Impact of outdated gene annotations on pathway enrichment analysis

@article{Wadi2016ImpactOO,
  title={Impact of outdated gene annotations on pathway enrichment analysis},
  author={Lina Wadi and M. Meyer and J. Weiser and Lincoln D. Stein and J. Reimand},
  journal={Nature Methods},
  year={2016},
  volume={13},
  pages={705-706}
}
To the Editor: 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 We analyzed the evolution of pathway knowledge and annotations over the past seven years and found that the use of outdated resources has strongly affected practical genomic analysis and recent literature: 67% of ~3,900 publications we surveyed in 2015 referenced outdated software that captured only 26% of… Expand
81 Citations

Figures and Topics from this paper

Monitoring changes in the Gene Ontology and their impact on genomic data analysis
  • 4
  • PDF
Monitoring changes in the Gene Ontology and their impact on genomic data analysis
  • 1
  • PDF
WocEA: The visualization of functional enrichment results in word clouds.
  • 5
  • PDF
Pathway enrichment analysis approach based on topological structure and updated annotation of pathway
  • Qian Yang, S. Wang, +6 authors Wei Jiang
  • Computer Science, Medicine
  • Briefings Bioinform.
  • 2019
  • 14
Comprehensive functional analysis of large lists of genes and proteins.
  • 35
  • PDF
Pathway and Network Analysis of Differentially Expressed Genes in Transcriptomes.
Summary Visualizations of Gene Ontology Terms With GO-Figure!
GOATOOLS: A Python library for Gene Ontology analyses
  • 202
  • PDF
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 10 REFERENCES
Gene Ontology: tool for the unification of biology
  • 29,007
  • PDF
Pathway and network analysis of cancer genomes
  • 246
  • PDF
Targeting Notch, Hedgehog, and Wnt pathways in cancer stem cells: clinical update
  • 724
N at ur e A m er ic a, In c. A ll rig ht s re se rv ed . np g © 2 01 6 N at ur e A m er
  • Nat. Rev. Clin. Oncol
  • 2015