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

The pipeline includes four major components:

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

Create disease gene expression signatures

Validate signatures using external sets

Predict drugs using CMap and LINCS

Analyze drug hits including niclosamide and NEN

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

Identify genes reversed by the drugs

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 ([email protected]) for any questions.