Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection

Noh, Heeju; Shoemaker, Jason E; Gunawan, Rudiyanto

For human PIN, we combined the protein-protein interactions from two databases, namely Enrichr (35) and STRING (36) . For mouse pancreatic cells, we obtained mouse (Mus musculus) PIN from the STRING database (36) . For each TF, we identified its protein partners, defined as proteins that are within a network distance of 2 from the TF in the PIN. When using the STRING database, we included all direct protein partners of TFs, and proteins with a network distance of 2 from TFs with a confidence score reported on STRING larger than 0.5. For human lymphoma, hepatocytes, and lung cancer cells, we identified 11 090 protein partners for a subset of 499 TFs (out of 515 TFs), 10 834 protein partners for a subset of 403 TFs (out of 413 TFs) and 6 175 protein partners for a subset of 504 TFs (out of 515 TFs), respectively. For mouse pancreatic cells, we found 6620 protein partners for a subset of 89 TFs (out of 95 TFs).