Supplemental website for the "Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm" publication.

Publication and Supplemental text references:
Manikandan Narayanan and Richard M. Karp. Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm. Journal of Computational Biology, 14(7): 892-907, 2007. [journal link, supplemental text]

Inputs:

The inputs for a two-species comparison using Match-and-Split are: (i) protein interaction networks of the two species, (ii) interaction reliabilities, and (iii) sequence-similar (or homologous) protein pairs between the two species. Please see manuscript and FAQ below for the exact inputs used to obtain the results in this page, and email us if you have any questions.

Software:

Match-and-Split method's source code (Version 0.1) is available here - match-and-split_VER_0_1.tar.gz .

Results:

Conserved modules or subnetworks (the *.csnets file) output by Match-and-Split (p=1 version, described in the manuscript) on pairwise protein network comparisons. Each line in species1-species2.csnets file is a candidate conserved module C between the two compared species in the format "(pvalue, score): {species1 proteins in C} | {species2 proteins in C}".

Yeast-Human conserved modules
Yeast-Fly conserved modules
Yeast-Worm conserved modules

More results and findings:

GO (Gene Ontology) analysis of the Yeast-Human conserved modules above.

Functional descriptions of Yeast-Human conserved modules
Functional predictions of Human proteins using Yeast-Human conserved modules

FAQ:

Q: Where are the input protein interaction networks and sequence-similar protein pairs used in obtaining the above results?
A: First the easy part: the tarball simpairs_MandS.tar.gz contains the sequence-similar protein pairs, along with a brief README file.
But regarding the input networks: licensing restrictions by DIP and HPRD prevent me from distributing them (sorry!) - however you can easily download the relevant version of the networks from DIP and HPRD websites (especially if you are in an academic institution).