Polycomb Protein BMI1 Overexpression Analysis in A375 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 Polycomb Protein BMI1 Overexpression Analysis in A375 Melanoma Cell Line. Journal of Interactive Notebooks Collection 2, 55.

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Using the BioJupies Jupyter Notebook Generator, this notebook analyzes gene expression in the A375 cell line after over-expression of BM1 via infection with lentivirus, compared with GFP over-expression controls; this data is available from GEO Dataset GSE71890. Gene Ontology (GO) Enrichment Analysis with BioJupies suggests up-regulation of genes related to voltage-gated calcium channel activity and embryonic skeletal system development in the perturbation sample, while Pathway Enrichment Analysis shows up regulation of muscle contraction, especially regarding cardiac muscle and cardiomyopathy. 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.