromosome location Homo sapiens * H_sapiens.CHR - chromosome location * H_sapiens.CYTO - cytogenetic map location * H_sapiens.CYTOD - detailed cytogenetic map location Mus musculus * M_musculus.CHR - chromosome location Saccharomyces cerevisiae * S_cerevisiae.CHR - chromosome location Corresponding description files are named as above, appended with a '.use' _______________________________________________________________________________ ########################### # Data Source and Details # ########################### ## Gene Ontology (GO) Annotations ## --- All GO species and multi-species collections --- Name: GO molecular function (.MF) - most specific annotations only Name: GO biological process (.BP) - most specific annotations only Name: GO cellular component (.CC) - most specific annotations only Name: GO molecular function (.hMF) - higher order (all parent terms) Name: GO biological process (.hBP) - higher order (all parent terms) Name: GO cellular component (.hCC) - higher order (all parent terms) Source: Gene Ontology Consortium Date: updated monthly Notes: Each file is prefixed with the date found in each .gaf gene association file as well as the originating gaf filename that provides the database source and type. ## Chromosome Location ## --- D. melanogaster --- Name: Chromosome Location (.CHR) Source: FlyBase Date: 12/28/2014 File: gene_map_table_fb_2014_06.tsv Notes: 2, 3, 4, X, Y, mitochondrion, UN. Arm and other labels removed. Scaffold and others unmapped labelled 'unknown' Name: Chromosome Arm Location (.CHARM) Source: FlyBase Date: 12/28/2014 File: gene_map_table_fb_2014_06.tsv Notes: 2L, 2R, 3L, 3R, 4, X, Y, mitochondrion, UN. Scaffold and others unmapped labelled 'unknown' Name: Cytogenetic Map Location (.CYTO) Source: FlyBase Date: 12/28/2014 File: gene_map_table_fb_2014_06.tsv Notes: Cytological range designations, e.g. '91A3-91A3' --- Drosophila species (12 genomes+) --- Name: Chromosome Location (.CHR) Source: FlyBase Date: 12/28/2014 File: gene_map_table_fb_2014_06.tsv Notes: 2, 3, 4, X, Y, mitochondrion, UN. Arm and other labels removed. Scaffold and unmapped labelled 'unknown'. Name: Chromosome Arm (.CHARM) Source: FlyBase Date: 12/28/2014 Notes: gene_map_table_fb_2014_06.tsv 2L, 2R, 3L, 3R, 4, X, Y, mitochondrion, UN, and chromosome subgroups, e.g., 'XL_group1a'. All details from table preserved including scaffold and supercontig IDs for unmapped genes, e.g., 'scaffold_10027', 'chr2h_Mrandom_022'. --- H. sapiens --- Name: Chromosome Location (.CHR) Source: HUGO Date: 1/15/2015 File: BioMart Query Notes: 1, 2, 3, 4..., X, Y, mitochrondrion Name: Cytogenetic Location (.CYTO) Source: HUGO Date: 1/15/2015 File: BioMart Query Notes: Xq22, 11q13, etc. Total of 355 regions. For genes with a range, only the first location is used (1740 of 19,828 genes). Name: Detailed Cytogenetic Location (.CYTOD) Source: HUGO Date: 1/15/2015 File: BioMart Query Notes: Xq22.1, 11q13.1, etc. Total of 2109 regions. --- M. musculus --- Name: Chromosome Location (.CHR) Source: MGI Date: 12/27/2014 File: MRK_List1.rpt Notes: 1, 2, 3... 19, X, Y, XY, MT, UN. Includes annotations for withdrawn marker symbols. --- S. cerevisiae --- Name: Chromosome Location (.CHR) Source: SGD Date: 1/15/2015 File: SGD_features.tab Notes: chromosome 1, 2, 3, 4... 17.