Collection No.2

Published 2018-08-02

Notebooks featured in Collection: 9

Perturbation Analysis Over Selected Metastatic Melanoma Cell Lines

The second collection of the Journal of Interactive Notebooks features nine Jupyter Notebooks performing perturbation analysis across five distinct malignant melanoma cell lines. Predominantly found in the skin, metastatic melanoma is one of the most aggressive forms of cancer; it can quickly spread to other internal organs and can consequently significantly lower life expectancy. The BioJupies Jupyter notebook generator performed data analysis on nine Gene Expression Omnibus (GEO) Datasets corresponding to knockdown, overexpression, and other forms of perturbation analysis in metastatic melanoma cell lines. Each notebook in this collection has performed dimensionality reduction of the dataset via Principal Component Analysis (PCA), as well as a Library Size analysis of the dataset and found Differential Expression signatures of affected proteins. Additional analysis tools such as Gene Ontology, Kinase Enrichment, and Transcription Factor Enrichment is shown, as well as visuzliation tools such as the Clustergrammer interactive heatmap and the L1000FWD small molecule query fireworks display.

Collection No.1

Published 2018-07-19

Notebooks featured in Collection: 11

p53-Related Perturbation Analysis Across Multiple Cell Lines in Cancer

For the first collection of the Journal of Interactive Notebooks (JOIN), we selected eleven Jupyter notebooks analyzing Gene Expression Omnibus (GEO) datasets on p53 gene expression. p53 is a tumor suppressor gene discovered in 1979 and regulates the expression of inhibitory proteins to induce cell cycle progression. Using the BioJupies online notebook generator, cell lines were analyzed pertaining to breast, colorectal and prostate cancer, as well as mouse embryonic fibroblasts and human umbilical cord endothelial cells. These datasets were taken from experiments where either knockout or knockdown was performed on p53, or a dependent gene such as MDM2 in mouse embryonic fibroblasts were silenced. In each notebook, Principal Component Analysis (PCA) dimensionality reduction was performed, as well as Gene Ontology (GO) Enrichment Analysis, Pathway Enrichment Analysis and Transcription Factor Analysis. Further examination is provided with the Clustergrammer interactive heatmap tool, as well as visualization methods like Volcano and MA plots.