Linked Life Data

21398384

Source:http://linkedlifedata.com/resource/pubmed/id/21398384

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2011-8-1
pubmed:abstractText
Detection of cis-regulatory elements, such as transcription factor binding sites (TFBS), through utilization of ortholog conservation is possible only if genomic data from closely related organisms are available. An alternative approach is the detection of TFBS based on their overrepresentation in promoters of co-regulated genes. However, this approach usually suffers from a high rate of false-positive prediction. Here, we have conducted a case study using promoters of genes known to be strongly induced by the phytohormone abscisic acid (ABA) in the model plant Physcomitrella patens, a moss. Putative TFBS were detected using three de novo motif detection tools in a strict consensus approach. The resulting motifs were validated using data from microarray expression profiling and were able to predict ABA-induced genes with high specificity (90.48%) at mediocre sensitivity (33.33%). In addition, 27 genes predicted to contain ABA-responsive TFBS were validated using real-time PCR. Here, a total of 37% of the genes could be shown to be induced upon ABA treatment, while 70% were found to be regulated by ABA. We conclude that the consensus approach for motif detection using co-regulation information can be used to identify genes that are regulated under a given stimulus. In terms of evolution, we find that the ABA response has apparently been conserved since the first land plants on the level of families involved in transcriptional regulation.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jul
pubmed:issn
1752-9867
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
4
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
713-29
pubmed:meshHeading
pubmed:year
2011
pubmed:articleTitle
Prediction and validation of promoters involved in the abscisic acid response in Physcomitrella patens.
pubmed:affiliation
Faculty of Biology, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't