Gene IDs for use with GeneMerge
The gene IDs used are the most stable identifiers
for each organism, often those used in organism-specific databases or those
used in GO annotations.
There is an updated (April 2007)
Gene Name Converter for human, fly, mouse, yeast, and Arabidopsis genes to translate
different gene names into the standard ones that you can use in GeneMerge. Please do this before running GeneMerge or you won't get anything out!
If you work with another organism make sure your gene names match the IDs below.
Below are example gene IDs for each species and where they come from
if I've figured it out.
| Species | Gene ID Example | ID Origin |
| Arabidopsis thaliana | AT3G61040.1 and CLE10 | TAIR ID |
| Bacillus anthracis Ames | BA0001 | TIGR ID |
| Bacillus subtilis | aapA | SubtiList genename |
| Bos taurus | ENSBTAP00000020276 / XP_001253159 / Q3T0Y3 | Mixture of ENSEMBL, NCBI Locus and UniProtKB Entries |
| Caenorhabditis elegans | unc-26 / R13A5.9 / CE0271 | Mixture of Wormbase genes (unc-26), predicted genes (R13A5.9), and protein IDs (CE0271) |
| Danio rerio | ZDB-GENE-000112-30 | ZFIN ID |
| Drosophila melanogaster | FBgn0002524 | FlyBase Identifier |
| Gallus gallus | Q5ZKI3 / XP_417416 | UniProtKB/TrEMBL and NCBI Loci |
| Glossina morsitans (Tsetse Fly) | CONTIG3098 | Sanger/TIGR ID |
| Homo sapiens | Q07666 / ENSP00000020673 / OTTHUMP00000167985 | Mixture of TrEMBL, ENSEMBL, and Sanger IDs |
| Leishmania major | L1156.01 | TIGR ID |
| Mus musculus | MGI:1913840 | MGI Identifier |
| Oryza sativa (Rice) | Q94LI7 | UniProtKB/SPDTrEMBL |
| Plasmodium falciparum | MAL13P1.109 | PlasmoDB ID |
| Rattus norvegicus | RGD:2007 / ENSRNOP00000018009 | RGD and ENSEMBL IDs |
| Saccharomyces cerevisiae | YGL011C | SGD Identifier |
| Schizosaccharomyces pombe | SPCC1795.01C | Sangner ID |
| Shewanella oneidensis MR-1 | SO0001 | TIGR ID |
| Trypanosoma brucei | Tb927.1.05 | TIGR/Sanger ID |
| Vibrio cholerae | VC0014 | TIGR ID |
| Virus Bioinformatics | 59500 | ? |
Note: I don't know why GO and the organism databases supply mixtures of gene names for the GO annotations. It's maddening I know... but please don't blame me!
GeneMerge - Post-genomic analysis, data mining, and hypothesis testing
Cristian I. Castillo-Davis
Department of Biology
University of Maryland
castill0@umd.edu