MDK Overexpression Analysis in Human LEC Melanoma Cell Line | BioJupies


Notebook Generator(s): Julia Zhao, Kevin Moses, Denis Torre, Avi Ma'ayan
Posted:2018-08-02
Collection No.2

Citation: Zhao, J., Moses, K., Torre, D., and Ma’ayan, A. (2018). BioJupies Notebook for MDK Overexpression Analysis in Human LEC Melanoma Cell Line. Journal of Interactive Notebooks Collection 2, 58.

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Using the BioJupies Jupyter Notebook Generator, this notebook analyzes gene expression in the human LEC cell line after over-expression of MDK; this data is available from GEO Dataset GSE94549. Gene Ontology (GO) Enrichment Analysis with BioJupies suggests upregulation in transmembrane transporter activity, inflammatory response signals, and downregulation in cholesterol biosynthetic processes. Pathway Enrichment Analysis seems to confirm down-regulation in Cholesterol biosynthesis pathways in human and mouse samples, as well as additional down-regulation in cell cycle pathways. Transcription Factor Enrichment Analysis with ARCHS4 coexpressed genes show downregulation in multiple E2F transcription factors responsible for the regulation and progression of the cell cycle. In addition to visualization of gene expression data with MA and Volcano Plots, PCA and the Clustergrammer web tool are also available for further analysis. A query using L1000CDS for small molecules which mimic or reverse the effects of the demonstrated gene expression was also performed, as well as a fireworks display of that query with L1000FWD.