Identification of RNA Transcript Makers Associated With Prognosis of Kidney Renal Clear Cell Carcinoma by a Competing Endogenous RNA Network Analysis

Frontiers in Genetics
Qiwei YangXingang Cui

Abstract

This study aims to identify several RNA transcripts associated with the prognosis of kidney renal clear cell carcinoma (KIRC). The differentially expressed mRNAs, lncRNAs, and miRNAs (DEmRNAs, DElncRNAs, and DEmiRNAs) between KIRC cases and controls were screened based on an RNA-seq dataset from The Cancer Genome Atlas (TCGA) database. Subsequently, miRcode, miRDB, and TargetScan database were used to predict interactions between lncRNAs, miRNAs and target mRNAs. Then, a ceRNA network was built using miRNAs-mRNAs and lncRNAs-miRNAs pairs. Functional analysis of mRNAs in ceRNA was performed. Finally, the survival analysis of RNA transcripts in ceRNA network and correlation analysis for key RNA regulators were carried out. There were 1527 DElncRNAs, 54 DEmiRNAs, and 2321 DEmRNAs. A ceRNA network was constructed among 81 lncRNAs, 9 miRNAs, and 197 mRNAs. Functional analysis showed that numerous mRNAs were significantly associated with regulation of cellular glucuronidation. In addition, 35 lncRNAs, 84 mRNAs and two miRNAs were significantly corelated to the survival of patients with KIRC (P < 0.05). Among them, miRNA-21 and miRNA-155 were negatively related to three lncRNAs (LINC00472, SLC25A5.AS1, and TCL6). Seven mRNA targets of...Continue Reading

References

Sep 5, 2002·Nature Reviews. Neuroscience·David F Owens, Arnold R Kriegstein
Dec 9, 2004·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Frede DonskovMarianne Hokland
Oct 21, 2005·Cancer Treatment Reviews·Beverly J Drucker
Oct 9, 2007·The Cancer Journal·Thomas E Hutson, Robert A Figlin
Mar 4, 2008·Cancer Treatment Reviews·Kiran GuptaClaudie Charbonneau
Sep 8, 2009·Nucleic Acids Research·Lu Ping TanAnke van den Berg
Aug 2, 2011·Cell·Leonardo SalmenaPier Paolo Pandolfi
Feb 22, 2012·PloS One·Mohd Saif ZamanRajvir Dahiya
Mar 9, 2012·Urologia Internationalis·Takehiro SejimaAtsushi Takenaka
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Sep 28, 2013·Cancer Discovery·Florian A Karreth, Pier Paolo Pandolfi
Jan 17, 2014·Nature·Yvonne TayPier Paolo Pandolfi
Dec 3, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima
Mar 10, 2017·Nature Reviews. Disease Primers·James J HsiehVincenzo Ficarra
Nov 18, 2017·Journal of the American Society of Hypertension : JASH·Dominika KlimczakLeszek Pączek
Dec 1, 2017·Neoplasia : an International Journal for Oncology Research·Tianhong PanRobert L Satcher
Jul 1, 2018·Critical Reviews in Oncology/hematology·Francesca De Felice, Vincenzo Tombolini
Aug 10, 2018·Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology·Peng LinGang Chen
Dec 7, 2018·Molecular Carcinogenesis·Seema KhadirnaikarSudhanshu Kumar Shukla
Aug 8, 2019·Biomedicine & Pharmacotherapy = Biomédecine & Pharmacothérapie·Tianbo XuXiaoping Zhang

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE40435

Methods Mentioned

BETA
surgical resection
RNA-seq
transfection

Software Mentioned

Database for Annotation , Visualization and Integrated Discove...
clusterProfiler
EdgeR
ggplot2
R Survival package
R
Cytoscape
EdgeR package

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.