dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis

dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis

Motivation: 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 im...

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Veröffentlicht in:Bioinformatics 2007-10, Vol.23 (19), p.2619-2621
Hauptverfasser: Bae, Seung-Hee, Tang, Haixu, Wu, Jing, Xie, Jun, Kim, Sun
Format: Artikel
Sprache:eng
Schlagworte:
Algorithms
Artificial Intelligence
Base Sequence
Binding Sites
Biological and medical sciences
Chromosome Mapping - methods
Discriminant Analysis
Fundamental and applied biological sciences. Psychology
Gene Expression Profiling - methods
General aspects
Genome, Human - genetics
Humans
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Molecular Sequence Data
Pattern Recognition, Automated - methods
Protein Binding
Sequence Analysis, DNA - methods
Software
Transcription Factors - chemistry
Transcription Factors - genetics
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Zusammenfassung:Motivation: 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. Availability: http://platcom.org/projects/dpattern Contact: sun.kim@acm.org or sunkim2@indiana.edu
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btm288