Mycobacterium tuberculosis

Tuberculosis Protein Network Server

Enter a M. tuberculosis ORF name (for example, ureA or Rv1848):

Approximately 2,906 unique functional linkages have been established between 2,772 (71%) of the 3,927 proteins of Mycobacterium tuberculosis by methods described in the following papers:

Assigning Protein Functions by Comparative Genome Analysis: Protein Phylogenetic Profiles (PNAS 96:4285-4288 (1999), link to PNAS abstract or Medline abstract),
Detecting Protein Function and Protein-Protein Interactions from Genome Sequences ( Science 285:751-753 (1999), link to Science abstract or Medline abstract), and
Predicting Functionally Linked Proteins from Gene Fusions with Confidence (Applied Bioinformatics 1 (2):93-100 (2002) )

Functional links are predicted between TB proteins that are coinherited (as measured with phylogenetic profiles), that are found as fusion genes in other genomes (using the Rosetta Stone method), and that are found as adjacent proteins in operons (using the method of Salgado et al., PNAS 97:6652-7 (2000). Annotions for the TB genes are taken from the Sanger Center.

Explanations of the prediction methods, error rates, etc. appear in the above papers and in A Combined Algorithm for Genome-Wide Prediction of Protein Function ( Nature 402:83-86 (1999), link to Nature abstract). We'll post proper explanations here soon (or you can contact us w/ specific questions.) As currently set up, all phylogenetic profile and Rosetta Stone links are considered very significant, estimated to have a less than 1 in 10^6 chance of occurring at random. Operon links are established between genes that are separated by less than 40 bp, a value shown to correctly discriminate operon partners from non-operon partners (for operon details, see Salgado et al.)


Visualize and interactively navigate the resulting networks

Please address comments to:
Edward Marcotte

A member of the Tuberculosis Structural Genomics Consortium.


Last modified: Fri Sep 6 14:58:46 CDT 2002

Copyright © 2002, Edward Marcotte, Shailesh Date, and Alex Adai. This site is not intended for commercial use. The tuberculosis protein network data and server is the property of the Regents of the University of Texas, and cannot be used for commercial purposes without written permission of Edward Marcotte and the Regents of UT. It is forbidden to redistribute, derivatize, or encapsulate the tuberculosis protein network server or data in another database without permission. Sale of information derived from it, whether directly or in revised form, is forbidden except by permission of UT and Edward Marcotte. All copies or mirrors of the tuberculosis protein network server must carry this notice.