Identification of a three-long noncoding RNA prognostic model involved competitive endogenous RNA in kidney renal clear cell carcinoma

Cancer Cell International
Di ZhangXiaopeng Hu

Abstract

Long noncoding RNA (lncRNA) is generally identified as competing endogenous RNA (ceRNA) that plays a vital role in the pathogenesis of kidney renal clear cell carcinoma (KIRC), the most common subtype of renal cell carcinoma with poor prognosis and unclear pathogenesis. This study established a novel ceRNA network and thus identified a three-lncRNA prognostic model in KIRC patients. Differentially expressed genes (DEGs) were screened out from The Cancer Genome Atlas (TCGA) database. The lncATLAS was applied to determine the differentially expressed lncRNAs (DElncRNAs) of the cytoplasm. The miRcode, miRDB, miRTarBase, and TargetScan databases were utilized to predict the interactions of DElncRNAs, DEmiRNAs, and DEmRNAs. Cytoscape was used to construct the ceRNA network. Then, a lncRNA prognostic model (LPM) was constructed based on ceRNA-related lncRNA that was significantly related to overall survival (OS), and its predictive ability was evaluated. Moreover, an LPM-based nomogram model was constructed. The significantly different expression of genes in the LPM was validated in an independent clinical cohort (N = 21) by quantitative RT-PCR. A novel ceRNA regulatory network, including 73 lncRNAs, 8 miRNAs, and 21 mRNAs was constr...Continue Reading

References

Nov 10, 2004·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Robert L CampDavid L Rimm
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Nov 14, 2006·Medical Decision Making : an International Journal of the Society for Medical Decision Making·Andrew J Vickers, Elena B Elkin
Oct 15, 2009·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Daniel Y C HengToni K Choueiri
Aug 2, 2011·Cell·Leonardo SalmenaPier Paolo Pandolfi
Nov 19, 2011·Cancer Discovery·John R Prensner, Arul M Chinnaiyan
Feb 18, 2012·Nature·Mitchell Guttman, John L Rinn
Mar 19, 2013·Cell·Pedro J Batista, Howard Y Chang
Jun 26, 2013·Nature Genetics·Yusuke SatoSeishi Ogawa
Nov 8, 2014·Nucleic Acids Research·Nathan Wong, Xiaowei Wang
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Feb 17, 2015·Clinical Epigenetics·Jasmine Jc BlondeauJörg Ellinger
Aug 4, 2015·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Huifang GuoZhiyong Ding
Aug 13, 2015·ELife·Vikram AgarwalDavid P Bartel
Sep 1, 2015·Lancet·Umberto Capitanio, Francesco Montorsi
Nov 22, 2015·Nucleic Acids Research·Chih-Hung ChouHsien-Da Huang
Dec 17, 2015·Nature Reviews. Genetics·Jeffrey J Quinn, Howard Y Chang
Apr 14, 2016·Cancer Cell·Adam M Schmitt, Howard Y Chang
Aug 9, 2016·Trends in Biochemical Sciences·Ling-Ling Chen
Sep 30, 2017·CA: a Cancer Journal for Clinicians·Pedro C Barata, Brian I Rini
Dec 25, 2017·Trends in Cell Biology·Chunru Lin, Liuqing Yang
Jul 25, 2018·Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology·Yan QuHongmei Yang
Oct 31, 2018·Biomedicine & Pharmacotherapy = Biomédecine & Pharmacothérapie·Xiaoxia LiuYanli Wang
Nov 6, 2018·Molecular Neurobiology·Manjari KiranAnindya Dutta
Feb 26, 2019·European Urology·Börje LjungbergAxel Bex
Jun 27, 2019·Seminars in Liver Disease·Abdelrahman Yousry AfifyAhmed Ihab Abdelaziz

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-Seq

Software Mentioned

DAVID
pheatmap
DESeq
GSEA
TargetScan
R
KOBAS
GEPIA2
tile
LASSO

Related Concepts

Related Feeds

Adenocarcinoma, Clear Cell

Clear Cell Adenocarcinoma is a tumor that arises in the female genital tract and is characterized by cells that appear clear under the microscope. Discover the latest research here.