Data Mining - worm to human genes

I am looking for public or private tools where I can paste in a list of C. elegans genes and have them converted to their human orthologs, and ideally also human homologs. Are there any other options besides OrthoList? Thank you.

You can use ENSEMBL’s BioMart to obtain a list of all worm-human orthologs, then your favorite text/database parser to limit the list to your subset of genes. Another option is the OMA browser, although you’ll also need to convert the gene names - they support several formats (e.g., RefSeq, Entrez), but not WormBase.

in addition to that, we got at WormBase:

  • WormMine should have PantherDB C.elegans → H.sapiens orthologs
  • ParaSite BioMart has EnsEMBL Compara C.elegans → H.sapiens orthologs
  • and from our work at AGR, the DIOPT tool should also accept WormBase identifiers.

We did actually cooperate with OMA to get our data in a few years back, so the WormBase WBGene identifiers should work, same with PantherDB.

Thanks very much!