title: Dissection of miRNA-miRNA interaction in esophageal squamous cell carcinoma.
abstract: The relationships between miRNAs and their regulatory influences in esophageal carcinoma remain largely unknown. Accumulated evidence suggests that delineation of subpathways within an entire pathway can underlie complex diseases. To analyze the regulation of differentially expressed miRNAs in subpathways of esophageal squamous cell carcinoma (ESCC), we constructed bipartite miRNA and subpathway networks to determine miRNA regulatory influences on subpathways. The miRNA-subpathway network indicated that miRNAs regulate numerous subpathways. Two principal biological networks were derived from the miRNA-subpathway network by the hypergeometric test. This miRNA-miRNA network revealed the co-regulation of subpathways between the upregulated and downregulated miRNAs. Subpathway-subpathway networks characterized scale free, small world, and modular architecture. K-clique analysis revealed co-regulation of subpathways between certain downregulated and upregulated miRNAs. When ESCC patients were grouped according to their expression levels of paired upregulation of miR-31 and downregulation of miR-338-3p, survival time analysis revealed a significant difference based on miR-31-miR-338-3p interaction. These findings can facilitate the understanding of the biological meaning of miRNA-miRNA interactions with either the same or opposite expression trend.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China ; Department of Biochemistry and Molecular Biology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: Bingli
authors.initials: B
authors.lastname: Wu
authors.forename: Chunquan
authors.initials: C
authors.lastname: Li
authors.forename: Pixian
authors.initials: P
authors.lastname: Zhang
authors.forename: Qianlan
authors.initials: Q
authors.lastname: Yao
authors.forename: Jianyi
authors.initials: J
authors.lastname: Wu
authors.forename: Junwei
authors.initials: J
authors.lastname: Han
authors.forename: Liandi
authors.initials: L
authors.lastname: Liao
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Xu
authors.forename: Ruijun
authors.initials: R
authors.lastname: Lin
authors.forename: Dawei
authors.initials: D
authors.lastname: Xiao
authors.forename: Liyan
authors.initials: L
authors.lastname: Xu
authors.forename: Enmin
authors.initials: E
authors.lastname: Li
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000378:metabolism / Q000401:mortality; D016000:Cluster Analysis; D004843:Epistasis, Genetic; D004938:Esophageal Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000401:mortality; D000077277:Esophageal Squamous Cell Carcinoma; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs
references.citation: Bioinformatics. 2008 Jan 15;24(2):282-4
references.pmid: 18006545
references.citation: Nature. 2005 Jun 9;435(7043):814-8
references.pmid: 15944704
references.citation: Nature. 2008 Oct 23;455(7216):1124-8
references.pmid: 18806776
references.citation: Cell Biochem Biophys. 2013 Nov;67(2):657-68
references.pmid: 23516093
references.citation: CA Cancer J Clin. 2011 Mar-Apr;61(2):69-90
references.pmid: 21296855
references.citation: Science. 1999 Oct 15;286(5439):509-12
references.pmid: 10521342
references.citation: Mol Cell Biochem. 2013 Sep;381(1-2):115-25
references.pmid: 23709326
references.citation: J Thorac Cardiovasc Surg. 2008 Feb;135(2):255-60; discussion 260
references.pmid: 18242245
references.citation: Oncogene. 2010 Apr 15;29(15):2161-4
references.pmid: 20190803
references.citation: World J Gastroenterol. 2011 Jan 7;17(1):79-88
references.pmid: 21218087
references.citation: Phys Rev Lett. 2005 Apr 29;94(16):160202
references.pmid: 15904198
references.citation: Nucleic Acids Res. 2009 Oct;37(19):e131
references.pmid: 19706733
references.citation: Bioinformatics. 2011 Feb 1;27(3):431-2
references.pmid: 21149340
references.citation: PLoS Genet. 2011 Dec;7(12):e1002415
references.pmid: 22194702
references.citation: Genome Res. 2009 Jan;19(1):92-105
references.pmid: 18955434
references.citation: Bioinformatics. 2004 Jun 12;20(9):1453-4
references.pmid: 14871861
references.citation: Biochem Biophys Res Commun. 2013 Jan 4;430(1):101-6
references.pmid: 23154181
references.citation: J Surg Oncol. 2012 Feb;105(2):175-82
references.pmid: 21882196
references.citation: BMC Cancer. 2011 Feb 07;11:57
references.pmid: 21299870
references.citation: Br J Cancer. 2003 Jul 7;89(1):140-5
references.pmid: 12838315
references.citation: N Engl J Med. 2005 Sep 15;353(11):1124-34
references.pmid: 16162883
references.citation: Oncol Rep. 2013 Jan;29(1):169-76
references.pmid: 23124769
references.citation: Nat Rev Genet. 2004 Feb;5(2):101-13
references.pmid: 14735121
references.citation: J Cell Physiol. 2011 Sep;226(9):2226-34
references.pmid: 21660946
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14
references.pmid: 22080510
references.citation: RNA. 2005 Dec;11(12):1753-61
references.pmid: 16314451
references.citation: Bioinformatics. 2004 Nov 22;20(17):3246-8
references.pmid: 15180930
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D98-104
references.pmid: 18927107
references.citation: Exp Cell Res. 2009 Feb 15;315(4):572-82
references.pmid: 18778701
references.citation: Biochim Biophys Acta. 2013 Aug;1832(8):1207-16
references.pmid: 23524237
references.citation: Int J Oncol. 2012 Nov;41(5):1653-61
references.pmid: 22940702
references.citation: Biochem Biophys Res Commun. 2012 May 18;421(4):640-5
references.pmid: 22450326
references.citation: Nucleic Acids Res. 2010 Jul;38(13):4476-86
references.pmid: 20299343
references.citation: Oncol Lett. 2013 May;5(5):1639-1642
references.pmid: 23761828
references.citation: Brief Bioinform. 2012 Mar;13(2):175-86
references.pmid: 21908864
references.citation: Nature. 2012 Feb 15;482(7385):347-55
references.pmid: 22337054
references.citation: Med Oncol. 2013 Mar;30(1):411
references.pmid: 23292834
references.citation: Clin Sci (Lond). 2011 Nov;121(10):437-47
references.pmid: 21658006
references.citation: Int J Cancer. 2009 Jun 1;124(11):2549-58
references.pmid: 19165868
references.citation: Nucleic Acids Res. 2011 Feb;39(3):825-36
references.pmid: 20929877
references.citation: Cancer Res. 2008 Jan 1;68(1):26-33
references.pmid: 18172293
references.citation: Dig Dis Sci. 2013 Jul;58(7):1863-70
references.pmid: 23504349
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D105-10
references.pmid: 18996891
references.citation: J Transl Med. 2011 Mar 22;9:30
references.pmid: 21426561
references.citation: PLoS One. 2011;6(6):e21131
references.pmid: 21695054
references.citation: Cancer Res. 2008 Oct 1;68(19):8164-72
references.pmid: 18829576
references.citation: Thorac Cancer. 2011 Nov;2(4):134-142
references.pmid: 27755846
references.citation: Digestion. 2010;82(3):138-44
references.pmid: 20588024