SELECT is a computational methodology to identify mutual exclusive and co-occurrent interactions between functional alterations in cancer.
This tool was originally introduced here:
Mina M., Raynaud F., Tavernari D., Battistello E., Sungalee S., Saghafinia S., Laessle T., Sanchez-Vega F., Schultz N., Oricchio E., Ciriello G. (2017) Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies. Cancer Cell, 32(2), 155-168
The latest version of this approach (v 1.6) was introduced here:
Mina M., Iyer A., Tavernari D., Raynaud F., Ciriello G. (2020) Discovery of functional evolutionary dependencies in human cancers Nature Genetics , DOI: 10.1038/s41588-020-0703-5
The R implementation of SELECT algorithm.
The Cancer Genome Atlas (TCGA) Pancan23 Genomic Alteration Matrix (GAM) is a binary representation of the occurrences of 505 Selected Functional Events (SFEs) across 6456 samples from 23 different tumor types. All data come from the TCGA Consortium.select_1.0.tar.gz
The R implementation of SELECT algorithm. (This version was used to generate the results in Mina et al. 2017.)
The Pancan23 dataset in R data file format and an example script to run Select on the Pancan23 dataset.
SELECT analysis of the Pancan23 dataset. The full set of pairwise interactions is included in this file.
Soon to appear. Please refer to the help pages in the R package.