ArticleNucleic acids research2002
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
56 citing papers in PubMed, 124 citations in OpenAlex.
- Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network.International journal of molecular sciences · 2019Article
- An Enhancer's Length and Composition Are Shaped by Its Regulatory Task.Frontiers in genetics · 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
- Evaluating tools for transcription factor binding site prediction.BMC bioinformatics · 2016Article
- Article
- Identification and computational analysis of gene regulatory elements.Cold Spring Harbor protocols · 2015Review
- GAMI-CRM: Using de novo motif inference to detect cis-regulatory modules.Proceedings of the ... Congress on Evolutionary Computation. Congress on Evolutionary Computation · 2014Article
- Large-scale investigation of human TF-miRNA relations based on coexpression profiles.BioMed research international · 2014Article
- Prediction of clustered RNA-binding protein motif sites in the mammalian genome.Nucleic acids research · 2013Article
- Spatial promoter recognition signatures may enhance transcription factor specificity in yeast.PloS one · 2013Article
- Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins.G3 (Bethesda, Md.) · 2012Article
- CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.Nucleic acids research · 2012Article
- Genomic approaches towards finding cis-regulatory modules in animals.Nature reviews. Genetics · 2012Review
- The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR.BMC genomics · 2012Article
- Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices.Nucleic acids research · 2012Article
- Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar.Plant physiology · 2012Article
- Article
- Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.Molecular systems biology · 2011Article
- Article
- Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns.BMC bioinformatics · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The human genome encodes the transcriptional control of its genes in clusters of cis-elements that constitute enhancers, silencers and promoter signals. The sequence motifs of individual cis- elements are usually too short and degenerate for confident detection. In most cases, the requirements for organization of cis-elements within these clusters are poorly understood. Therefore, we have developed a general method to detect local concentrations of cis-element motifs, using predetermined matrix representations of the cis-elements, and calculate the statistical significance of these motif clusters. The statistical significance calculation is highly accurate not only for idealized, pseudorandom DNA, but also for real human DNA. We use our method 'cluster of motifs E-value tool' (COMET) to make novel predictions concerning the regulation of genes by transcription factors associated with muscle. COMET performs comparably with two alternative state-of-the-art techniques, which are more complex and lack E-value calculations. Our statistical method enables us to clarify the major bottleneck in the hard problem of detecting cis-regulatory regions, which is that many known enhancers do not contain very significant clusters of the motif types that we search for. Thus, discovery of additional signals that belong to these regulatory regions will be the key to future progress.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.