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 We analyzed the evolution of pathway knowledge and annotations over the past seven years and found that the use of outdated resources has strongly affected practical genomic analysis and recent literature: 67% of ~3,900 publications we surveyed in 2015 referenced outdated software that captured only 26% of biological processes and pathways identified using current resources.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Questions about functional enrichment and pathway tools being out of date seem to show up on Biostars often.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.