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  4. A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans
 
research article

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

Pavlidis, Pavlos
•
Jensen, Jeffrey D.  
•
Stephan, Wolfgang
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2012
Molecular Biology And Evolution

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.

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Type
research article
DOI
10.1093/molbev/mss136
Web of Science ID

WOS:000309927900034

Author(s)
Pavlidis, Pavlos
Jensen, Jeffrey D.  
Stephan, Wolfgang
Stamatakis, Alexandros
Date Issued

2012

Publisher

Oxford University Press

Published in
Molecular Biology And Evolution
Volume

29

Issue

10

Start page

3237

End page

3248

Subjects

genome scanning

•

positive selection

•

gene ontology

•

validation

•

literature mining

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
UPJENSEN  
Available on Infoscience
February 27, 2013
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/89416
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