title: In Silico Expression Analysis.
abstract: Information on the specificity of cis-sequences enables the design of functional synthetic plant promoters that are responsive to specific stresses. Potential cis-sequences may be experimentally tested, however, correlation of genomic sequence with gene expression data enables an in silico expression analysis approach to bioinformatically assess the stress specificity of candidate cis-sequences prior to experimental verification. The present chapter demonstrates an example for the in silico validation of a potential cis-regulatory sequence responsive to cold stress. The described online tool can be applied for the bioinformatic assessment of cis-sequences responsive to most abiotic and biotic stresses of plants. Furthermore, a method is presented based on a reverted in silico expression analysis approach that predicts highly specific potentially functional cis-regulatory elements for a given stress.
authors.affiliation: Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
authors.forename: Julio
authors.initials: J
authors.lastname: Bolívar
authors.affiliation: Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Hehl
authors.affiliation: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany. lorenz.buelow@julius-kuehn.de.
authors.forename: Lorenz
authors.initials: L
authors.lastname: Bülow
mesh_terms: D058639:Cold-Shock Response / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D010944:Plants / Q000235:genetics; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014158:Transcription, Genetic
keywords: Cis-elements; Cis-regulatory sequences; Expression analysis; In silico validation; PathoPlant; Promoter sequences