A tool for discovering essential genes in cancer metabolism
We present gMCtool, a user-friedly web-tool to predict essential genes in the latest reconstruction of the human metabolism, Human1, freely available in GitHub.
We have chosen the game 'jenga' as the icon of our tool, because the jenga tower falls when you take out the most vulnerable part of the structure. In our case, we are searching for the most vulnerable parts of the metabolism of cancer cells in order to disrupt cellular proliferation.
In order to fin metabolic vulnerabilities in cancer cells, we employ the concept of genetic Minimal Cut Sets (gMCSs), a metabolic network-based approach to synthetic lethality, and RNA-seq data.
gMCtool has been developed to achieve the following analysis:
- Find essential genes for cancer metabolism based on RNA-seq data.
- Predict putative companion biomarkers for predicted essential genes.
- Identify essential tasks or essential metabolites associated with predicted essential genes.
GMCtool has been developed using R and Shiny. It can be launched either on the public web application of GMCtool, on a local machine using R and RShiny or within Docker.
link: GMCtool
Clone the repository
git clone https://github.com/PlanesLab/gmctool.git
Run RShiny
shiny::runApp('app.R')The code is prepared to adjust the amount of available RAM and number of cores, based on the information of the PC. Furthermore, there are two variables to activate real-time tables in the tabs 4 and 5.
Run the following command:
sudo docker run -p 3838:3838 lvalcarcel/gmctool R -e 'shiny::runApp("/root/GMCtool")'
Now, you can point your browser to http://localhost:3838 and use GMCtool!
There is a complete manual of PDF, in the help tab of the tool or in or in YouTube.
Luis V. Valcárcel, Edurne San José-Enériz, Raquel Ordoñez, Iñigo Apaolaza, Danel Olaverri-Mendizabal, Naroa Barrena, Ana Valcárcel, Leire Garate, Jesús San Miguel, Antonio Pineda-Lucena, Xabier Agirre, Felipe Prósper, Francisco J. Planes "gMCSool App"