Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks.MicroRNAs (miRNAs) inhibit expression of target genes by binding to their RNA transcripts.  Here we propose a computational method called Cancerin to identify cancer-associated ceRNA interactions.  Cancerin incorporates DNA methylation, copy number alteration, gene and miRNA expression datasets to construct cancer-specific ceRNA networks.  We applied Cancerin to three cancer datasets from the Cancer Genome Atlas (TCGA) project.  Using LINCS-L1000 shRNA-mediated gene knockdown experiment in breast cancer cell line to assess accuracy, Cancerin was able to predict expression outcome of ceRNA genes with high accuracy.
Cancerin
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks.MicroRNAs (miRNAs) inhibit expression of target genes by binding to their RNA transcripts.  Here we propose a computational method called Cancerin to identify cancer-associated ceRNA interactions.  Cancerin incorporates DNA methylation, copy number alteration, gene and miRNA expression datasets to construct cancer-specific ceRNA networks.  We applied Cancerin to three cancer datasets from the Cancer Genome Atlas (TCGA) project.  Using LINCS-L1000 shRNA-mediated gene knockdown experiment in breast cancer cell line to assess accuracy, Cancerin was able to predict expression outcome of ceRNA genes with high accuracy.
Cancerin