SMAD1 Overexpression and GDF6 Knockdown Analysis in A375 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 SMAD1 Overexpression and GDF6 Knockdown Analysis in A375 Melanoma Cell Line. Journal of Interactive Notebooks Collection 2, 60.

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This notebook uses the BioJupies Jupyter Notebook Generator to analyze GEO Dataset GSE83342, which tests a knockdown perturbation of GDFP6 versus overexpression of SMAD1 combined with a GDF6 Knockdown. Gene Ontology (GO) Analysis indicates downregulation of the perturbation sample with regards to chemokine and cytokine activity; Pathway Enrichment Analysis with Reactome also suggests chemokine and peptide ligand-binding receptor downregulation. 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.