Monitoring changes in the Gene Ontology and their impact on genomic data analysis
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Abstract
Background
The Gene Ontology (GO) is one of the most widely used resources in molecular and cellular biology, largely through the use of “enrichment analysis.” To facilitate informed use of GO, we present GOtrack (https://gotrack.msl.ubc.ca), which provides access to historical records and trends in the GO and GO annotations.
Findings
GOtrack gives users access to gene- and term-level information on annotations for nine model organisms as well as an interactive tool that measures the stability of enrichment results over time for user-provided “hit lists” of genes. To document the effects of GO evolution on enrichment, we analyzed more than 2,500 published hit lists of human genes (most older than 9 years ); 53% of hit lists were considered to yield significantly stable enrichment results.
Conclusions
Because stability is far from assured for any individual hit list, GOtrack can lead to more informed and cautious application of GO to genomics research.
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Now published in GigaScience doi: 10.1093/gigascience/giy103
Matthew Jacobson 1Michael Smith Laboratories, University of British Columbia2Department of Psychiatry, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdriana Estela Sedeño-Cortés 3Graduate Program in Bioinformatics, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaul Pavlidis 1Michael Smith Laboratories, University of British Columbia2Department of Psychiatry, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Paul PavlidisFor correspondence: paul@msl.ubc.ca
A version of this preprint has been published in the Open Access journal …
Now published in GigaScience doi: 10.1093/gigascience/giy103
Matthew Jacobson 1Michael Smith Laboratories, University of British Columbia2Department of Psychiatry, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdriana Estela Sedeño-Cortés 3Graduate Program in Bioinformatics, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaul Pavlidis 1Michael Smith Laboratories, University of British Columbia2Department of Psychiatry, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Paul PavlidisFor correspondence: paul@msl.ubc.ca
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy103 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101302 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101303
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