Related Experiment Video
Updated: May 15, 2026

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
Assessing identity, redundancy and confounds in Gene Ontology annotations over time
1Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 192B Genome Research Center, 500 Sunnyside Boulevard, Woodbury, NY 11797, USA.
Motivation:
The Gene Ontology (GO) is heavily used in systems biology, but the potential for redundancy, confounds with other data sources and problems with stability over time have been little explored.
Results:
We report that GO annotations are stable over short periods, with 3% of genes not being most semantically similar to themselves between monthly GO editions. However, we find that genes can alter their 'functional identity' over time, with 20% of genes not matching to themselves (by semantic similarity) after 2 years. We further find that annotation bias in GO, in which some genes are more characterized than others, has declined in yeast, but generally increased in humans. Finally, we discovered that many entries in protein interaction databases are owing to the same published reports that are used for GO annotations, with 66% of assessed GO groups exhibiting this confound. We provide a case study to illustrate how this information can be used in analyses of gene sets and networks.
Availability:
Data available at http://chibi.ubc.ca/assessGO.
Related Concept Videos
Genome Annotation and Assembly
Gene Duplication and Divergence
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Genomics
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Gene Families
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

