Fig. 1

The workflow of cogena for drug repositioning. 0. Differential expression analysis of a disease or compound (drug) dataset. Cogena requires the gene expression signature of differentially expressed genes as an input. 1. Co-expression analysis on the expression profile of differentially expressed genes. Ten clustering methods are available in cogena. 2.1 Pathway Analysis. Hypergeometric test and KEGG gene sets are used for the pathway analysis for each co-expressed gene cluster. 2.2 Drug repositioning. The same test and CMap gene set from Connectivity Map are used for drug repositioning for each co-expressed gene cluster. The pathways enriched for a gene cluster may imply the MoA of drugs enriched for the same gene cluster. The main steps are outlined in the circles, methods in ellipses, while data streams are described in the rectangles