Co-targeting BET and MEK inhibitors in M93047 Melanoma Cell Line | BioJupies

Notebook Generator(s): Julia Zhao, Kevin Moses, Denis Torre, Avi Ma'ayan
Collection No.2

Citation: Zhao, J., Moses, K., Torre, D., and Ma’ayan, A. (2018). BioJupies Notebook for Co-targeting BET and MEK inhibitors in M93047 Melanoma Cell Line. Journal of Interactive Notebooks Collection 2, 61.

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Using the BioJupies Jupyter Notebook Generator, this notebook analyzes gene expression in the M93047 cell line after combined treatment of BET and MEK inhibitors with JQ1 and PD901; this data is available from GEO Dataset GSE95153. Differential Expression Analysis shows that the expression of Histone Cluster 2 was significantly altered. Gene Ontology (GO) Enrichment Analysis with BioJupies suggests down-regulation of genes related to extracellular matrix organization, protein kinase binding, as well as centromere and ER activity, while Pathway Enrichment Analysis shows additional downregulation of extracellular matrix pathways, as well as cell cycle pathways in perturbation cells. In addition to visualization of gene expression data with MA and Volcano Plots, PCA and the Clustergrammer web tool are also available for further analysis. A query using L1000CDS for small molecules which mimic or reverse the effects of the demonstrated gene expression was also performed, as well as a fireworks display of that query with L1000FWD.