ArticleBMC bioinformatics2005
Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Bioinformatics tools for the sequence complexity estimates.Biophysical reviews · 2023Review
- Review
- A study on the application of topic models to motif finding algorithms.BMC bioinformatics · 2016Article
- Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation.Nucleic acids research · 2014Article
- A statistical thin-tail test of predicting regulatory regions in the Drosophila genome.Theoretical biology & medical modelling · 2013Article
- A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis.PLoS genetics · 2012Article
- Formation of regulatory modules by local sequence duplication.PLoS computational biology · 2011Article
- Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Most transcription factor binding sites are in a few mosaic classes of the human genome.BMC genomics · 2010Article
- Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse.Developmental cell · 2009Article
- Article
- Comparative analysis of distinct non-coding characteristics potentially contributing to the divergence of human tissue-specific genes.Genetica · 2009Article
- Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs.BMC bioinformatics · 2009Article
- Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses.Genome biology · 2007Article
- Using hexamers to predict cis-regulatory motifs in Drosophila.BMC bioinformatics · 2005Article
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4 authors.
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Abstract
backgroundThis paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. Experimental procedures for this are slow and costly, and computational methods are hard, because they lack positional information.
resultsWe present a novel statistical method, the "fluffy-tail test", to recognise regulatory DNA. We exploit one of the basic informational properties of regulatory DNA: abundance of over-represented transcription factor binding site (TFBS) motifs, although we do not look for specific TFBS motifs, per se . Though overrepresentation of TFBS motifs in regulatory DNA has been intensively exploited by many algorithms, it is still a difficult problem to distinguish regulatory from other genomic DNA.
conclusionWe show that, in the data used, our method is able to distinguish cis-regulatory modules by exploiting statistical differences between the probability distributions of similar words in regulatory and other DNA. The potential application of our method includes annotation of new genomic sequences and motif discovery.
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