Curated model organism gene functional annotations

Question

[ian.will]

Hi,

I'm working with a model organism for the first time - C. elegans nematodes - and have created a list of differential expressed genes from some RNAseq data the lab had. One of the things I like to do is look for enrichment/over-representation patterns of functional annotations (e.g. Interpro/PFAM, GO terms, secretion signals, etc.)

I've put together [geneID] x [annotation1/2/3...] master sheets for my own projects before with non-model organisms ... but does anyone know of a curated and publicly available resource for these worms? It'd be a time-saver and be a trustworthy source of info. I looked at WormBase hoping to find something but didn't see it.

Thanks!

[manaswwm]

I thought Interproscan already has species-specific information, for example this page for Buchnera aphidicola. You can try to search if they also have this for C. elegans, preferably by downloading the inferred domains per species through their Download portal. Another way of doing it would probably be through UniProt - filter all possible entries on Uniprot to keep only for the taxonomy ID of C. elegans (I think it is 6239). In the output table, edit the columns using the "Customize columns" button and add "Domain(CC)" and "Domain(FT)" columns. Now you will have a functional annotation of all possible domains within proteins

[ian.will]

The Uniprot approach worked pretty well for me, great head start on lots of annotations and what should be matchable geneIDs to my txi/deseq outputs. Didn't have to run interproscan or a bunch of extra tools, lovely. Thanks!

[manaswwm]

Glad to read that it was helpful!