ArticleNucleic acids research2010
Modeling tissue-specific structural patterns in human and mouse promoters.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it, 41 citations in OpenAlex.
- GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements.Nature communications · 2022Pooled it
- TiSMeD: A tissue-specific methylation and expression database for biomarker and translational applications.Molecular therapy. Nucleic acids · 2026Article
- The Genetic Landscape of Familial Pulmonary Fibrosis.American journal of respiratory and critical care medicine · 2023Article
- Trichome-Specific Analysis and Weighted Gene Co-Expression Correlation Network Analysis (WGCNA) Reveal Potential Regulation Mechanism of Artemisinin Biosynthesis inInternational journal of molecular sciences · 2023Article
- Robust and rigorous identification of tissue-specific genes by statistically extending tau score.BioData mining · 2022Article
- SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups.BMC bioinformatics · 2020Article
- A benchmark of gene expression tissue-specificity metrics.Briefings in bioinformatics · 2017Article
- Modeling thePeerJ · 2017Article
- Rosa26 locus supports tissue-specific promoter driving transgene expression specifically in pig.PloS one · 2014Article
- A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster.PloS one · 2014Article
- A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription.BMC genomics · 2012Article
- GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group.BMC genomics · 2012Article
- Distance and helical phase dependence of synergistic transcription activation in cis-regulatory module.PloS one · 2012Article
- Functional characterization of liver enhancers that regulate drug-associated transporters.Clinical pharmacology and therapeutics · 2011Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sets of genes expressed in the same tissue are believed to be under the regulation of a similar set of transcription factors, and can thus be assumed to contain similar structural patterns in their regulatory regions. Here we present a study of the structural patterns in promoters of genes expressed specifically in 26 human and 34 mouse tissues. For each tissue we constructed promoter structure models, taking into account presences of motifs, their positioning to the transcription start site, and pairwise positioning of motifs. We found that 35 out of 60 models (58%) were able to distinguish positive test promoter sequences from control promoter sequences with statistical significance. Models with high performance include those for liver, skeletal muscle, kidney and tongue. Many of the important structural patterns in these models involve transcription factors of known importance in the tissues in question and structural patterns tend to be conserved between human and mouse. In addition to that, promoter models for related tissues tend to have high inter-tissue performance, indicating that their promoters share common structural patterns. Together, these results illustrate the validity of our models, but also indicate that the promoter structures for some tissues are easier to model than those of others.
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