IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0183517.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183517
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0183517&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0183517?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Shivali Patel & Alec N. Sexton & Madison S. Strine & Craig B. Wilen & Matthew D. Simon & Anna Marie Pyle, 2023. "Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Tian Tian & Chunjian Li & Jing Xiao & Yi Shen & Yihua Lu & Liying Jiang & Xun Zhuang & Minjie Chu, 2016. "Quantitative Assessment of the Polymorphisms in the HOTAIR lncRNA and Cancer Risk: A Meta-Analysis of 8 Case-Control Studies," PLOS ONE, Public Library of Science, vol. 11(3), pages 1-11, March.
    3. Lihui Liu & Ziyang Liu & Qinghua Liu & Wei Wu & Peng Lin & Xing Liu & Yuechuan Zhang & Dongpeng Wang & Briana C. Prager & Ryan C. Gimple & Jichuan Yu & Weixi Zhao & Qiulian Wu & Wei Zhang & Erzhong Wu, 2023. "LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2’-O-methylation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    4. Roberta Esposito & Andrés Lanzós & Tina Uroda & Sunandini Ramnarayanan & Isabel Büchi & Taisia Polidori & Hugo Guillen-Ramirez & Ante Mihaljevic & Bernard Mefi Merlin & Lia Mela & Eugenio Zoni & Lusin, 2023. "Tumour mutations in long noncoding RNAs enhance cell fitness," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    5. Federica Conte & Giulia Fiscon & Matteo Chiara & Teresa Colombo & Lorenzo Farina & Paola Paci, 2017. "Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer," PLOS ONE, Public Library of Science, vol. 12(2), pages 1-22, February.
    6. Harshita Sharma & Matthew N. Z. Valentine & Naoko Toki & Hiromi Nishiyori Sueki & Stefano Gustincich & Hazuki Takahashi & Piero Carninci, 2024. "Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0183517. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.