siControl vs siRNA Knockout Analysis of p53 and PKM2 in Human Umbilical Vein Endothelial Cells | BioJupies


Notebook Generator(s): Rachel Werner, Kevin Moses, Denis Torre, Avi Ma'ayan
Posted:2018-07-24
Collection No.1

Citation: Werner, R., Moses, K., Torre, D., and Ma’ayan, A. (2018). BioJupies Notebook for siControl vs siRNA Knockout Analysis of p53 and PKM2 in Human Umbilical Vein Endothelial Cells. Journal of Interactive Notebooks Collection 1, 45.

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This notebook analyzes changes in gene expression associated with a double knockdown of PKM2 and p53 using the BioJupies Jupyter Notebook Generator developed by the Ma'ayan Lab at the Icahn School of Medicine at Mount Sinai. Top hits from ChEA and ARCHS4 coexpressed gene libraries suggest significant downregulation in genes involved in neural differentiation and development such as MYT1 and MTF2 in siRNA. Gene Ontology (GO) enrichment analysis also suggests upregulation of antimicrobial humoral responses and downregulation of hydrolase and phospholipase activity in siRNA. MA Plots and Volcano Plots show visualization of this downrregulation; PCA and the Clustergrammer web tool is also provided.