title: Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice.
abstract: One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.
authors: Plant and Environmental Sciences, Clemson University, Clemson, South Carolina 29634, USA.
authors: Stephen P
authors: SP
authors: Ficklin
authors: F Alex
authors: FA
authors: Feltus
references: Methods Mol Biol. 2011;678:247-75
references: 20931385
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D987-91
references: 18953027
references: Bioinformatics. 2010 May 1;26(9):1267-8
references: 20305269
references: Nucleic Acids Res. 2011 Apr;39(7):e41
references: 21149270
references: Pac Symp Biocomput. 2008;:303-14
references: 18229695
references: Bioinformatics. 2009 Jun 15;25(12):i259-67
references: 19477997
references: BMC Bioinformatics. 2005 Sep 14;6:227
references: 16162296
references: Nat Rev Genet. 2010 Dec;11(12):843-54
references: 21085203
references: Plant Physiol. 2010 Sep;154(1):13-24
references: 20668062
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D1016-22
references: 21081562
references: Plant Mol Biol. 2005 Jul;58(5):739-50
references: 16158246
references: Plant Cell. 2003 Aug;15(8):1771-80
references: 12897251
references: Nat Genet. 2009 Mar;41(3):299-307
references: 19234471
references: BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S61
references: 20122237
references: Science. 2009 Nov 20;326(5956):1112-5
references: 19965430
references: Nat Protoc. 2009;4(1):44-57
references: 19131956
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D883-7
references: 17145706
references: BMC Bioinformatics. 2009 Oct 21;10:346
references: 19845953
references: Biostatistics. 2003 Apr;4(2):249-64
references: 12925520
references: Nucleic Acids Res. 2001 Jan 1;29(1):37-40
references: 11125043
references: Nat Rev Genet. 2004 Feb;5(2):101-13
references: 14735121
references: Nat Genet. 2002 May;31(1):64-8
references: 11967538
references: Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8633-8
references: 15932943
references: Plant Physiol. 2009 Jun;150(2):535-46
references: 19357200
references: Plant Physiol. 2010 Jan;152(1):29-43
references: 19889879
references: Plant Cell Physiol. 2007 Mar;48(3):381-90
references: 17251202
references: Nat Genet. 2000 May;25(1):25-9
references: 10802651
references: Plant Physiol. 2009 Sep;151(1):16-33
references: 19605550
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5
references: 17526522
references: BMC Plant Biol. 2008 Jul 11;8:76
references: 18616834
references: Plant Cell Environ. 2009 Dec;32(12):1633-51
references: 19712066
references: J Comput Biol. 2009 Aug;16(8):1001-22
references: 19645599
references: Genome Biol. 2003;4(5):P3
references: 12734009
references: Bioinformatics. 2009 Feb 1;25(3):415-6
references: 19106121
references: Int J Bioinform Res Appl. 2010;6(2):101-19
references: 20223734
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W504-9
references: 16845059
references: Bioinformatics. 2005 Jun;21 Suppl 1:i213-21
references: 15961460
references: Science. 2002 Aug 30;297(5586):1551-5
references: 12202830
references: Genome Biol. 2004;5(10):R80
references: 15461798
references: Algorithms Mol Biol. 2010 Nov 12;5:36
references: 21073720
references: BMC Res Notes. 2009 Jul 20;2:142
references: 19619323
references: Plant Physiol. 2006 Oct;142(2):762-74
references: 16920875
references: Nat Biotechnol. 2010 Feb;28(2):149-56
references: 20118918
references: BMC Syst Biol. 2009 Sep 03;3:86
references: 19728874
references: Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7783-8
references: 8755553
references: Bioinformatics. 2009 Jun 15;25(12):i253-8
references: 19477996
references: J Comput Biol. 2009 Aug;16(8):989-99
references: 19624266
references: Genome Res. 2006 Mar;16(3):428-35
references: 16510899
references: BMC Bioinformatics. 2008 Dec 29;9:559
references: 19114008
references: BMC Genomics. 2010 Feb 26;11:142
references: 20187945
references: Bioinformatics. 2008 Feb 1;24(3):319-24
references: 18042555
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
references: 18077471
references: Plant Physiol. 2009 Jan;149(1):125-31
references: 19126703
references: BMC Bioinformatics. 2009 Oct 14;10:332
references: 19828039
references: Science. 2003 Oct 10;302(5643):249-55
references: 12934013
references: Int J Mol Sci. 2009 Jan;10(1):116-32
references: 19333437
references: Pac Symp Biocomput. 2010;:123-32
references: 19908365
references: Science. 2002 Oct 25;298(5594):824-7
references: 12399590
references: J R Soc Interface. 2010 Sep 6;7(50):1341-54
references: 20236959
references: BMC Bioinformatics. 2009 Oct 08;10 Suppl 11:S4
references: 19811688
references: BMC Bioinformatics. 2007 Aug 14;8:299
references: 17697349