p53 Knockdown Analysis in HCT-116 Cell Line | BioJupies

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

Citation: Werner, R., Moses, K., Torre, D., and Ma’ayan, A. (2018). BioJupies Notebook for p53 Knockdown Analysis in HCT-116 Cell Line. Journal of Interactive Notebooks Collection 1, 44.

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Using the BioJupies Jupyter Notebook Generator, this notebook analyzes gene expression in the human HCT-116 cell line with and without a p53 knockout, which is associated with colorectal cancer. Pathway Enrichment Analysis done with Reactome shows noticeable upregulation of SHC and Fibroblast Growth Factor Receptor (FGFR) genes in the knockout sample. Gene Ontology Enrichment analysis, moreover, shows downregulation of genes involved in extracellular matrix organization and collagen development, as well as sulfotransferase activity and multiple interleukin receptor complexes. In addition to visualization of gene expression data with MA and Volcano Plots, further visualization of siRNA and siControl can be seen with Principal Component Analysis and the Clustergrammer tool.