A critical assessment of storytelling

Gene ontology categories and the importance of validating genomic scans

Pavlos Pavlidis, Jeffrey Jensen, Wolfgang Stephan, Alexandros Stamatakis

Research output: Contribution to journalArticle

103 Citations (Scopus)

Abstract

In the age of whole-genome population genetics, so-called genomic scan studies often conclude with a long list of putatively selected loci. These lists are then further scrutinized to annotate these regions by gene function, corresponding biological processes, expression levels, or gene networks. Such annotations are often used to assess and/or verify the validity of the genome scan and the statistical methods that have been used to perform the analyses. Furthermore, these results are frequently considered to validate true-positives if the identified regions make biological sense a posteriori. Here, we show that this approach can be potentially misleading. By simulating neutral evolutionary histories, we demonstrate that it is possible not only to obtain an extremely high false-positive rate but also to make biological sense out of the false-positives and construct a sensible biological narrative. Results are compared with a recent polymorphism data set from Drosophila melanogaster.

Original languageEnglish (US)
Pages (from-to)3237-3248
Number of pages12
JournalMolecular Biology and Evolution
Volume29
Issue number10
DOIs
StatePublished - Oct 2012
Externally publishedYes

Fingerprint

Gene Ontology
genomics
genome
Genome
Biological Phenomena
gene
Gene Regulatory Networks
Population Genetics
Drosophila melanogaster
biological processes
population genetics
polymorphism
statistical analysis
genes
genetic polymorphism
history
loci
Genes
Datasets
gene regulatory networks

Keywords

  • gene ontology
  • genome scanning
  • literature mining
  • positive selection
  • validation

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

A critical assessment of storytelling : Gene ontology categories and the importance of validating genomic scans. / Pavlidis, Pavlos; Jensen, Jeffrey; Stephan, Wolfgang; Stamatakis, Alexandros.

In: Molecular Biology and Evolution, Vol. 29, No. 10, 10.2012, p. 3237-3248.

Research output: Contribution to journalArticle

Pavlidis, Pavlos ; Jensen, Jeffrey ; Stephan, Wolfgang ; Stamatakis, Alexandros. / A critical assessment of storytelling : Gene ontology categories and the importance of validating genomic scans. In: Molecular Biology and Evolution. 2012 ; Vol. 29, No. 10. pp. 3237-3248.
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