Notes on outdated gene annotations paper - bcb420-2024/Dien_Nguyen GitHub Wiki

Wadi, L., Meyer, M., Weiser, J. et al. Impact of outdated gene annotations on pathway enrichment analysis. Nat Methods 13, 705–706 (2016). https://doi.org/10.1038/nmeth.3963

• Pathway enrichment analysis success depends on quality of gene annotations
• Issue lies in software no updating functional information for years even though GO and Reactome are updated daily and quarterly, respectively

What has changed:

• From 2009-2016, # of biological processes doubled in GO and Reactome, vocabulary details increase, interconnected GO terms have longer paths and more parents
• Knowledge of individual genes have increased significantly, high-confidence experimental annotations are more common

How is functional analysis affected:

• 74% enrichment 2016 terms were missed when using 2010 era annotations (77 breast cancer cell lines for testing)
• Using high-confidence data set, 2010 annotations captured only 20% of current results
• 2010 annotations are often based on low-quality information (inferred from electronic annotations)

Bottom line:

• Researchers need to be mindful of timeliness of data. Document software updates in publications.
• Software needs to update gene annotations regularly.