Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling.

ABSTRACT:

Background

The use of computational methods for predicting protein interaction networks will continue to grow with the number of fully sequenced genomes available. The Co-Conservation method, also known as the Phylogenetic profiles method, is a well-established computational tool for predicting functional relationships between proteins.

Results

Here, we examined how various aspects of this method affect the accuracy and topology of protein interaction networks. We have shown that the choice of reference genome influences the number of predictions involving proteins of previously unknown function, the accuracy of predicted interactions, and the topology of predicted interaction networks. We show that while such results are relatively insensitive to the E-value threshold used

SUBMITTER: Karimpour-Fard A 

PROVIDER: S-EPMC2204017 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature