Title page for ETD etd-06162005-140525

Type of Document Master's Thesis
Author Rivera, Corban G.
Author's Email Address cgrivera@vt.edu
URN etd-06162005-140525
Title Identifying Evolutionarily Conserved Protein Interaction Networks
Degree Master of Science
Department Computer Science
Advisory Committee
Advisor Name Title
Murali, T. M. Committee Chair
Potts, Malcolm Committee Member
Zhang, Liqing Committee Member
  • Orthologues
  • Protein-Protein Interaction
  • Species Hopping
  • Conserved Networks
Date of Defense 2005-05-31
Availability unrestricted
Our goal is to investigate protein networks conserved between different organisms. Given the protein interaction networks for two species and a list of homologous pairs of protein in the two species, we propose a model for measuring whether two subnetworks, one in each protein interaction network, are conserved. Our model separately measures the degree of conservation of the two subnetworks and the quality of the edges in each subnetwork. We propose an algorithm for finding pairs of networks, one in each protein interaction network, with high conservation and high quality. When applied to publicly-available protein-protein interaction data and gene sequences for baker's yeast and fruit fly, our algorithm finds many conserved networks with a high degree of functional enrichment. Using our method, we find many conserved protein interaction networks involved in functions such as DNA replication, protein folding, response to heat, protein serine/threonine phosphatase activity, kinase activity, and ATPase activity.

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