Research in Computational Molecular Biology

Volume 3500 of the series Lecture Notes in Computer Science pp 1-13

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks

  • Jacob ScottAffiliated withComputer Science Division, U. C. Berkeley
  • , Trey IdekerAffiliated withDept. of Bioengineering, U. C. San Diego
  • , Richard M. KarpAffiliated withInternational Computer Science Institute
  • , Roded SharanAffiliated withSchool of Computer Science, Tel-Aviv University

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The interpretation of large-scale protein network data depends on our ability to identify significant sub-structures in the data, a computationally intensive task. Here we adapt and extend efficient techniques for finding paths in graphs to the problem of identifying pathways in protein interaction networks. We present linear-time algorithms for finding paths in networks under several biologically-motivated constraints. We apply our methodology to search for protein pathways in the yeast protein-protein interaction network. We demonstrate that our algorithm is capable of reconstructing known signaling pathways and identifying functionally enriched paths in an unsupervised manner. The algorithm is very efficient, computing optimal paths of length 8 within minutes and paths of length 10 in less than two hours.