Triple Knockout Analysis in Mouse Embryonic Stem Cell Differentiation | 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 Triple Knockout Analysis in Mouse Embryonic Stem Cell Differentiation. Journal of Interactive Notebooks Collection 1, 47.

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This notebook was generated with the BioJupies Jupyter Notebook Generator and analyzes the GSE70486 dataset from the Gene Expression Omnibus (GEO). This dataset compares wild type mouse control samples in the E14Tg2a embryonic stem cell line with p53/p63shRNA/p74shRNA triple knockout samples. Gene Ontology Enrichment Analysis seems to show down-regulation in the KO sample pertaining to a wide range of hormone activities, with Neural Crest Differentiation slightly up-regulated. Transcription Factor Analysis indicates upregulation in EZH2, JARID2, SUZ12 and other genes involved with the Polycomb-group (PcG) family. In addition to Volcano and MA Plots describing up and down-regulation, 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.