DynaMod: dynamic functional modularity analysis.
A comprehensive analysis of enriched functional categories in differentially expressed genes is important to extract the underlying biological processes of genome-wide expression profiles. Moreover, identification of the network of significant functional modules in these dynamic processes is an interesting challenge. This study introduces DynaMod, a web-based application that identifies significant functional modules reflecting the change of modularity and differential expressions that are correlated with gene expression profiles under different conditions. DynaMod allows the inspection of a wide variety of functional modules such as the biological pathways, transcriptional factor-target gene groups, microRNA-target gene groups, protein complexes and hub networks involved in protein interactome. The statistical significance of dynamic functional modularity is scored based on Z-statistics from the average of mutual information (MI) changes of involved gene pairs under different conditions. Significantly correlated gene pairs among the functional modules are used to generate a correlated network of functional categories. In addition to these main goals, this scoring strategy supports better performance to detect significant genes in microarray analyses, as the scores of correlated genes show the superior characteristics of the significance analysis compared with those of individual genes. DynaMod also offers cross-comparison between different analysis outputs. DynaMod is freely accessible at http://piech.kaist.ac.kr/dynamod.
Sun
Choong-Hyun
CH
Department of Computer Science, KAIST, Daejeon 305-701, South Korea.
Hwang
Taeho
T
Oh
Kimin
K
Yi
Gwan-Su
GS
D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D020407:Internet; D035683:MicroRNAs / Q000378:metabolism; D046912:Multiprotein Complexes / Q000378:metabolism; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D014584:User-Computer Interface
D035683:MicroRNAs; D046912:Multiprotein Complexes; D014157:Transcription Factors
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51
14681454
Curr Cancer Drug Targets. 2005 Aug;5(5):365-80
16101384
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D108-10
16381825
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7
16381885
Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72
18988627
Cell. 1995 Oct 6;83(1):111-9
7553862
Mol Syst Biol. 2008;4:169
18277385
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
16199517
J Mol Biol. 2001 Oct 26;313(3):465-71
11676531
Bioinformatics. 2007 Dec 1;23(23):3251-3
17644558
Cancer Cell. 2006 Apr;9(4):287-300
16616334
Artif Intell Med. 2004 Jun;31(2):91-103
15219288
BMC Bioinformatics. 2005 Jun 08;6:144
15941488
Mol Syst Biol. 2007;3:89
17353931
Nat Rev Cancer. 2004 Mar;4(3):177-83
14993899
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D418-24
15608229
Bioinformatics. 2007 Jul 1;23(13):1697-9
17468122
Nat Genet. 2004 May;36(5):431-2
15118671
BMC Bioinformatics. 2010 Jan 26;11:50
20100357
Nucleic Acids Res. 2010 Jan;38(Database issue):D532-9
19897547
Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5
17145710
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W350-5
19429688
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7
15608251
Nat Biotechnol. 2009 Feb;27(2):199-204
19182785
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W592-5
15980543
Bioinformatics. 2005 Mar;21(6):832-4
15531608
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W186-92
17526521
Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40
18000002