Searching for transcription factor binding site cl...[J Bioinform Comput Biol. 2004]

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1: J Bioinform Comput Biol. 2004 Jun;2(2):413-6. Links

Searching for transcription factor binding site clusters: how true are true positives?

Krivan W.

ZymoGenetics, Inc., 1201 Eastlake Avenue East, Seattle, Washington 98102, USA. krivan@zgi.com

The computational detection of functional transcription factor binding sites in genomic sequence is one of the challenges of the post-genomic era. Several groups have approached this problem from different directions and have demonstrated considerable success. The purpose of this communication, however, is to point out an imperfection in the way computational results are commonly reported that may lead to a distorted picture of the performance of existing algorithms.

PMID: 15297989 [PubMed - indexed for MEDLINE]

Context specific transcription factor prediction. [Ann Biomed Eng. 2007]
Transcription regulatory region analysis using signal detection and fuzzy clustering. [Bioinformatics. 1998]
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. [Bioinformatics. 2003]
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. [BMC Bioinformatics. 2007]
Integrating genomic data to predict transcription factor binding. [Genome Inform. 2005]
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Searching for transcription factor binding site clusters: how true are true positives?

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