Despite growing appreciation of the importance of long noncoding RNAs (lncRNAs) in normal physiology and disease, our knowledge of cancer-related lncRNAs remains limited. By repurposing microarray probes, we constructed expression profiles of 10,207 lncRNA genes in approximately 1,300 tumors over four different cancer types. Through integrative analysis of the lncRNA expression profiles with clinical outcome and somatic copy-number alterations, we identified lncRNAs that are associated with cancer subtypes and clinical prognosis and predicted those that are potential drivers of cancer progression. We validated our predictions by experimentally confirming prostate cancer cell growth dependence on two newly identified lncRNAs. Our analysis provides a resource of clinically relevant lncRNAs for the development of lncRNA biomarkers and the identification of lncRNA therapeutic targets. It also demonstrates the power of integrating publically available genomic data sets and clinical information for discovering disease-associated lncRNAs.

How to cite our work

Zhou Du, Teng Fei, Roel G W Verhaak, Zhen Su, Yong Zhang, Myles Brown*, Yiwen Chen* & X Shirley Liu*. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nature Structural & Molecular Biology. [Full Paper]

Download supplementary data

LncRNA classification  [Download]
LncRNA annotation in GTF format [Download]
Probe sequences and lncRNA-alignment results in multiple platforms*  [Sequences] [Alignment]
Subtype specific lncRNA [Lung SCC] [OvCa] [GBM]
Candidate driver lncRNAs in Prostate Cancer [Download]
LncRNA associated with overall survival [Lung SCC] [OvCa] [GBM]
LncRNA associated with progression-free survival [Prostate Cancer] [OvCa]
LncRNA associated with recurrent SCNL [Prostate Cancer] [Lung SCC] [OvCa] [GBM]
LncRNA associated with recurrent SCNG [Prostate Cancer] [Lung SCC] [OvCa] [GBM]
Expression level measured by Exon Array [Prostate Cancer] [Lung SCC] [OvCa] [GBM]
Up/down-regulated lncRNA in Prostate Cancer patients [Up-regulated] [Down-regulated]

*The exon array probe ID was generated based on annotation in probe sequence file. For example, for the probe in sequence file

>probe:HG_U95Av2:1138_at:395:301; Interrogation_Position=2631; Antisense;

I generated a ID "395_301" using a segment of this line (395:301).


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