In silico modelling of hormone response elements.
BACKGROUND
An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA binding preferences, it is a challenging problem to establish an accurate model for recognition of functional regulatory elements in promoters of eukaryotic genes.


RESULTS
We present a method for precise prediction of a large group of transcription factor binding sites - steroid hormone response elements. We use a large training set of experimentally confirmed steroid hormone response elements, and adapt a sequence-based statistic method of position weight matrix, for identification of the binding sites in the query sequences. To estimate the accuracy level, a table of correspondence of sensitivity vs. specificity values is constructed from a number of independent tests. Furthermore, feed-forward neural network is used for cross-verification of the predicted response elements on genomic sequences.


CONCLUSIONS
The proposed method demonstrates high accuracy level, and therefore can be used for prediction of hormone response elements de novo. Experimental results support our analysis by showing significant improvement of the proposed method over previous HRE recognition methods.
Stepanova
Maria
M
Bioinformatics Research Centre, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore. mstepanova@pmail.ntu.edu.sg
Lin
Feng
F
Lin
Valerie C-L
VC
D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D012739:Gonadal Steroid Hormones / Q000235:genetics*; D008957:Models, Genetic; D010363:Pattern Recognition, Automated; D011485:Protein Binding; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D020218:Response Elements / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics*
D012739:Gonadal Steroid Hormones; D014157:Transcription Factors