Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways.
* Mitogen activated protein kinase (MAPK) pathways are signal transduction modules with layers of protein kinases having c. 120 genes in Arabidopsis, but only a few have been linked experimentally to functions. * We analysed microarray expression data for 114 MAPK signalling genes represented on the ATH1 Affymetrix arrays; determined their expression patterns during development, and in a wide range of time-course microarray experiments for their signal-dependent transcriptional regulation and their coregulation with other signalling components and transcription factors. * Global expression correlation of the MAPK genes with each of the represented 21 692 Arabidopsis genes was determined by calculating Pearson correlation coefficients. To group MAPK signalling genes based on similarities in global regulation, we performed hierarchical clustering on the pairwise correlation values. This should allow inferring functional information from well-studied MAPK components to functionally uncharacterized ones. Statistical overrepresentation of specific gene ontology (GO) categories in the gene lists showing high expression correlation values with each of the MAPK components predicted biological themes for the gene functions. * The combination of these methods provides functional information for many uncharacterized MAPK genes, and a framework for complementary future experimental dissection of the function of this complex family.
Menges
Margit
M
Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK.
Dóczi
Róbert
R
School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK.
Ökrész
László
L
Institute of Plant Biology, Biological Research Centre, POB 521, H-6701, Szeged, Hungary.
Morandini
Piero
P
Department of Biology, University of Milan and CNR Biophysics Institute (Milan Section), Via Celoria 26, I-20133 Milan, Italy.
Mizzi
Luca
L
Department of Biomolecular Sciences and Biotechnology, University of Milan and CNR Biophysics Institute (Milan Section), Via Celoria 26, I-20133 Milan, Italy.
Soloviev
Mikhail
M
School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK.
Murray
James A H
JAH
Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK.
Bögre
László
L
School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK.
D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000382:microbiology / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D049109:Cell Proliferation; D016000:Cluster Analysis; D015870:Gene Expression; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D020935:MAP Kinase Signaling System; D020411:Oligonucleotide Array Sequence Analysis; D010937:Plant Growth Regulators / Q000494:pharmacology
D029681:Arabidopsis Proteins; D010937:Plant Growth Regulators