Analysis of KMT2D Knockdown in MM13 Metastatic 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 Analysis of KMT2D Knockdown in MM13 Metastatic Melanoma Cell Line. Journal of Interactive Notebooks Collection 2, 56.

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This notebook analyzes gene expression regulation of KMT2D-associated target genes and transcriptional enhancers; this data was gathered from GEO Dataset GSE71854. After knockdown of KMT2D via infection with lentiviral vectors, Gene Ontology (GO) Enrichment Analysis with the BioJupies Jupyter Notebook Generator suggests significant down regulation in genes associated with the mitotic spindle and protein kinase binding, while Pathway Enrichment Analysis indicates further down regulation in pathways related to G1 to S mitotic cell cycle control, as well as p53 signaling in mouse pathways. Kinase Enrichment seems to confirm down regulation of substrates related to CDK1 and AURKB, kinases associated with cell cycle control. BioJupies provides further tools such as Differential Expression Analysis and miRNA Enrichment, as well as the L1000CDS Small Molecule Query. Visualization tools such as L1000FWD, PCA, and a Clustergrammer interactive heat map is also provided.