Academic Projects:

4. Large scale analysis of protein:protein interaction networks

(Collaborators: J Gowrishankar, Ranjan Sen, Abhijit A Sardesai, Manjula Reddy)

Cellular functions are determined by intricate interactions among many components of cells. Proteins being the dominant molecules of life, interactions among all the cellular proteins direct many of the cellular responses. We have recently become interested in the analysis of genome-wide protein:protein interactions. Our interest primarily is in applying graph theory to protein:protein interactions and attempt to understand how cells respond to external environmental signals.

We have recently proposed a genome-wide collection of functional linkages among all the proteins of Escherichia coli. This was carried out by training a Support Vector Machine on the known high quality protein:protein complexes in the EcoCyc database. The average sensitivity and specificity of our predictions is of the order of 87%. Moreover, our data also is in overall agreement with the known gene essentiality data available for E. coli. This may be accessed via our web server: http://sunserver.cdfd.org.in:8080/protease/PPI/ . Our current focus is on mapping gene expression data on these interactions, and study the dynamic changes in the interactome with different environmental signals.

· Inferring genome-wide functional linkages in Escherichia coli by combining improved genome context methods: comparison with high throughput experimental data (PDF)

S. Yellaboina, K. Goyal and S. C. Mande

Genome Res. (2007) 17, 527- 535.

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