MDM2 Deletion on p53 Activity and Gene Expression in Mouse Fibroblasts | 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 MDM2 Deletion on p53 Activity and Gene Expression in Mouse Fibroblasts. Journal of Interactive Notebooks Collection 1, 49.

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The BioJupies Online Jupyter Notebook Generator was used to analyze GEO Dataset GSE98705, which contains expression profiling by high throughput sequencing on p53-null mouse fibroblast cell types after deletion of MDM2. a gene that negatively regulates and ubiquitinates p53 activity. Analysis with BioJupies reveals after MDM2 deletion, significant up-regulation of chemokine activity and chemokine receptor signaling pathways in mouse fibroblast cell lines. Pathway enrichment analysis also suggests further upregulation of interferon and cytokine signaling after MDM2 deletion, especially pointing to the STAT1, STAT2, IRF1 and IRF8 transcription factors. 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.