title: miRNA functional synergistic network analysis of mice with ischemic stroke.
abstract: This study aimed to identify potential miRNAs highly associated with the response to brain ischemic stroke. The miRNAs microarray expression profiles data were downloaded from Gene Expression Omnibus database under accession number GSE51586, including three ischemia and three ipsilateral normal samples from mouse brain tissues. Limma package was used to identify differentially expressed miRNAs between ischemia and ipsilateral normal samples. The common target genes of miRNA predicted from TargetScan, PicTar, miRanda and DIANA-microT databases were used as the candidate subset in which functional modules were identified by performing gene ontology enrichment analysis using ClusterProfile. Finally, the miRNA functional synergistic network was constructed by assembling all miRNA synergistic pairs. Fifty-one differentially expressed miRNAs were identified between ischemia and ipsilateral normal samples, including 32 up- and 19 down-regulated miRNAs. Among them, 24 miRNAs can commonly regulate at least one target gene and thus were used to construct a network, which included 274 pairs of co-regulating miRNAs. Further, 242 pairs of miRNAs interaction involving 23 miRNAs were shown to be synergetic in function. Sixteen miRNAs forming 20 miRNAs interaction pairs participated in inflammatory response, such as mir-185 and mir-674-3p. The 16 miRNAs related to inflammatory response during ischemic stroke may provide underlying targets for prevention and treatment of stroke.
authors.affiliation: Department of Neurology, Fourth People's Hospital of Jinan, No 50 Shifan Road, Jinan, 250031, Shangdong, China, shupingxx@gmail.com.
authors.forename: Shuping
authors.initials: S
authors.lastname: Xiao
authors.forename: Yingwen
authors.initials: Y
authors.lastname: Ma
authors.forename: Haiying
authors.initials: H
authors.lastname: Zhu
authors.forename: Hongyu
authors.initials: H
authors.lastname: Sun
authors.forename: Yanling
authors.initials: Y
authors.lastname: Yin
authors.forename: Guangkun
authors.initials: G
authors.lastname: Feng
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism*; D002545:Brain Ischemia / Q000378:metabolism*; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D020521:Stroke / Q000378:metabolism*
chemical_list: D035683:MicroRNAs
references.citation: Nat Med. 2009 Feb;15(2):192-9
references.pmid: 19169263
references.citation: FASEB J. 2011 Aug;25(8):2515-27
references.pmid: 21507901
references.citation: Nature. 2007 Oct 18;449(7164):919-22
references.pmid: 17943132
references.citation: Arch Neurol. 2001 Apr;58(4):672-4
references.pmid: 11296003
references.citation: Cell. 2007 Apr 6;129(1):147-61
references.pmid: 17382377
references.citation: Curr Opin Neurol. 2007 Jun;20(3):334-42
references.pmid: 17495630
references.citation: BMC Genomics. 2006 Oct 09;7:252
references.pmid: 17029630
references.citation: BMC Syst Biol. 2009 Jun 26;3:65
references.pmid: 19558649
references.citation: Apoptosis. 2001 Feb-Apr;6(1-2):69-81
references.pmid: 11321043
references.citation: Stroke. 2008 Nov;39(11):e186
references.pmid: 18802201
references.citation: Trends Neurosci. 1999 Sep;22(9):391-7
references.pmid: 10441299
references.citation: PLoS One. 2013 Dec 20;8(12):e83717
references.pmid: 24376737
references.citation: J Exp Med. 2006 Oct 30;203(11):2519-27
references.pmid: 17060477
references.citation: Immunity. 2007 Jul;27(1):123-34
references.pmid: 17613256
references.citation: Circulation. 2008 Jan 29;117(4):e25-146
references.pmid: 18086926
references.citation: Cell Mol Neurobiol. 2006 Oct-Nov;26(7-8):1057-83
references.pmid: 16710759
references.citation: Stroke. 2007 Feb;38(2 Suppl):770-3
references.pmid: 17261736
references.citation: Neuron. 2010 Jul 29;67(2):181-98
references.pmid: 20670828
references.citation: Ann Neurol. 2006 Mar;59(3):467-77
references.pmid: 16453316
references.citation: FEBS Lett. 2009 Oct 20;583(20):3349-55
references.pmid: 19786024
references.citation: J Exp Med. 2005 Jul 18;202(2):261-9
references.pmid: 16009718
references.citation: Oncogene. 2008 Sep 18;27(42):5643-7
references.pmid: 18504431
references.citation: Science. 2008 Mar 28;319(5871):1789-90
references.pmid: 18369137
references.citation: J Exp Med. 2005 May 2;201(9):1367-73
references.pmid: 15867090
references.citation: Science. 2004 Jan 2;303(5654):83-6
references.pmid: 14657504
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: Trends Pharmacol Sci. 2003 Aug;24(8):402-8
references.pmid: 12915049
references.citation: J Cereb Blood Flow Metab. 2010 Jan;30(1):92-101
references.pmid: 19724284
references.citation: Stroke. 2006 Feb;37(2):345-50
references.pmid: 16397184
references.citation: Arch Neurol. 2001 Apr;58(4):674
references.pmid: 11296004
references.citation: Free Radic Res. 2009 Apr;43(4):348-64
references.pmid: 19241241
references.citation: Brain Res. 2001 Jun 1;902(2):171-7
references.pmid: 11384610
references.citation: Nat Rev Neurosci. 2003 May;4(5):399-415
references.pmid: 12728267
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1604-9
references.pmid: 17242365
references.citation: Stroke. 2008 Mar;39(3):959-66
references.pmid: 18258830
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W145-8
references.pmid: 21551220