Data Mining - worm to human genes

Model Organism: Worms Scientific Discussion
1

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.

2

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.

3

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.

4

Thanks very much!