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Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study

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  • Weiwei Han
  • Zhenyu Zhang
  • Bangshun He
  • Yijun Xu
  • Jun Zhang
  • Weijun Cao

Abstract

Accumulating evidence highlights the important role of long non-coding RNAs (lncRNAs) in a large number of biological processes. However, the knowledge of genome scale expression of lncRNAs and their potential biological function in gastric cancer is still lacking. Using RNA-seq data from 420 gastric cancer patients in The Cancer Genome Atlas (TCGA), we identified 1,294 lncRNAs differentially expressed in gastric cancer compared with adjacent normal tissues. We also found 247 lncRNAs differentially expressed between intestinal subtype and diffuse subtype. Survival analysis revealed 33 lncRNAs independently associated with patient overall survival, of which 6 lncRNAs were validated in the internal validation set. There were 181 differentially expressed lncRNAs located in the recurrent somatic copy number alterations (SCNAs) regions and their correlations between copy number and RNA expression level were also analyzed. In addition, we inferred the function of lncRNAs by construction of a co-expression network for mRNAs and lncRNAs. Together, this study presented an integrative analysis of lncRNAs in gastric cancer and provided a valuable resource for further functional research of lncRNAs in gastric cancer.

Suggested Citation

  • Weiwei Han & Zhenyu Zhang & Bangshun He & Yijun Xu & Jun Zhang & Weijun Cao, 2017. "Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-12, August.
    • Handle: RePEc:plo:pone00:0183517
    DOI: 10.1371/journal.pone.0183517
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    References listed on IDEAS

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    1. Mitchell Guttman & John L. Rinn, 2012. "Modular regulatory principles of large non-coding RNAs," Nature, Nature, vol. 482(7385), pages 339-346, February.
    2. Yuen-Yi Tseng & Branden S. Moriarity & Wuming Gong & Ryutaro Akiyama & Ashutosh Tiwari & Hiroko Kawakami & Peter Ronning & Brian Reuland & Kacey Guenther & Thomas C. Beadnell & Jaclyn Essig & George M, 2014. "PVT1 dependence in cancer with MYC copy-number increase," Nature, Nature, vol. 512(7512), pages 82-86, August.
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