ArticleGenome research2004
Decoding human regulatory circuits.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
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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.
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Who cites it
41 citing papers in PubMed, 106 citations in OpenAlex.
- Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Review
- GAMI-CRM: Using de novo motif inference to detect cis-regulatory modules.Proceedings of the ... Congress on Evolutionary Computation. Congress on Evolutionary Computation · 2014Article
- 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
- Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction.Scientifica · 2012Review
- Article
- Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns.BMC bioinformatics · 2011Article
- Flanking region sequence information to refine microRNA target predictions.Journal of biosciences · 2010Article
- Genome-wide discovery of human heart enhancers.Genome research · 2010Article
- Transcription factor site dependencies in human, mouse and rat genomes.BMC bioinformatics · 2009Article
- Identifying regulatory elements in eukaryotic genomes.Briefings in functional genomics & proteomics · 2009Review
- DISCOVER: a feature-based discriminative method for motif search in complex genomes.Bioinformatics (Oxford, England) · 2009Article
- Integrating sequence, evolution and functional genomics in regulatory genomics.Genome biology · 2009Review
- Conservation and implications of eukaryote transcriptional regulatory regions across multiple species.BMC genomics · 2008Article
- Ab initio identification of functionally interacting pairs of cis-regulatory elements.Genome research · 2008Article
- Identification of the sensory neuron specific regulatory region for the mouse gene encoding the voltage-gated sodium channel NaV1.8.Journal of neurochemistry · 2008Article
- Extracting sequence features to predict protein-DNA interactions: a comparative study.Nucleic acids research · 2008Article
- DiRE: identifying distant regulatory elements of co-expressed genes.Nucleic acids research · 2008Article
- Measuring global credibility with application to local sequence alignment.PLoS computational biology · 2008Article
- ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?Genome biology · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitute cis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling, which locates, de novo, the cis features of these CRMs, their component TFBSs, and the properties of their spatial distribution. The algorithm finds 69% of experimentally reported TFBSs and 85% of the CRMs in a reference data set of regions upstream of genes differentially expressed in skeletal muscle cells. A discriminant procedure based on the output of the model specifically discriminated regulatory sequences in muscle-specific genes in an independent test set. Application of the method to the analysis of 2710 10-kb fragments upstream of annotated human genes identified 17 novel candidate modules with a false discovery rate </=0.05, demonstrating the applicability of the method to genome-scale data.
Indexed as
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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.