DGPsubNet: Drug-Gene-Disease coherent SUBNETworks

• Version 0.0.1
• Last updated: Oct. 12, 2013

References#

• Lin Wang, Yong Wang, Qinghua Hu and Shao Li. Exploring drug-gene-disease coherent subnetworks for elucidating drug-disease associations. In submission.

Motivation#

How to analyze transcriptional response data to identify meaningful gene modules shared by both drugs and diseases is still a critical issue to elucidate the molecular basis of drug-disease associations.

Method#

Here, we propose the drug-gene-disease coherent subnetwork concept to group the biological function related drugs, diseases and genes. Based on disease-related and drug-induced transcriptional response profiles, we develop a multiple non-negative matrix factorization method to identify drug-gene-disease coherent subnetworks. Additional heterogeneous data are simultaneously integrated in a regularized manner. Meanwhile, the sparsity penalties are employed to achieve modular solutions.

Software#

This version of the program is in very preliminary stage and provided just for testing purpose. The program is still under development.

• DGPsubNet.rar

Data#

• Data.zip