title: Prospecting for genes involved in transcriptional regulation of plant defenses, a bioinformatics approach.
abstract: BACKGROUND
  In order to comprehend the mechanisms of induced plant defense, knowledge of the biosynthesis and signaling pathways mediated by salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) is essential. Potentially, many transcription factors could be involved in the regulation of these pathways, although finding them is a difficult endeavor. Here we report the use of publicly available Arabidopsis microarray datasets to generate gene co-expression networks.
  
  
  RESULTS
  Using 372 publicly available microarray data sets, a network was constructed in which Arabidopsis genes for known components of SA, JA and ET pathways together with the genes of over 1400 transcription factors were assayed for co-expression. After determining the Pearson Correlation Coefficient cutoff to obtain the most probable biologically relevant co-expressed genes, the resulting network confirmed the presence of many genes previously reported in literature to be relevant for stress responses and connections that fit current models of stress gene regulation, indicating the potential of our approach. In addition, the derived network suggested new candidate genes and associations that are potentially interesting for future research to further unravel their involvement in responses to stress.
  
  
  CONCLUSIONS
  In this study large sets of stress related microarrays were used to reveal co-expression networks of transcription factors and signaling pathway components. These networks will benefit further characterization of the signal transduction pathways involved in plant defense.
authors: Institute of Biology, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
authors: Marcel C
authors: MC
authors: van Verk
authors: John F
authors: JF
authors: Bol
authors: Huub J M
authors: HJ
authors: Linthorst
references: PLoS Pathog. 2006 Nov;2(11):e123
references: 17096590
references: Plant Physiol. 2005 Oct;139(2):949-59
references: 16183832
references: Plant Physiol. 2004 Sep;136(1):2621-32
references: 15375207
references: Plant Physiol. 2008 Sep;148(1):212-22
references: 18599650
references: Plant Mol Biol. 2007 Sep;65(1-2):63-76
references: 17587183
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D77-82
references: 17932064
references: Bioinformatics. 2004 Dec 12;20(18):3647-51
references: 15247097
references: Nature. 2002 Feb 28;415(6875):977-83
references: 11875555
references: Plant Cell. 2007 Mar;19(3):805-18
references: 17369371
references: Nat Chem Biol. 2009 May;5(5):308-16
references: 19377457
references: EMBO J. 2003 Mar 17;22(6):1282-8
references: 12628921
references: Plant Cell. 2010 Jul;22(7):2384-401
references: 20647342
references: Plant Cell. 2007 Jul;19(7):2225-45
references: 17616737
references: Mol Plant Microbe Interact. 2003 Apr;16(4):295-305
references: 12744458
references: Nature. 2009 Feb 26;457(7233):1154-8
references: 19122675
references: Plant Cell. 2006 Nov;18(11):3289-302
references: 17114354
references: Nature. 2008 Feb 14;451(7180):789-95
references: 18273012
references: EMBO J. 2001 Oct 1;20(19):5400-11
references: 11574472
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D987-91
references: 18953027
references: Plant Signal Behav. 2007 Jan;2(1):30-2
references: 19516965
references: Nucleic Acids Res. 2002 Jan 1;30(1):207-10
references: 11752295
references: BMC Res Notes. 2009 Dec 02;2:240
references: 19954523
references: Plant Mol Biol. 2009 Mar;69(4):473-88
references: 19083153
references: Plant Cell. 2003 Jul;15(7):1619-31
references: 12837951
references: Science. 2003 Dec 12;302(5652):1956-60
references: 14671301
references: Plant Physiol. 2008 Jul;147(3):1004-16
references: 18467456
references: BMC Plant Biol. 2011 May 19;11:89
references: 21595875
references: Plant Physiol. 2007 Feb;143(2):661-9
references: 17142480
references: Cell. 2006 May 5;125(3):563-75
references: 16678099
references: Trends Plant Sci. 2003 Aug;8(8):365-8
references: 12927968
references: Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8633-8
references: 15932943
references: Nature. 2007 Aug 9;448(7154):661-5
references: 17637677
references: J Biol Chem. 2005 Feb 4;280(5):3697-706
references: 15569682
references: Plant Cell Physiol. 2007 Mar;48(3):381-90
references: 17251202
references: Plant Cell. 2004 Dec;16(12):3386-99
references: 15539472
references: Plant Cell Environ. 2009 Dec;32(12):1633-51
references: 19712066
references: Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6478-83
references: 17420480
references: Plant Physiol. 2009 Apr;149(4):1797-809
references: 19176718
references: In Silico Biol. 2008;8(3-4):339-45
references: 19032166
references: Plant J. 2004 Apr;38(2):366-79
references: 15078338
references: Nucleic Acids Res. 2003 Jan 1;31(1):68-71
references: 12519949
references: Trends Plant Sci. 2001 Sep;6(9):420-5
references: 11544131
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W504-9
references: 16845059
references: Plant J. 2009 May;58(4):578-91
references: 19175769
references: Trends Plant Sci. 2005 Sep;10(9):407-9
references: 16081312
references: Genome Res. 2007 Nov;17(11):1614-25
references: 17921353
references: Plant Cell. 2008 Jun;20(6):1678-92
references: 18586869
references: EMBO J. 2005 Jul 20;24(14):2579-89
references: 15990873
references: Plant J. 2005 Jul;43(1):153-63
references: 15960624
references: Plant Cell. 2006 May;18(5):1310-26
references: 16603654
references: Mol Plant. 2008 May;1(3):459-70
references: 19825553
references: Adv Bioinformatics. 2008;2008:420747
references: 19956698
references: Nature. 2007 Aug 9;448(7154):666-71
references: 17637675
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D863-9
references: 17130150
references: Plant J. 2006 Aug;47(4):532-46
references: 16813576
references: Plant Cell. 2005 Mar;17(3):944-56
references: 15705956
references: Plant Physiol. 2004 Jun;135(2):1113-28
references: 15181213