ArticleNucleic acids research2000
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
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98 citing papers in PubMed, 314 citations in OpenAlex.
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- RSAT 2022: regulatory sequence analysis tools.Nucleic acids research · 2022Article
- Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example.Plant physiology · 2021Article
- SUPPRESSOR OF GAMMA RESPONSE 1 acts as a regulator coordinating crosstalk between DNA damage response and immune response in Arabidopsis thaliana.Plant molecular biology · 2020Article
- TFregulomeR reveals transcription factors' context-specific features and functions.Nucleic acids research · 2020Article
- RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach.Frontiers in microbiology · 2020Article
- Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.Current protocols in bioinformatics · 2019Article
- A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.BMC biology · 2018Article
- RSAT 2018: regulatory sequence analysis tools 20th anniversary.Nucleic acids research · 2018Article
- Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets.Nucleic acids research · 2018Article
- Machine learning for epigenetics and future medical applications.Epigenetics · 2017Review
- A study on the application of topic models to motif finding algorithms.BMC bioinformatics · 2016Article
- Parametric bootstrapping for biological sequence motifs.BMC bioinformatics · 2016Article
- Black perithecial pigmentation in Fusarium species is due to the accumulation of 5-deoxybostrycoidin-based melanin.Scientific reports · 2016Article
- BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.Bioinformatics (Oxford, England) · 2015Article
- Hypoxia and Temperature Regulated Morphogenesis in Candida albicans.PLoS genetics · 2015Article
- RSAT 2015: Regulatory Sequence Analysis Tools.Nucleic acids research · 2015Article
- Signaling domains of mucin Msb2 in Candida albicans.Eukaryotic cell · 2015Article
- The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.Nucleic acids research · 2015Article
38 more citing papers are in PubMed but not listed here.
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3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The application of microarray and related technologies is currently generating a systematic catalog of the transcriptional response of any single gene to a multiplicity of experimental conditions. Clustering genes according to the similarity of their transcriptional response provides a direct hint to the regulons of the different transcription factors, many of which have still not been characterized. We have developed a new method for deciphering the mechanism underlying the common transcriptional response of a set of genes, i.e. discovering cis -acting regulatory elements from a set of unaligned upstream sequences. This method, called dyad analysis, is based on the observation that many regulatory sites consist of a pair of highly conserved trinucleotides, spaced by a non-conserved region of fixed width. The approach is to count the number of occurrences of each possible spaced pair of trinucleotides, and to assess its statistical significance. The method is highly efficient in the detection of sites bound by C(6)Zn(2)binuclear cluster proteins, as well as other transcription factors. In addition, we show that the dyad and single-word analyses are efficient for the detection of regulatory patterns in gene clusters from DNA chip experiments. In combination, these programs should provide a fast and efficient way to discover new regulatory sites for as yet unknown transcription factors.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.