Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Nat Chem Biol. 2010 Jan;6(1):34-40. doi: 10.1038/nchembio.266. Epub 2009 Nov 22.

Automatic policing of biochemical annotations using genomic correlations.

Author information

  • 1Center for Computational Biology and Bioinformatics and Department of Biomedical Informatics, Columbia University, Irving Cancer Research Center, New York, New York, USA.

Abstract

With the increasing role of computational tools in the analysis of sequenced genomes, there is an urgent need to maintain high accuracy of functional annotations. Misannotations can be easily generated and propagated through databases by functional transfer based on sequence homology. We developed and optimized an automatic policing method to detect biochemical misannotations using context genomic correlations. The method works by finding genes with unusually weak genomic correlations in their assigned network positions. We demonstrate the accuracy of the method using a cross-validated approach. In addition, we show that the method identifies a significant number of potential misannotations in Bacillus subtilis, including metabolic assignments already shown to be incorrect experimentally. The experimental analysis of the mispredicted genes forming the leucine degradation pathway in B. subtilis demonstrates that computational policing tools can generate important biological hypotheses.

PMID:
19935659
[PubMed - indexed for MEDLINE]
PMCID:
PMC2935526
Free PMC Article

Images from this publication.See all images (4)Free text

Figure 1
Figure 2
Figure 3
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Nature Publishing Group Icon for PubMed Central
    Loading ...
    Write to the Help Desk