Gene-Association files

Below are descriptions of gene-association files currently available for use with GeneMerge. It lists the source of the data, who prepared it, and a reference, if any. If you would like the most up-to-date GeneMerge files for your organism please let me know. Functional genomic information for the following organisms is available:

Arabidopsis thaliana | Bacillus anthracis Ames| Bacillus subtilis | *New*Bos taurus | Caenorhabditis elegans | Coxiella burnetii RSA 493 | Danio rerio | Drosophila melanogaster | *New*Gallus gallus| Glossina morsitans (Tsetse Fly) | Homo sapiens | Leishmania major| Mus musculus | Oryza sativa (Rice) | Plasmodium falciparum | Rattus norvegicus | Saccharomyces cerevisiae | Schizosaccharomyces pombe | Shewanella oneidensis MR-1 | Trypanosoma brucei | Vibrio cholerae | Virus Bioinformatics

Updated GO files for Human, Mouse, Worm, Yeast, Arabidopsis, Plasmodium, Zebrafish, Rat, Rice, Chicken, and Cow (April 2007)

Download These Files

Arabidopsis thaliana
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Bacillus anthracis AMES
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Bacillus subtilis
Gene-Association FileSourceDateAuthorReferenceNotes
Functions/Pathways/ProcessesSubtiList Database1/22/03Castillo-DavisMoszer, Glaser, and Danchin (1995) SubtiList DB Annotated Categories
Specific Text-based FunctionsSubtiList Database1/22/03Castillo-DavisMoszer, Glaser, and Danchin (1995) derived from SubtiList DB
General Text-based FunctionsSubtiList Database1/22/03Castillo-DavisMoszer, Glaser, and Danchin (1995) derived from SubtiList DB ignoring parenthetical text, e.g. ATP synthase (subunit alpha)
Spore and Sporulation Categories Plus General FunctionsSubtiList Database1/22/03Castillo-DavisMoszer, Glaser, and Danchin (1995) same as General Text but with special "spore" and "sporulation" categories for genes with these words in their description
Bos taurus
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Caenorhabditis elegans
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/19/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/19/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/19/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/19/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/19/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/19/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
RNAi PhenotypeWormbase2/27/03Castillo-DavisKamath et al. (2003) RNAi phenotype (embryonic lethality, slow growth, etc.)
RNAi Embryonic LethalityWormbase2/27/03Castillo-DavisKamath et al. (2003) RNAi Phenotype Embryonic Lethality: 100% vs Not
RNAi Embryonic LethalityWormbase2/27/03Castillo-DavisKamath et al. (2003) RNAi Phenotype Embryonic Lethality: 6 Percentage categories
Coxiella burnetii RSA 493
Molecular FunctionGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium6/03/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Danio rerio
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Drosophila melanogaster
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Chromosomal LocationSpreadsheet from Hey and Kliman (2002)4/1/02Castillo-DavisHey and Kliman (2002) chromosome X, Y, 2, 3, 4dot
Chromosomal ArmSpreadsheet from Hey and Kliman (2002)4/1/02Castillo-DavisHey and Kliman (2002) chromosome X, Y, 2R, 2L, 3R, 3L, 4dot
Chrosomal Map PositionSpreadsheet from Hey and Kliman (2002)4/1/02Castillo-DavisHey and Kliman (2002) 10A, 10B, etc.
Metabolic/Regulatory PathwayKEGG Database4/1/02Castillo-DavisKanehisa et al. (2002) pyruvate metabolism, wnt signaling pathway, etc.
Gallus gallus
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Glossina morsitans (Tsetse Fly)
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Homo sapiens
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
MeSH Major Topic TermsNational Library of Medicine Medical Subject Headings04/27/07Louiqa Raschid & Adam LeeRaschid Group Derived from MeSH 'Major Topic' Annotations
Leishmania major
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Mus musculus
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Oryza sativa (Rice)
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Plasmodium falciparum
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Rattus norvegicus
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Saccharomyces cerevisiae
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium3/20/07Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Deletion ViabilitySaccharomyces Genome Database7/18/02Castillo-DavisGiaever et al. (2002) Deletion viability phenotype (via/inviable)
Metabolic/Regulatory PathwayKEGG Database5/26/02Castillo-DavisKanehisa et al. (2002) pyruvate metabolism, signaling pathways, etc.
Schizosaccharomyces pombe
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Shewanella oneidensis MR-1
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Trypanosoma brucei
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Vibrio cholerae
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Virus Bioinformatics
Gene-Association FileSourceDateAuthorReferenceNotes
Molecular FunctionGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Biological ProcessGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Cellular ComponentGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGene Ontology Consortium6/3/03Castillo-DavisAshburner et al. (2000) All levels in GO hierarchy



GeneMerge - Post-genomic analysis, data mining, and hypothesis testing

Cristian I. Castillo-Davis
Department of Biology
University of Maryland
castill0@umd.edu