ArticleGenome research2007
Predicting tissue-specific enhancers in the human genome.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 1 of them a synthesis that pooled it.
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Who cites it
89 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation.BMC genomics · 2009Pooled it
- The combinatorial binding syntax of transcription factors in forebrain-specific enhancers.Biology open · 2025Article
- HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.BMC genomics · 2024Article
- DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements.Computational and structural biotechnology journal · 2024Article
- HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.bioRxiv : the preprint server for biology · 2024Article
- Hemizygous Moesin (MSN) Gene Deletion in an Adult With Chronic Neutropenia.Case reports in immunology · 2024Article
- RNA editing: Expanding the potential of RNA therapeutics.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Review
- Deciphering the multi-scale, quantitative cis-regulatory code.Molecular cell · 2023Review
- Promoter/enhancer-based controllability of regulatory networks.Scientific reports · 2022Article
- Enhancers with tissue-specific activity are enriched in intronic regions.Genome research · 2021Article
- Nuclear Respiratory Factor 1 (NRF1) Transcriptional Activity-Driven Gene Signature Association with Severity of Astrocytoma and Poor Prognosis of Glioblastoma.Molecular neurobiology · 2020Article
- Dissecting myogenin-mediated retinoid X receptor signaling in myogenic differentiation.Communications biology · 2020Article
- Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers.Bioinformatics (Oxford, England) · 2019Article
- Intronic CNVs and gene expression variation in human populations.PLoS genetics · 2019Article
- Dichotomy in redundant enhancers points to presence of initiators of gene regulation.BMC genomics · 2018Article
- Dual Roles for Ikaros in Regulation of Macrophage Chromatin State and Inflammatory Gene Expression.Journal of immunology (Baltimore, Md. : 1950) · 2018Article
- Genome-wide Identification and Characterization of Enhancers Across 10 Human Tissues.International journal of biological sciences · 2018Article
- Gene networks activated by specific patterns of action potentials in dorsal root ganglia neurons.Scientific reports · 2017Article
- In Vivo Hepatic Enhancer Elements in the Human ABCG2 Locus.Drug metabolism and disposition: the biological fate of chemicals · 2017Article
- Estrogenic Endocrine Disrupting Chemicals Influencing NRF1 Regulated Gene Networks in the Development of Complex Human Brain Diseases.International journal of molecular sciences · 2016Review
29 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Determining how transcriptional regulatory signals are encoded in vertebrate genomes is essential for understanding the origins of multicellular complexity; yet the genetic code of vertebrate gene regulation remains poorly understood. In an attempt to elucidate this code, we synergistically combined genome-wide gene-expression profiling, vertebrate genome comparisons, and transcription factor binding-site analysis to define sequence signatures characteristic of candidate tissue-specific enhancers in the human genome. We applied this strategy to microarray-based gene expression profiles from 79 human tissues and identified 7187 candidate enhancers that defined their flanking gene expression, the majority of which were located outside of known promoters. We cross-validated this method for its ability to de novo predict tissue-specific gene expression and confirmed its reliability in 57 of the 79 available human tissues, with an average precision in enhancer recognition ranging from 32% to 63% and a sensitivity of 47%. We used the sequence signatures identified by this approach to successfully assign tissue-specific predictions to approximately 328,000 human-mouse conserved noncoding elements in the human genome. By overlapping these genome-wide predictions with a data set of enhancers validated in vivo, in transgenic mice, we were able to confirm our results with a 28% sensitivity and 50% precision. These results indicate the power of combining complementary genomic data sets as an initial computational foray into a global view of tissue-specific gene regulation in vertebrates.
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