ReviewNature reviews. Genetics2012
Genomic approaches towards finding cis-regulatory modules in animals.
Review in Nature reviews. Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
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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.
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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
133 citing papers in PubMed.
- A putativebioRxiv : the preprint server for biology · 2026Article
- UnlockingNAR genomics and bioinformatics · 2026Article
- NovelbioRxiv : the preprint server for biology · 2026Article
- Gene-centered identification of cis-regulatory islands highlights regulatory landscapes complementary to motif-centric approaches.BMC genomics · 2026Article
- CRM-TI: an enhanced pipeline for computationally assigning the target genes of cis-regulatory modules by considering comprehensive long-range regulation mechanisms.BioData mining · 2026Article
- A scalable computational framework for predicting gene expression from candidateGenome research · 2026Article
- RNA-programmable cell-type monitoring and manipulation in the human cortex with CellREADR.Cell reports · 2025Article
- Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.BMC biology · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Unveiling Novel Mechanism of CIDEB in Fatty Acid Synthesis Through ChIP-Seq and Functional Analysis in Dairy Goat.International journal of molecular sciences · 2024Article
- Article
- Notch-Dependent Expression of theGenes · 2024Article
- Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.Nature communications · 2024Article
- DMLS: an automated pipeline to extract the Drosophila modular transcription regulators and targets from massive literature articles.Database : the journal of biological databases and curation · 2024Article
- Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells.Nature genetics · 2024Article
- Towards a comprehensive regulatory map of Mammalian Genomes.Research square · 2023Article
- Machine-guided design of synthetic cell type-specificbioRxiv : the preprint server for biology · 2023Article
- Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening.Nature biotechnology · 2023Article
- Detecting clusters of transcription factors based on a nonhomogeneous poisson process model.BMC bioinformatics · 2022Article
- Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence.Nature communications · 2022Article
73 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
2 authors.
Funding
Abstract
Differential gene expression is the fundamental mechanism underlying animal development and cell differentiation. However, it is a challenge to identify comprehensively and accurately the DNA sequences that are required to regulate gene expression: namely, cis-regulatory modules (CRMs). Three major features, either singly or in combination, are used to predict CRMs: clusters of transcription factor binding site motifs, non-coding DNA that is under evolutionary constraint and biochemical marks associated with CRMs, such as histone modifications and protein occupancy. The validation rates for predictions indicate that identifying diagnostic biochemical marks is the most reliable method, and understanding is enhanced by the analysis of motifs and conservation patterns within those predicted CRMs.
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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.