BRG1 Knockdown Analysis in 501Mel 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 BRG1 Knockdown Analysis in 501Mel Metastatic Melanoma Cell Line. Journal of Interactive Notebooks Collection 2, 54.

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This notebook uses the BioJupies Jupyter Notebook Generator to analyze GEO Dataset GSE61966, which tests a knockdown perturbation of BRG1 on the expression of MITF and SOX10 transcription factors. Transcription Factor Enrichment Analysis with ARCHS4 coexpressed genes suggest down-regulation of SOX10 and SOX8, part of a family of transcription factors involved with the regulation of embryonic development. Gene Ontology (GO) Enrichment Analysis also indicates down-regulation of maltose transport complexes, while Pathway Enrichment Analysis indicates up-regulation of pathways related to collagen fibril assembly. BioJupies provides further analysis via Kinase Enrichment and miRNA Enrichment, as well as L1000CDS Small Molecule Query. Visualization tools such as L1000FWD, PCA, and a Clustergrammer interactive heat map is also provided.