rkiprev

This repo contains data and scripts to generate figures for a book chapter titled:

Anti-cancer effect of RKIP via modulating autophagy during metastasis

The following is Appendix A from the text which describes the data sources and the method used to generate the figures

Appendix A. RKIP profile in cancer data & method

Gene expression in tumor & normal tissues

The expression level of RKIP in different types of tumor and their corresponding normal tissue were obtained through GEPIA. The web server was accessed through the link http://gepia.cancer-pku.cn. The term "PEBP1" was queried and relevant data were retrieved. The dataset consisted of the expression of RKIP in (n=31) tumor and normal tissues from which the cumulative distribution functions were calculated.

Mutations & copy number alterations in cancer tissue

The mutations and copy number alterations data were obtained from cBioPortal. The web server was accessed through the link http://www.cbioportal.org. The gene name "PEBP1" was used to query and download the genetic alterations for "All listed studies". The dataset consisted of RKIP mutations and copy number alterations in (n=240) cancer studies. The entries were classified into Altered vs Not altered and Mutated vs Not mutated and used to count the cumulative distribution function.

Source code & reproducibility

The data were imported and processed in R software environment and used to generate the graph. The source code for reproducing the graph is available online https://github.com/BCMSLab/rkiprev.

To reproduce the figures, clone this repo and run make.

git clone https://github.com/BCMSLab/rkiprev
cd rkiprev
make

The only requirement in the for running the code properly in R, is the tidyverse package. The docker image rocker/verse can be used for this purpose.

docker pull rocker/verse

The final version of the book chapter can be viewed here