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Bioinformatics Advance Access originally published online on March 3, 2005
Bioinformatics 2005 21(10):2161-2166; doi:10.1093/bioinformatics/bti375
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading frames

Prachee Prakash 1, Sailu Yellaboina 2, Akash Ranjan 2 and Seyed E. Hasnain 1,3,*

1Laboratory of Molecular and Cellular Biology, Centre for DNA Fingerprinting and Diagnostics Hyderabad 500 076, India
2Laboratory of Computational and Functional Genomics, Centre for DNA Fingerprinting and Diagnostics Hyderabad 500 076, India
3Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur, Bangalore 560064, India

*To whom correspondence should be addressed.

IdeR (iron-dependent regulator) is a key regulator of virulence factors and iron acquisition systems in Mycobacterium tuberculosis. Despite the wealth of information available on IdeR-regulated genes of M.tuberculosis, there is still an underlying possibility that there are novel genes/pathways that have gone undetected, the identification of which could give new insights into understanding the pathogenesis of M.tuberculosis. We describe an in silico approach employing the positional relative entropy method to identify potential IdeR binding sites in the upstream sequences of all the 3919 ORFs of M.tuberculosis. While many of the predictions made by this approach overlapped with the ones already identified by microarray experiments and binding assays, pointing to the accuracy of our method, a few genes for which there has been no evidence for IdeR regulation were additionally identified. Our results have implications on the iron-dependent regulatory mechanism of M.tuberculosis vis-a-vis the activity of urease operon and novel transcription regulators and transporters.

Contact: hasnain{at}cdfd.org.in


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Home page
 Nucleic Acids ResHome page
S. Ranjan, J. Seshadri, V. Vindal, S. Yellaboina, and A. Ranjan
iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W584 - W587.
[Abstract] [Full Text] [PDF]


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