Systematical Identification of Breast Cancer-Related Circular RNA Modules for Deciphering circRNA Functions Based on the Non-Negative Matrix Factorization Algorithm

International Journal of Molecular Sciences
Shuyuan WangChaohan Xu

Abstract

Circular RNA (circRNA), a kind of special endogenous RNA, has been shown to be implicated in crucial biological processes of multiple cancers as a gene regulator. However, the functional roles of circRNAs in breast cancer (BC) remain to be poorly explored, and relatively incomplete knowledge of circRNAs handles the identification and prediction of BC-related circRNAs. Towards this end, we developed a systematic approach to identify circRNA modules in the BC context through integrating circRNA, mRNA, miRNA, and pathway data based on a non-negative matrix factorization (NMF) algorithm. Thirteen circRNA modules were uncovered by our approach, containing 4164 nodes (80 circRNAs, 2703 genes, 63 miRNAs and 1318 pathways) and 67,959 edges in total. GO (Gene Ontology) function screening identified nine circRNA functional modules with 44 circRNAs. Within them, 31 circRNAs in eight modules having direct relationships with known BC-related genes, miRNAs or disease-related pathways were selected as BC candidate circRNAs. Functional enrichment results showed that they were closely related with BC-associated pathways, such as 'KEGG (Kyoto Encyclopedia of Genes and Genomes) PATHWAYS IN CANCER', 'REACTOME IMMUNE SYSTEM' and 'KEGG MAPK SIGNALIN...Continue Reading

References

Jun 5, 2002·Genome Research·W James KentDavid Haussler
Jun 3, 2006·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Kun YuPatrick Tan
Aug 6, 2008·BMC Bioinformatics·Meeta Mistry, Paul Pavlidis
May 7, 2011·Bioinformatics·Arthur LiberzonJill P Mesirov
Dec 6, 2011·Nucleic Acids Research·Miri DananRotem Sorek
Feb 22, 2012·Circulation Research·Maha Abdellatif
Jan 24, 2013·Proteomics. Clinical Applications·Kenneth D ColeLili Wang
Sep 17, 2013·Molecular Cell·Yang ZhangLing-Ling Chen
Mar 5, 2014·Disease Markers·Bruna Karina Banin HirataMaria Angelica Ehara Watanabe
Aug 27, 2014·Cancer Science·Eriko TokunagaYoshihiko Maehara
Nov 13, 2014·CPT: Pharmacometrics & Systems Pharmacology·L WangS Li
Jan 7, 2015·Journal of Zhejiang University. Science. B·Wei Wang, Yun-ping Luo
Mar 15, 2015·Cell·Simon J ConnGregory J Goodall
Apr 22, 2015·Postȩpy higieny i medycyny doświadczalnej·Jarosław KozłowskiJanusz Kocki
Sep 29, 2015·Advances in Clinical Chemistry·Michael J DuffyJohn Crown
Oct 22, 2015·Japanese Journal of Clinical Oncology·Akiko MatsumotoYuko Kitagawa
Feb 14, 2016·Nucleic Acids Research·Xiaofeng SongWange Lu
Jul 28, 2016·Breast Cancer Research : BCR·Ruben Nogales-CadenasZhengdong D Zhang
Nov 1, 2014·CPT: Pharmacometrics & Systems Pharmacology·L WangS Li
May 26, 2017·Molecular Cancer·Shujuan MengMinghua Wu
Jun 22, 2017·Frontiers in Molecular Biosciences·John GreeneStephen P Finn
Jul 20, 2017·Breast Cancer : the Journal of the Japanese Breast Cancer Society·He-da ZhangZhen-Ling Ji
Oct 4, 2017·CA: a Cancer Journal for Clinicians·Carol E DeSantisAhmedin Jemal
Nov 11, 2017·Nucleic Acids Research·Chih-Hung ChouHsien-Da Huang
Apr 28, 2018·Bioinformatics·Xing ChenHongsheng Liu
May 26, 2018·Cell Death and Differentiation·Ling FangBurton B Yang
Aug 7, 2018·EBioMedicine·Zhongrong ZhangJunjie Xiao

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

package ‘
clusterMaker
package ‘ clusterProfiler
clusterProfiler ’
UROBORUS
Cytoscape
Cufflinks
TopHat2
MCL
R

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