title: Coexpression network analysis associated with call of rice seedlings for encountering heat stress.
abstract: Coexpression network analysis is useful tool for identification of functional association of coexpressed genes. We developed a coexpression network of rice from heat stress transcriptome data. Global transcriptome of rice leaf tissues was performed by microarray at three time points--post 10 and 60 min heat stress at 42 °C and 30 min recovery at 26 °C following 60 min 42 °C heat stress to investigate specifically the early events in the heat stress and recovery response. The transcriptome profile was significantly modulated within 10 min of heat stress. Strikingly, the number of up-regulated genes was higher than the number of down-regulated genes in 10 min of heat stress. The enrichment of GO terms protein kinase activity/protein serine threonine kinase activity, response to heat and reactive oxygen species in up-regulated genes after 10 min signifies the role of signal transduction events and reactive oxygen species during early heat stress. The enrichment of transcription factor (TF) binding sites for heat shock factors, bZIPs and DREBs coupled with up-regulation of TFs of different families suggests that the heat stress response in rice involves integration of various regulatory networks. The interpretation of microarray data in the context of coexpression network analysis identified several functionally correlated genes consisting of previously documented heat upregulated genes as well as new genes that can be implicated in heat stress. Based on the findings on parallel analysis of growth of seedlings, associated changes in transcripts of selected Hsps, genome-wide microarray profiling and the coexpression network analysis, this study is a step forward in understanding heat response of rice, the world's most important food crop.
authors: Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
authors: Neelam K
authors: NK
authors: Sarkar
authors: Yeon-Ki
authors: YK
authors: Kim
authors: Anil
authors: A
authors: Grover
mesh_terms: D016000:Cluster Analysis; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D006358:Hot Temperature; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction; D013312:Stress, Physiological / Q000235:genetics / Q000502:physiology*; D059467:Transcriptome
chemical_list: D010940:Plant Proteins
references: Bioinformatics. 2008 Dec 15;24(24):2915-7
references: 18922805
references: BMC Genomics. 2011 Mar 16;12:149
references: 21406116
references: BMC Genomics. 2008 Sep 22;9:432
references: 18808683
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D1214-21
references: 23180784
references: Genome Res. 2003 Nov;13(11):2498-504
references: 14597658
references: PLoS Genet. 2010 Sep 09;6(9):e1001114
references: 20844575
references: Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18822-7
references: 17030801
references: Plant Cell Physiol. 2010 Mar;51(3):448-62
references: 20089509
references: BMC Genomics. 2008 Sep 23;9:439
references: 18811975
references: Plant Cell. 2007 Mar;19(3):1065-80
references: 17400895
references: Ann Bot. 2006 Aug;98(2):279-88
references: 16740587
references: Plant Physiol. 2008 Feb;146(2):748-61
references: 18055584
references: BMC Genomics. 2010 Feb 08;11:95
references: 20141629
references: Plant Cell. 2007 Dec;19(12):4111-9
references: 18156219
references: Plant Sci. 2009 Apr;176(4):583-90
references: 26493149
references: Plant J. 2009 Oct;60(1):10-21
references: 19500308
references: Plant Mol Biol. 2003 Mar;51(4):543-53
references: 12650620
references: Mol Plant. 2012 Mar;5(2):504-14
references: 22199238
references: Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):9971-5
references: 15226500
references: PLoS One. 2012;7(11):e49652
references: 23155476
references: Planta. 2011 Jun;233(6):1237-52
references: 21336597
references: Plant Cell Physiol. 2010 May;51(5):795-809
references: 20304786
references: Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15898-903
references: 12456878
references: Plant Cell. 2009 Sep;21(9):2829-43
references: 19773386
references: Plant Cell Environ. 2008 Feb;31(2):218-26
references: 17996015
references: Plant Physiol. 2005 May;138(1):341-51
references: 15834008
references: Plant J. 2007 Apr;50(1):54-69
references: 17346263
references: Proteomics. 2010 Aug;10(16):3001-19
references: 20645384
references: Plant Physiol. 2006 Apr;140(4):1297-305
references: 16500991
references: Wiley Interdiscip Rev RNA. 2011 Nov-Dec;2(6):875-89
references: 21766458
references: Plant Cell Physiol. 2012 Jan;53(1):144-53
references: 22084314
references: J Exp Bot. 2013 Jan;64(2):569-83
references: 23202132
references: Mol Genet Genomics. 2010 Feb;283(2):185-96
references: 20049613
references: Plant J. 2011 Jun;66(5):844-51
references: 21457365
references: Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18548-53
references: 22042862
references: Mol Cell Biol. 2004 Jun;24(12):5249-56
references: 15169889
references: Plant J. 2008 Jan;53(2):264-74
references: 17999647
references: Mol Genet Genomics. 2008 Dec;280(6):535-46
references: 18813955
references: Plant Physiol. 2008 May;147(1):316-30
references: 18375600
references: New Phytol. 2013 Feb;197(3):825-837
references: 23252708
references: Nat Genet. 2000 May;25(1):25-9
references: 10802651
references: Plant Physiol. 2009 Sep;151(1):16-33
references: 19605550
references: Plant Cell. 2009 Feb;21(2):642-54
references: 19244141
references: Plant Mol Biol. 2006 Jul;61(4-5):733-46
references: 16897488
references: BMC Genomics. 2007 Jun 18;8:175
references: 17577400
references: Nucleic Acids Res. 2002 Feb 15;30(4):e15
references: 11842121
references: Plant J. 2012 Mar;69(6):946-56
references: 22050533
references: Plant Cell Physiol. 2012 Aug;53(8):1481-91
references: 22722767
references: Plant Mol Biol. 2003 Mar;51(5):677-86
references: 12678556
references: Plant Cell. 2011 Mar;23(3):895-910
references: 21441431
references: BMC Plant Biol. 2010 Jan 25;10:16
references: 20100339
references: Cell Stress Chaperones. 2013 Jul;18(4):427-37
references: 23264228
references: Planta. 2008 Apr;227(5):957-67
references: 18064488
references: Plant J. 2009 Aug;59(3):387-99
references: 19366428
references: Plant Mol Biol. 2007 Jan;63(2):237-55
references: 17080288
references: Genome Biol. 2003;4(4):R28
references: 12702209
references: Plant Cell. 2009 Dec;21(12):4031-43
references: 20028842
references: Plant J. 2005 Jan;41(1):1-14
references: 15610345
references: Plant Cell Physiol. 2004 May;45(5):627-34
references: 15169945
references: Plant Biotechnol J. 2011 Apr;9(3):315-27
references: 20809928
references: Plant Physiol. 2010 Sep;154(1):13-24
references: 20668062
references: Plant Biotechnol J. 2008 Oct;6(8):782-98
references: 18643947
references: Plant Physiol. 2012 Jul;159(3):1111-24
references: 22566494
references: Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16398-403
references: 18849477
references: Plant Cell Environ. 2013 Jul;36(7):1242-55
references: 23305614
references: Plant Physiol. 2013 May;162(1):512-21
references: 23503691
references: PeerJ. 2013 Apr 02;1:e59
references: 23638397
references: J Plant Physiol. 2010 Aug 15;167(12):959-66
references: 20417985
references: Plant J. 2008 Sep;55(5):760-73
references: 18466301
references: Plant Physiol. 2008 May;147(1):381-90
references: 18359842
references: Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2940-5
references: 10717008
references: BMC Genomics. 2009 Aug 24;10:393
references: 19703271
references: Plant Cell Environ. 2007 Feb;30(2):156-64
references: 17238907
references: Cell Stress Chaperones. 2013 May;18(3):321-31
references: 23160806
references: PLoS One. 2012;7(7):e40899
references: 22815860
references: Plant Cell. 2011 Feb;23(2):741-55
references: 21307284
references: Stat Appl Genet Mol Biol. 2004;3:Article3
references: 16646809
references: Biochem Biophys Res Commun. 2010 Oct 15;401(2):238-44
references: 20849812
references: Plant Cell Rep. 2009 Jan;28(1):21-30
references: 18818929
references: Plant Cell Rep. 2011 Dec;30(12):2155-65
references: 21769604
references: Mol Cells. 2010 May;29(5):475-83
references: 20396965
references: Plant Cell Environ. 2013 Apr;36(4):775-88
references: 22994594
references: Plant Physiol. 2003 Dec;133(4):1755-67
references: 14645724
references: J Mol Model. 2012 Oct;18(10):4665-73
references: 22653607
references: J Biol Chem. 2008 Apr 4;283(14):9269-75
references: 18201973