liver cancer project
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disease_sig
drug_prediction
reverse_genes
tumor_cell_line
.DS_Store
LICENSE
README.md
main.R
workflow_general.pdf
workflow_general.png

README.md

This pipeline is used to identify drug hits for hepatocellular carcinoma (Chen B. Gastroenterology, 2017). It can be applied to other cancers as well.

alt text

The pipeline includes four major components:

tumor_cell_line

Correlate tumor samples and cell lines

Select tumor samples that are not correlated to cell lines

Select cell lines that are correlated to tumor samples

disease_sig

Create disease gene expression signatures

Validate signatures using external sets

drug_prediction

Predict drugs using CMap and LINCS

Analyze drug hits including niclosamide and NEN

reverse_genes

Examine correlation between disease gene signatures and drug gene signatures derived from in vitro/in vivo studies

Identify genes reversed by the drugs

To run the scripts

  1. dowload data from https://www.synapse.org/#!Synapse:syn6173892/files/

  2. set up workspace in main.R

  3. run workflow.R in each component.

Contact Bin Chen (binchengroup@gmail.com) for any questions.