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Impact of knowledge accumulation on pathway enrichment analysis

Lina Wadi, Mona Meyer, Joel Weiser, Lincoln D. Stein, Jüri Reimand
doi: https://doi.org/10.1101/049288
Lina Wadi
1Ontario Institute for Cancer Research
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Mona Meyer
1Ontario Institute for Cancer Research
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Joel Weiser
1Ontario Institute for Cancer Research
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Lincoln D. Stein
1Ontario Institute for Cancer Research
3Department of Molecular Genetics, University Of Toronto
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Jüri Reimand
1Ontario Institute for Cancer Research
2Department of Medical Biophysics, University Of Toronto
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  • For correspondence: juri.reimand@utoronto.ca
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Abstract

Pathway-based interpretation of gene lists is a staple of genome analysis. It depends on frequently updated gene annotation databases. We analyzed the evolution of gene annotations over the past seven years and found that the vocabulary of pathways and processes has doubled. This strongly impacts practical analysis of genes: 80% of publications we surveyed in 2015 used outdated software that only captured 20% of pathway enrichments apparent in current annotations.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 19, 2016.
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Impact of knowledge accumulation on pathway enrichment analysis
Lina Wadi, Mona Meyer, Joel Weiser, Lincoln D. Stein, Jüri Reimand
bioRxiv 049288; doi: https://doi.org/10.1101/049288
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Impact of knowledge accumulation on pathway enrichment analysis
Lina Wadi, Mona Meyer, Joel Weiser, Lincoln D. Stein, Jüri Reimand
bioRxiv 049288; doi: https://doi.org/10.1101/049288

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