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TimeXNet executable with sample files and documentation


Sample input files

TimeXNet can be run with these sample files:

  1. Mouse interaction network (all_network): This file contains protein-protein interactions, protein DNA interactions and post-translational modifications scored for reliability.

  2. Source genes (source_genes): The genes showing the highest change in expression between 0.5-1 hours after LPS stimulation of dendritic cells. The genes are scored based on the change in their expression on LPS stimulation.

  3. Intermediate genes (inter_genes): The genes showing the highest change in expression between 2-4 hours after LPS stimulation of dendritic cells. The genes are scored based on the change in their expression on LPS stimulation.

  4. Late genes (late_genes): The genes showing the highest change in expression between 6-8 hours after LPS stimulation of dendritic cells. The genes are scored based on the change in their expression on LPS stimulation.

Suggested gamma values for this dataset: gamma1 = 1, gamma2 = 0;

This dataset is further described in the following manuscript:

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response. Patil A, Kumagai Y, Liang KC, Suzuki Y, Nakai K. PLoS Comput Biol. 2013 Nov;9(11):e1003323. PDF

Human Genome Centre, Institute of Medical Science, University of Tokyo