Gene-Association files

Below are descriptions of gene-association files currently available for use with GeneMerge. It lists the source of the data and a reference, if available. If you would like the most up-to-date GeneMerge files for your organism please let me know. Or, learn how to make your own association files.

Download Individual Files

Species

Functional genomic information for the following organisms is available:

Agrobacterium tumefaciens str. C58 | Arabidopsis thaliana | Bos taurus | Caenorhabditis elegans | Candida albicans | Canis lupus familiaris | Danio rerio | Dickeya dadantii | Dictyostelium discoideum | Drosophila melanogaster | Escherichia coli | Gallus gallus | Homo sapiens | Magnaporthe grisea | Mus musculus | Oomycetes | Oryza sativa | Plasmodium falciparum | Pseudomonas aeruginosa | Rattus norvegicus | Saccharomyces cerevisiae | Schizosaccharomyces pombe | Sus scrofa | Trypanosoma brucei


Multi-Species Collections

Aspergillus species (AGD) | Comprehensive Microbial Resource (JCVI) | Drosophila species (12 Genomes+)(FlyBase)


Gene-Association Data

Different types of gene-association data are available for different species. These are listed below and include Gene Ontology annotations, chromosome location, RNAi phenotypes, and others.

Chromosome Location
Gene Ontology Annotations
RNAi Phenotypes
Metabolic Pathways
Deletion Viability


Chromosome Location

D. melanogaster

Gene-Association Source Date* Reference Notes
Chromosome Location FlyBase 12/28/2014 gene_map_table_fb_2014_06.tsv 2, 3, 4, X, Y, mitochondrion, UN. Arm and other labels removed. Scaffold and others unmapped --> unknown
Chromosome Arm Location FlyBase 12/28/2014 gene_map_table_fb_2014_06.tsv 2L, 2R, 3L, 3R, 4, X, Y, mitochondrion, UN. Scaffold and others unmapped --> unknown
Cytogenetic Map Location FlyBase 12/28/2014 gene_map_table_fb_2014_06.tsv Cytological range designations, e.g. '91A3-91A3'

Drosophila species (12 genomes+)

Gene-Association Source Date* Reference Notes
Chromosome Location FlyBase 12/28/2014 gene_map_table_fb_2014_06.tsv 2, 3, 4, X, Y, mitochondrion, UN. Arm and other labels removed. Scaffold and unmapped labelled 'unknown'.
Chromosome Arm Location FlyBase 12/28/2014 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

Gene-Association Source Date* Reference Note
Chromosome Location HUGO 1/15/2015 BioMart Query 1, 2, 3, 4..., X, Y, mitochrondrion
Cytogenetic Location HUGO 1/15/2015 BioMart Query Xq22, 11q13, etc. Total of 355 regions. For genes with a range, only the first location is used (1740 of 19,828 genes).
Detailed Cytogenetic Location HUGO 1/15/2015 BioMart Query Xq22.1, 11q13.1, etc. Total of 2109 regions.

M. musculus

Gene-Association Source Date* Reference Note
Chromosome Location MGI 12/27/2014 MRK_List1.rpt 1, 2, 3..19, X, Y, XY, MT, UN. Inlcudes annotations for withdrawn marker symbols.

S. cerevisiae

Gene-Association Source Date* Reference Note
Chromosome Location SGD 1/15/2015 SGD_features.tab chromosome 1, 2, 3, 4..., 17.

Gene Ontology

- All species -

Gene-Association File Source Date* Reference Notes
Molecular FunctionGO Consortium1/9/2015Ashburner et al. (2000) Most specific annotation only
Biological ProcessGO Consortium1/9/2015Ashburner et al. (2000) Most specific annotation only
Cellular ComponentGO Consortium1/9/2015Ashburner et al. (2000) Most specific annotation only
Molecular Function HierarchicalGO Consortium1/9/2015Ashburner et al. (2000) All levels in GO hierarchy
Biological Process HierarchicalGO Consortium1/9/2015Ashburner et al. (2000) All levels in GO hierarchy
Cellular Component HierarchicalGO Consortium1/9/2015Ashburner et al. (2000) All levels in GO hierarchy

Metabolic/Regulatory Pathway

D. melanogaster

Gene-Association File Source Date* Reference Notes
Metabolic/Regulatory Pathway KEGG Database 4/1/02 Kanehisa et al. (2002) pyruvate metabolism, wnt signaling pathway, etc.

S. cerevesiae

Gene-Association File Source Date* Reference Notes
Metabolic/Regulatory PathwayKEGG Database 5/26/02 Kanehisa et al. (2002) pyruvate metabolism, signaling pathways, etc.

RNAi Phenotypes

C. elegans

Gene-Association File Source Date* Reference Notes
RNAi Phenotype Wormbase 02/27/2003 Kamath et al. (2003) All phenotypes - embryonic lethality, slow growth, etc.
RNAi Embryonic Lethality Wormbase 02/27/2003 Kamath et al. (2003) Embryonic lethality - 6 percentage categories
RNAi Embryonic Lethality Wormbase 02/27/2003 Kamath et al. (2003) Embryonic lethality - 100% vs Not

Deletion Viability

S. cerevesiae

Gene-Association File Source Date* Reference Notes
Deletion Viability SGD 7/18/02 Giaever et al. (2002) Deletion viability phenotype (viable/inviable)


* Refers to the date a file was downloaded from the source. Please check the source for date of data creation.



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