The human genome contains ~25,000 protein-coding genes, representing less than 2% of the total genome, whereas up to 70% of the human genome is transcribed into non-coding RNA. The discovery of long noncoding RNA (lncRNA) has dramatically altered our understanding of cancer. Here, we describe a comprehensive analysis of lncRNA alterations at transcriptional, genomic, and epigenetic levels in 5,037 tumor specimens across 13 cancer types from the Cancer Genome Atlas (TCGA). Our results suggest that the expression and dysregulation of lncRNAs are highly cancer-type specific compared to protein-coding genes. Using the integrative data generated by this analysis, we present a clinically guided small interfering RNA screening strategy and a co-expression analysis approach to identify cancer driver lncRNAs and predict their functions. This provides a resource for investigating lncRNAs in cancer and lays the groundwork for the development of new diagnostics and treatments.
Statistics Cancer Types: 13
Tumor Specimens: 5,037
Data Types: 4 ( Expression; CNV; Methylation; SNP )
LncRNAs subject to analysis: 13,562
Pseudogenes subject to analysis: 14,181