News:Impact of outdated gene annotations on pathway enrichment analysis

Question

[pld]

Pathway enrichment analysis is a common technique for interpreting
gene lists derived from high-throughput experiments1. Its success
depends on the quality of gene annotations. We analyzed the evolution
of pathway knowledge and annotations over the past seven years and
found that the use of outdated resources has strongly affected
practical genomic analysis and recent literature: 67% of ~3,900
publications we surveyed in 2015 referenced outdated software that
captured only 26% of biological processes and pathways identified
using current resources.

http://www.nature.com/nmeth/journal/v13/n9/full/nmeth.3963.html

Questions about functional enrichment and pathway tools being out of date seem to show up on Biostars often. Thought this would be of use.

[WouterDeCoster]

First published as preprint: http://biorxiv.org/content/early/2016/04/19/049288 (I read it before it was in nature, hipster scientist).

And "coincidentally", a bit later DAVID got finally updated.

[Istvan Albert]

I read it on Biostar before it was even on arxiv - I match your hipster and raise it to a nerd.

C: GO analysis: DAVID vs GREAT vs GOrilla

[Egon Willighagen]

A shame that WikiPathways was not included in the analysis :(