Reverse Engineering Cancer: Inferring Transcriptional Gene Signatures from Copy Number Aberrations with ICAro.

ABSTRACT: The characterization of a gene product function is a process that involves multiple laboratory techniques in order to silence the gene itself and to understand the resulting cellular phenotype via several omics profiling. When it comes to tumor cells, usually the translation process from in vitro characterization results to human validation is a difficult journey. Here, we present a simple algorithm to extract mRNA signatures from cancer datasets, where a particular gene has been deleted at the genomic level, ICAro. The process is implemented as a two-step workflow. The first one employs several filters in order to select the two patient subsets: the inactivated one, where the target gene is deleted, and the control one, where large genomic rearrangements should be absent. The second step

SUBMITTER: Angeli D 

PROVIDER: S-EPMC6406408 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature