p53-depletion by siRNA and LncRNA Analysis in WA-09 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-depletion by siRNA and LncRNA Analysis in WA-09 Cell Line. Journal of Interactive Notebooks Collection 1, 46.

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This notebook, generated by the BioJupies Jupyter Notebeook Generator, compares gene expression in the WA-09 cell line, specifically after depletion of p53 by siRNA. In this cell line, p53 is associated with differentiation of human embryonic stem cells. Pathway Enrichment Analysis describes down-regulation of signaling by NODAL as well as DNA methylation in general; Neurogenesis in mouse and human samples seem to be up-regulated. Transcription Factor Analysis with ENCODE, ChEA and coexpressed genes show downregulation in TFs for the development of endothelial cells (GRHL3, GATA6, SUZ12).In addition to Volcano and MA Plots describing up and down-regulation of genes, differential gene expression analysis was performed and displayed in table format, as well as an interactive heatmap generated with Clustergrammer, PCA, and Library Size Analysis.