ArticleNucleic acids research2007
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Genome wide analysis of W-box element in Arabidopsis thaliana reveals TGAC motif with genes down regulated by heat and salinity.Scientific reports · 2019Article
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- Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes.Genome biology and evolution · 2017Review
- Balancing selection maintains polymorphisms at neurogenetic loci in field experiments.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.BMC bioinformatics · 2016Article
- Identification and characterization of an hnRNP E1 translational silencing motif.Nucleic acids research · 2016Article
- A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors.Nucleic acids research · 2016Article
- Evolutionary Footprints of Short Tandem Repeats in Avian Promoters.Scientific reports · 2016Article
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- Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition.PloS one · 2015Article
- Abundance, arrangement, and function of sequence motifs in the chicken promoters.BMC genomics · 2014Article
- Patterns and evolution of ACGT repeat cis-element landscape across four plant genomes.BMC genomics · 2013Article
- A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.BMC bioinformatics · 2013Article
- DLocalMotif: a discriminative approach for discovering local motifs in protein sequences.Bioinformatics (Oxford, England) · 2013Article
- Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways.PLoS genetics · 2013Article
- A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.Nucleic acids research · 2012Article
- Distance and helical phase dependence of synergistic transcription activation in cis-regulatory module.PloS one · 2012Article
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3 authors.
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Abstract
Computational discovery of cis-regulatory elements remains challenging. To cope with the high false positives, evolutionary conservation is routinely used. However, conservation is only one of the attributes of cis-regulatory elements and is neither necessary nor sufficient. Here, we assess two additional attributes--positional and inter-motif distance specificity--that are critical for interactions between transcription factors. We first show that for a greater than expected fraction of known motifs, the genes that contain the motifs in their promoters in a position-specific or distance-specific manner are related, both in function and/or in expression pattern. We then use the position and distance specificity to discover novel motifs. Our work highlights the importance of distance and position specificity, in addition to the evolutionary conservation, in discovering cis-regulatory motifs.
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