dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis.
BACKGROUND
Transcription factor binding sites (TFBSs) are typically short in length, thus search with a profile model from known TFBSs produces many false positives. When combined with additional information, gene expression data in this article, sensitivity and specificity of TFBS search can be improved significantly.


RESULTS
By modifying our previous REFINEMENT approach, we developed dPattern that searches for occurrences of TFBSs in the promotor regions of up/down regulated or random genes.
Bae
Seung-Hee
SH
Department of Computer Science, Indiana University - Bloomington, IN 47404, USA.
Tang
Haixu
H
Wu
Jing
J
Xie
Jun
J
Kim
Sun
S
D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D016002:Discriminant Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics*
D014157:Transcription Factors