Comprehensive Genomic Characterization of Long Non-Coding RNAs across Human Cancers

By Xiaohui Yan, Zhongyi Hu, Yi Feng, Xiaowen Hu, Jiao Yuan, S. Zhao, Youyou Zhang, Lu Yang, Weiwei Shan, Qun He and 20 more. Cancer Cell, 2015

606 citations recorded by the source corpus.

SUMMARY The discovery of long non-coding 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 human 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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/592014f6d8332c25cc189e2e38fbf4175b0eecbe

Citations in the corpus

• CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells (2016, neutral): “Full model AUC 0.753 Expression only model AUC 0.681 False positive rate Tr ue p os iti ve r at e 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 Variable odds P value Expression level C 1.62 4.52E-28 100 Near FANTOM Enhancer D 1.34 6.44E-09 100 Near cancer associated SNP D 1.10 1.84E-03 81 Number o”