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Nucleic Acids Research Advance Access originally published online on July 25, 2007
Nucleic Acids Research 2007 35(15):5085-5095; doi:10.1093/nar/gkm518
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Nucleic Acids Research, 2007, Vol. 35, No. 15 5085-5095
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

A predicted operon map for Mycobacterium tuberculosis

P. Roback1, J. Beard2, D. Baumann2, C. Gille3, K. Henry2, S. Krohn2, H. Wiste2, M.I. Voskuil4, C. Rainville5 and R. Rutherford5,*

1Department of Mathematics, Statistics and Computer Science, 2Center for Interdisciplinary Research and 3Department of Biology St. Olaf College, Northfield MN 55057, 4Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and 5Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA

*To whom correspondence should be addressed. Tel: +1 206 296 2501; Fax: +1 206 296 5634; Email: robertr{at}seattleu.edu

Received October 16, 2006. Revised June 18, 2007. Accepted June 19, 2007.

The prediction of operons in Mycobacterium tuberculosis (MTB) is a first step toward understanding the regulatory network of this pathogen. Here we apply a statistical model using logistic regression to predict operons in MTB. As predictors, our model incorporates intergenic distance and the correlation of gene expression calculated for adjacent gene pairs from over 474 microarray experiments with MTB RNA. We validate our findings with known examples from the literature and experimentation. From this model, we rank each potential operon pair by the strength of evidence for cotranscription, choose a classification threshold with a true positive rate of over 90% at a false positive rate of 9.1%, and use it to construct an operon map for the MTB genome.

The authors wish it to be known that, in their opinion, the first two authors and the last author should be regarded as joint First Authors.


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