Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction.

Microbial Informatics and Experimentation
Seshan AnanthasubramanianMadhavi Ganapathiraju

Abstract

Protein-protein interaction (PPI) networks (interactomes) of most organisms, except for some model organisms, are largely unknown. Experimental methods including high-throughput techniques are highly resource intensive. Therefore, computational discovery of PPIs can accelerate biological discovery by presenting "most-promising" pairs of proteins that are likely to interact. For many bacteria, genome sequence, and thereby genomic context of proteomes, is readily available; additionally, for some of these proteomes, localization and functional annotations are also available, but interactomes are not available. We present here a method for rapid development of computational system to predict interactome of bacterial proteomes. While other studies have presented methods to transfer interologs across species, here, we propose transfer of computational models to benefit from cross-species annotations, thereby predicting many more novel interactions even in the absence of interologs. Mycobacterium tuberculosis (Mtb) and Clostridium difficile (CD) have been used to demonstrate the work. We developed a random forest classifier over features derived from Gene Ontology annotations and genetic context scores provided by STRING database for...Continue Reading

References

Mar 1, 1996·Microbiological Reviews·P AlifanoC B Bruni
Oct 27, 1998·Trends in Biochemical Sciences·T DandekarP Bork
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·M PellegriniT O Yeates
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
May 14, 2003·Archives of Internal Medicine·Elizabeth L CorbettChristopher Dye
Dec 19, 2003·Nucleic Acids Research·Suraj PeriAkhilesh Pandey
Oct 20, 2004·BMC Bioinformatics·Nan LinHongyu Zhao
Feb 3, 2005·Proceedings of the National Academy of Sciences of the United States of America·Roded SharanTrey Ideker
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Mar 11, 2006·Science·Weiwei Zhong, Paul W Sternberg
May 17, 2006·Anaerobe·Cynthia L Sears
May 1, 2007·International Journal of Medical Microbiology : IJMM·Helmy Rachman, Stefan H E Kaufmann
Nov 21, 2007·Methods in Molecular Biology·Kiyoko F Aoki-Kinoshita, Minoru Kanehisa
Dec 9, 2008·Nature Methods·Kavitha VenkatesanMarc Vidal
Apr 7, 2009·Briefings in Bioinformatics·Iakes EzkurdiaMichael L Tress
Feb 23, 2010·Molecular BioSystems·Karthik RamanNagasuma Chandra
Nov 4, 2010·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Nov 13, 2010·Nucleic Acids Research·Chris StarkMike Tyers
Apr 5, 2011·Tuberculosis·Nagasuma ChandraKanury Rao
Apr 9, 2011·Nature Reviews. Immunology·Gerhard WalzlAlimuddin Zumla

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Methods Mentioned

BETA
two-hybrid
tandem affinity purification
Y2H
2-hybrid
interaction prediction

Software Mentioned

STRING
GO
KEGG
- Orthology
Weka

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