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Automatic policing of biochemical annotations using genomic correlations
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 a...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935526/ https://www.ncbi.nlm.nih.gov/pubmed/19935659 http://dx.doi.org/10.1038/nchembio.266 |
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author | Hsiao, Tzu-Lin Revelles, Olga Chen, Lifeng Sauer, Uwe Vitkup, Dennis |
author_facet | Hsiao, Tzu-Lin Revelles, Olga Chen, Lifeng Sauer, Uwe Vitkup, Dennis |
author_sort | Hsiao, Tzu-Lin |
collection | PubMed |
description | 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 B. 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. |
format | Text |
id | pubmed-2935526 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
record_format | MEDLINE/PubMed |
spelling | pubmed-29355262010-09-08 Automatic policing of biochemical annotations using genomic correlations Hsiao, Tzu-Lin Revelles, Olga Chen, Lifeng Sauer, Uwe Vitkup, Dennis Nat Chem Biol Article 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 B. 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. 2009-11-22 2010-01 /pmc/articles/PMC2935526/ /pubmed/19935659 http://dx.doi.org/10.1038/nchembio.266 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms |
spellingShingle | Article Hsiao, Tzu-Lin Revelles, Olga Chen, Lifeng Sauer, Uwe Vitkup, Dennis Automatic policing of biochemical annotations using genomic correlations |
title | Automatic policing of biochemical annotations using genomic correlations |
title_full | Automatic policing of biochemical annotations using genomic correlations |
title_fullStr | Automatic policing of biochemical annotations using genomic correlations |
title_full_unstemmed | Automatic policing of biochemical annotations using genomic correlations |
title_short | Automatic policing of biochemical annotations using genomic correlations |
title_sort | automatic policing of biochemical annotations using genomic correlations |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935526/ https://www.ncbi.nlm.nih.gov/pubmed/19935659 http://dx.doi.org/10.1038/nchembio.266 |
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