Detection of locally over-represented GO terms in protein-protein interaction networks (supplementary material)

Detection of locally over-represented GO terms in protein-protein interaction networks

Mathieu Lavallee-Adam, Benoit Coulombe, Mathieu Blanchette

Java Program (with documentation) implementing an algorithm identifying protein annotation which are clustered in a given protein-protein interaction network: GoNet

The MathUtils.java of the org.apache.commons.math.util was downloaded from the apache project website.

Protein-protein interaction network was obtained from the Krogan et al. paper
Protein GO annotations were downloaded from the Gene Ontology website

Supplementary Material

Supplementary File F1: file1.txt
File containing all GO terms with p-value below 0.05 in Krogan et al. "core" network with TPD measure

Supplementary File F2: file2.txt
File containing all GO terms with p-value below 0.05 in Jeronimo et al. network with PSF measure

Supplementary File F3:file3.txt
File containing all GO terms with p-value below 0.05 in Jeronimo et al. network with WPSF measure

If you have questions about executing the program, feel free to email us at mathieu.lavallee-adam@mail.mcgill.ca