Multi-task learning for Host-Pathogen protein interactions

Meghana Kshirsagar, Jaime Carbonell and Judith Klein-Seetharaman, ISMB 2013

Supplementary Information

Supplementary document accompanying the paper. This has a detailed description of the features used in Section 2.
Supplementary and Features notes

Predicted interactions of human proteins with the four bacterial species:
Format of files: Bacterial-uniprotID Bacterial-geneSymbol Human-uniprotID Human-geneSymbol
B. anthracis
F. tularensis
Y. pestis
S. typhi

Pathways enriched by the human genes from the predicted interactions:
Pathways enriched by interaction with B. anthracis
Pathways enriched by interaction with F. tularensis
Pathways enriched by interaction with Y. pestis
Pathways enriched by interaction with S. typhi

Training data (PPIs) used in the paper

Here's the README file so you know what's in there. Here's the training data:

Code and sample data to run it

Download it here: This contains a README.TXT which has additional information about compiling/running and the sample datasets. Feel free to contact me if you have any questions or for the datasets used in the paper (too large to upload here).