Sensitive and specific identification of protein complexes in "perturbed" protein interaction networks from noisy pull-down data

William Hendrix, Tatiana Karpinets, Byung Hoon Park, Eric Schendel, Alok Nidhi Choudhary, Nagiza F. Samatova*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

High-throughput mass-spectrometry technology has enabled genome-scale discovery of protein-protein interactions. Yet, computational inference of protein interaction networks and their functional modules from large-scale pull-down data is challenging. Over-expressed or "sticky" bait is not specific; it generates numerous false positives. This "curse" of the technique is also its "blessing" - the sticky bait can pull-down interacting components of other complexes, thus increase sensitivity. Finding optimal trade-offs between coverage and accuracy requires tuning multiple "knobs," i.e., method parameters. Each selection leads to a putative network, where each network in the set of "perturbed" networks differs from the others by a few added or removed edges. Identification of functional modules in such networks is often based on graph-theoretical methods such as maximal clique enumeration. Due to the NP-hard nature of the latter, the number of tunings to explore is limited. This paper presents an efficient iterative framework for sensitive and specific detection of protein complexes from noisy protein interaction data.

Original languageEnglish (US)
Title of host publication2011 IEEE International Symposium on Parallel and Distributed Processing, Workshops and Phd Forum, IPDPSW 2011
Pages512-522
Number of pages11
DOIs
StatePublished - Dec 20 2011
Event25th IEEE International Parallel and Distributed Processing Symposium, Workshops and Phd Forum, IPDPSW 2011 - Anchorage, AK, United States
Duration: May 16 2011May 20 2011

Publication series

NameIEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum

Other

Other25th IEEE International Parallel and Distributed Processing Symposium, Workshops and Phd Forum, IPDPSW 2011
CountryUnited States
CityAnchorage, AK
Period5/16/115/20/11

Keywords

  • Cliques
  • Databases
  • Parallel algorithms
  • Protein complexes
  • Protein interaction networks
  • Proteomics
  • Systems biology

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Software
  • Theoretical Computer Science

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