title: 'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences.
abstract: Using bioinformatics, putative cis-regulatory sequences can be easily identified using pattern recognition programs on promoters of specific gene sets. The abundance of predicted cis-sequences is a major challenge to associate these sequences with a possible function in gene expression regulation. To identify a possible function of the predicted cis-sequences, a novel web tool designated 'in silico expression analysis' was developed that correlates submitted cis-sequences with gene expression data from Arabidopsis thaliana. The web tool identifies the A. thaliana genes harbouring the sequence in a defined promoter region and compares the expression of these genes with microarray data. The result is a hierarchy of abiotic and biotic stress conditions to which these genes are most likely responsive. When testing the performance of the web tool, known cis-regulatory sequences were submitted to the 'in silico expression analysis' resulting in the correct identification of the associated stress conditions. When using a recently identified novel elicitor-responsive sequence, a WT-box (CGACTTTT), the 'in silico expression analysis' predicts that genes harbouring this sequence in their promoter are most likely Botrytis cinerea induced. Consistent with this prediction, the strongest induction of a reporter gene harbouring this sequence in the promoter is observed with B. cinerea in transgenic A. thaliana. DATABASE URL: http://www.pathoplant.de/expression_analysis.php.
authors.affiliation: Institut für Genetik, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany.
authors.forename: Julio C
authors.initials: JC
authors.lastname: Bolívar
authors.forename: Fabian
authors.initials: F
authors.lastname: Machens
authors.forename: Yuri
authors.initials: Y
authors.lastname: Brill
authors.forename: Artyom
authors.initials: A
authors.lastname: Romanov
authors.forename: Lorenz
authors.initials: L
authors.lastname: Bülow
authors.forename: Reinhard
authors.initials: R
authors.lastname: Hehl
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D018521:Plant Physiological Phenomena; D010944:Plants / Q000235:genetics / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012984:Software; D013312:Stress, Physiological / Q000502:physiology*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors
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