Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways

Margit Menges, Róbert Dóczi, L. Ökrész, Piero Morandini, Luca Mizzi, Mikhail Soloviev, James A H Murray, László Bögre

Research output: Contribution to journalArticle

73 Citations (Scopus)

Abstract

• 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.

Original languageEnglish
Pages (from-to)643-662
Number of pages20
JournalNew Phytologist
Volume179
Issue number3
DOIs
Publication statusPublished - Aug 2008

Fingerprint

MAP Kinase Signaling System
Atlases
mitogen-activated protein kinase
Arabidopsis
Gene expression
Mitogen-Activated Protein Kinases
Phosphotransferases
Genes
Gene Expression
gene expression
genes
Microarrays
Gene Ontology
Dissection
Signal transduction
Protein Kinases
Cluster Analysis
Signal Transduction
protein kinases
Transcription Factors

Keywords

  • Arabidopsis
  • Functional prediction
  • Gene expression
  • Microarray
  • Mitogen activated protein kinase (MAPK)
  • Signalling

ASJC Scopus subject areas

  • Plant Science
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry

Cite this

Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways. / Menges, Margit; Dóczi, Róbert; Ökrész, L.; Morandini, Piero; Mizzi, Luca; Soloviev, Mikhail; Murray, James A H; Bögre, László.

In: New Phytologist, Vol. 179, No. 3, 08.2008, p. 643-662.

Research output: Contribution to journalArticle

Menges, M, Dóczi, R, Ökrész, L, Morandini, P, Mizzi, L, Soloviev, M, Murray, JAH & Bögre, L 2008, 'Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways', New Phytologist, vol. 179, no. 3, pp. 643-662. https://doi.org/10.1111/j.1469-8137.2008.02552.x
Menges, Margit ; Dóczi, Róbert ; Ökrész, L. ; Morandini, Piero ; Mizzi, Luca ; Soloviev, Mikhail ; Murray, James A H ; Bögre, László. / Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways. In: New Phytologist. 2008 ; Vol. 179, No. 3. pp. 643-662.
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