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Bioinformatics. 2012 May 1;28(9):1239-45. doi: 10.1093/bioinformatics/bts119. Epub 2012 Mar 13.

PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction.

Author information

  • 1Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College, London, UK.

Abstract

MOTIVATION:

Analysis of protein-protein interaction networks (PPINs) at the system level has become increasingly important in understanding biological processes. Comparison of the interactomes of different species not only provides a better understanding of species evolution but also helps with detecting conserved functional components and in function prediction. Method and

RESULTS:

Here we report a PPIN alignment method, called PINALOG, which combines information from protein sequence, function and network topology. Alignment of human and yeast PPINs reveals several conserved subnetworks between them that participate in similar biological processes, notably the proteasome and transcription related processes. PINALOG has been tested for its power in protein complex prediction as well as function prediction. Comparison with PSI-BLAST in predicting protein function in the twilight zone also shows that PINALOG is valuable in predicting protein function. Availability and implementation: The PINALOG web-server is freely available from http://www.sbg.bio.ic.ac.uk/~pinalog. The PINALOG program and associated data are available from the Download section of the web-server.

CONTACT:

m.sternberg@imperial.ac.uk

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22419782
[PubMed - indexed for MEDLINE]
PMCID:
PMC3338015
Free PMC Article

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