Drug network reconstruction
CLUEreg is a webserver that finds small molecule candidates that reverse a given regulatory signature. The regulatory signature of each compound was estimated from their differential expression from the CLUE resource.
Using PANDA to reconstruct TF-gene bipartite regulatory network, we computed differential targeting scores for 19789 small molecules and derived the drug-induced up-targeted and down-targeted
genes among 12328 genes. The targeting score for each gene is the weighted in-degree for that gene in the network. You can submit your list of up-targeted and down-targeted genes for a given condition or disease and get back a list of compounds that
optimally either reverse or exacerbate the input signature.
Similarly, TF targeting of genes can be used as a surrograte for drug activity. We computed the TF targeting of 644 TFs from PANDA drug networks as the weighted outdegree of each TF.
If you would like to perform the analysis on gene expression, check these excellent tools: CLUE, L1000 Fireworks, L1000 CDS2, and L1000 Canvas Browser.