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 |
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| container_issue | 19 |
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| container_title | Bioinformatics |
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| creator | Bae, Seung-Hee Tang, Haixu Wu, Jing Xie, Jun Kim, Sun |
| description | 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 |
| doi_str_mv | 10.1093/bioinformatics/btm288 |
| format | Article |
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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</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btm288</identifier><identifier>PMID: 17550915</identifier><identifier>CODEN: BOINFP</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Algorithms ; Artificial Intelligence ; Base Sequence ; Binding Sites ; Biological and medical sciences ; Chromosome Mapping - methods ; Discriminant Analysis ; Fundamental and applied biological sciences. 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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</description><subject>Algorithms</subject><subject>Artificial Intelligence</subject><subject>Base Sequence</subject><subject>Binding Sites</subject><subject>Biological and medical sciences</subject><subject>Chromosome Mapping - methods</subject><subject>Discriminant Analysis</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Profiling - methods</subject><subject>General aspects</subject><subject>Genome, Human - genetics</subject><subject>Humans</subject><subject>Mathematics in biology. 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| subjects | 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 |
| title | dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis |
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