ArticleBMC bioinformatics2011
MotifMap: integrative genome-wide maps of regulatory motif sites for model species.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers, 2 of them syntheses that pooled it.
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
114 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity.Communications biology · 2023Pooled it
- Genome-wide meta-analysis of SNP-by9-ACEI/ARB and SNP-by-thiazide diuretic and effect on serum potassium in cohorts of European and African ancestry.The pharmacogenomics journal · 2019Pooled it
- UnlockingNAR genomics and bioinformatics · 2026Article
- The impact of sex on the immune system explored at the single-cell level.American journal of human genetics · 2026Article
- Programming Next-Generation Synthetic Biosensors by Genetic Circuit Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Chronic intermittent hypoxia reshapes circadian metabolic architecture in a model of sleep apnea.Science advances · 2026Article
- Exploring potential transcription factors and their regulatory relationships based on asymmetric covariance natural vector encoding method and machine learning algorithms.Briefings in bioinformatics · 2026Article
- Defective vascular smooth muscle cell tafazzin impairs mitochondrial function and promotes atherosclerosis in preclinical models.Nature communications · 2025Article
- Activating NEDD4L suppresses EGFR-driven lung adenocarcinoma growth via facilitating EGFR proteasomal degradation.Journal of experimental & clinical cancer research : CR · 2025Article
- Multifaceted regulation of the HOX cluster and its implications in oral cancer.Clinical epigenetics · 2025Article
- MAFin: motif detection in multiple alignment files.Bioinformatics (Oxford, England) · 2025Article
- Exploring Genetic Influences on Equine Meat Quality: A Bioinformatics Approach.Foods (Basel, Switzerland) · 2025Article
- TFTG: A comprehensive database for human transcription factors and their targets.Computational and structural biotechnology journal · 2024Article
- An unexpected role of neurite outgrowth inhibitor A as regulator of tooth enamel formation.International journal of oral science · 2024Article
- Article
- XRCC2 driven homologous recombination subtypes and therapeutic targeting in lung adenocarcinoma metastasis.NPJ precision oncology · 2024Article
- Common and novel haplotype structures between different types of cancer.Cancer reports (Hoboken, N.J.) · 2024Article
- Review
- CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing.RNA (New York, N.Y.) · 2024Article
- Identification of DNA motif pairs on paired sequences based on composite heterogeneous graph.Frontiers in genetics · 2024Article
54 more citing papers are in PubMed but not listed here.
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.
Funding
Abstract
backgroundA central challenge of biology is to map and understand gene regulation on a genome-wide scale. For any given genome, only a small fraction of the regulatory elements embedded in the DNA sequence have been characterized, and there is great interest in developing computational methods to systematically map all these elements and understand their relationships. Such computational efforts, however, are significantly hindered by the overwhelming size of non-coding regions and the statistical variability and complex spatial organizations of regulatory elements and interactions. Genome-wide catalogs of regulatory elements for all model species simply do not yet exist.
resultsThe MotifMap system uses databases of transcription factor binding motifs, refined genome alignments, and a comparative genomic statistical approach to provide comprehensive maps of candidate regulatory elements encoded in the genomes of model species. The system is used to derive new genome-wide maps for yeast, fly, worm, mouse, and human. The human map contains 519,108 sites for 570 matrices with a False Discovery Rate of 0.1 or less. The new maps are assessed in several ways, for instance using high-throughput experimental ChIP-seq data and AUC statistics, providing strong evidence for their accuracy and coverage. The maps can be usefully integrated with many other kinds of omic data and are available at http://motifmap.igb.uci.edu/.
conclusionsMotifMap and its integration with other data provide a foundation for analyzing gene regulation on a genome-wide scale, and for automatically generating regulatory pathways and hypotheses. The power of this approach is demonstrated and discussed using the P53 apoptotic pathway and the Gli hedgehog pathways as examples.
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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.