ArticleNature methods2008
Systematic identification of mammalian regulatory motifs' target genes and functions.
Article in Nature methods, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Inferring gene-regulatory networks using epigenomic priors.iScience · 2026Article
- Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics.PLoS computational biology · 2022Article
- Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.Molecular cell · 2020Article
- Identification and Characterization of Cis-Regulatory Elements for Photoreceptor-Type-Specific Transcription in ZebraFish.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Computational Biology Solutions to Identify Enhancers-target Gene Pairs.Computational and structural biotechnology journal · 2019Review
- Recurrent Neural Network for Predicting Transcription Factor Binding Sites.Scientific reports · 2018Article
- Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation.BMC genomics · 2018Article
- Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia.Genome biology and evolution · 2017Article
- Article
- Imputation for transcription factor binding predictions based on deep learning.PLoS computational biology · 2017Article
- Frapid: achieving full automation of FRAP for chemical probe validation.Biomedical optics express · 2016Article
- Two Forkhead transcription factors regulate cardiac progenitor specification by controlling the expression of receptors of the fibroblast growth factor and Wnt signaling pathways.Development (Cambridge, England) · 2016Article
- Control of lysosomal biogenesis and Notch-dependent tissue patterning by components of the TFEB-V-ATPase axis in Drosophila melanogaster.Autophagy · 2016Article
- Nuclear respiratory factor 2 induces SIRT3 expression.Aging cell · 2015Article
- MicroRNA214 Is Associated With Progression of Ulcerative Colitis, and Inhibition Reduces Development of Colitis and Colitis-Associated Cancer in Mice.Gastroenterology · 2015Article
- Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models.Molecular biology and evolution · 2015Article
- Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.Genome research · 2014Article
- iRegulon: from a gene list to a gene regulatory network using large motif and track collections.PLoS computational biology · 2014Article
- Transcriptional enhancers: from properties to genome-wide predictions.Nature reviews. Genetics · 2014Review
- Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification.Development (Cambridge, England) · 2014Article
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6 authors.
Funding
Abstract
We developed an algorithm, Lever, that systematically maps metazoan DNA regulatory motifs or motif combinations to sets of genes. Lever assesses whether the motifs are enriched in cis-regulatory modules (CRMs), predicted by our PhylCRM algorithm, in the noncoding sequences surrounding the genes. Lever analysis allows unbiased inference of functional annotations to regulatory motifs and candidate CRMs. We used human myogenic differentiation as a model system to statistically assess greater than 25,000 pairings of gene sets and motifs or motif combinations. We assigned functional annotations to candidate regulatory motifs predicted previously and identified gene sets that are likely to be co-regulated via shared regulatory motifs. Lever allows moving beyond the identification of putative regulatory motifs in mammalian genomes, toward understanding their biological roles. This approach is general and can be applied readily to any cell type, gene expression pattern or organism of interest.
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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.