Author: Noh, Heeju; Shoemaker, Jason E; Gunawan, Rudiyanto
Title: Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection Document date: 2018_4_6
ID: j80hnhpb_44
Snippet: We tested ProTINA's performance in predicting drug targets using gene expression data from three drug treatment studies employing human and mouse cell lines. The first dataset came from the NCI-DREAM drug synergy study using human diffuse large B cell lymphoma OCI-LY3 (24), the second from the compound genotoxicity study using human liver cancer cells HepG2 (25) , and the third from the chromatin-targeting compound study using mouse pancreatic ce.....
Document: We tested ProTINA's performance in predicting drug targets using gene expression data from three drug treatment studies employing human and mouse cell lines. The first dataset came from the NCI-DREAM drug synergy study using human diffuse large B cell lymphoma OCI-LY3 (24), the second from the compound genotoxicity study using human liver cancer cells HepG2 (25) , and the third from the chromatin-targeting compound study using mouse pancreatic cells (26) . We compared ProTINA to the state-ofthe-art network-based analytical method DeMAND (23) , and to the traditional DE analysis. For the analysis of datasets from human cell lines, we constructed cell-type specific PGRNs by combining human PIN from STRING (36) and Enrichr database (35) and human cell-type specific protein-DNA networks from Regulatory Circuit resource (33) . Meanwhile, for the construction of mouse pancreatic
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