Cross-species cluster co-conservation: a new method for generating protein interaction networks

Genome Biol. 2007;8(9):R185. doi: 10.1186/gb-2007-8-9-r185.


Co-conservation (phylogenetic profiles) is a well-established method for predicting functional relationships between proteins. Several publicly available databases use this method and additional clustering strategies to develop networks of protein interactions (cluster co-conservation (CCC)). CCC has previously been limited to interactions within a single target species. We have extended CCC to develop protein interaction networks based on co-conservation between protein pairs across multiple species, cross-species cluster co-conservation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Biofilms
  • Cluster Analysis
  • Computational Biology / methods*
  • Databases, Protein
  • Escherichia coli / metabolism
  • Gammaproteobacteria / metabolism*
  • Likelihood Functions
  • Models, Biological
  • Models, Genetic
  • Models, Statistical
  • Phylogeny
  • Protein Interaction Mapping
  • Shigella flexneri / metabolism
  • Species Specificity