ArticleNucleic acids research2003
A non-parametric model for transcription factor binding sites.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Evaluating tools for transcription factor binding site prediction.BMC bioinformatics · 2016Article
- Sequence information gain based motif analysis.BMC bioinformatics · 2015Article
- Identification and computational analysis of gene regulatory elements.Cold Spring Harbor protocols · 2015Review
- Effective automated feature construction and selection for classification of biological sequences.PloS one · 2014Article
- NPEST: a nonparametric method and a database for transcription start site prediction.Quantitative biology (Beijing, China) · 2013Article
- Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites.BMC genomics · 2012Article
- Improved models for transcription factor binding site identification using nonindependent interactions.Genetics · 2012Article
- An information transmission model for transcription factor binding at regulatory DNA sites.Theoretical biology & medical modelling · 2012Article
- Identification of cis-regulatory sequence variations in individual genome sequences.Genome medicine · 2011Article
- Tree-based position weight matrix approach to model transcription factor binding site profiles.PloS one · 2011Article
- Article
- Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction.Nucleic acids research · 2010Article
- On the detection and refinement of transcription factor binding sites using ChIP-Seq data.Nucleic acids research · 2010Article
- Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix.PloS one · 2010Article
- Modeling the quantitative specificity of DNA-binding proteins from example binding sites.PloS one · 2009Article
- Identifying regulatory elements in eukaryotic genomes.Briefings in functional genomics & proteomics · 2009Review
- New scoring schema for finding motifs in DNA Sequences.BMC bioinformatics · 2009Article
- Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering.Genome research · 2008Article
- An efficient method for statistical significance calculation of transcription factor binding sites.Bioinformation · 2007Article
- Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.BMC bioinformatics · 2007Article
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Authors and funding
2 authors.
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Abstract
We introduce a non-parametric representation of transcription factor binding sites which can model arbitrary dependencies between positions. As two parameters are varied, this representation smoothly interpolates between the empirical distribution of binding sites and the standard position-specific scoring matrix (PSSM). In a test of generalization to unseen binding sites using 10-fold cross-validation on known binding sites for 95 TRANSFAC transcription factors, this representation outperforms PSSMs on between 65 and 89 of the 95 transcription factors, depending on the choice of the two adjustable parameters. We also discuss how the non- parametric representation may be incorporated into frameworks for finding binding sites given only a collection of unaligned promoter regions.
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