ArticleDevelopmental cell2009
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse.
Article in Developmental cell, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Article
- Mechanisms of transcriptional regulation inProceedings. Biological sciences · 2024Article
- Cell-type-directed design of synthetic enhancers.Nature · 2024Article
- Article
- Article
- Mechanisms of transcriptional regulation inbioRxiv : the preprint server for biology · 2023Article
- A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait.PLoS genetics · 2023Article
- Review
- Identification of new Anopheles gambiae transcriptional enhancers using a cross-species prediction approach.Insect molecular biology · 2021Article
- Annotating the Insect Regulatory Genome.Insects · 2021Review
- Transcriptional Enhancers inGenetics · 2020Review
- Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster.Nucleic acids research · 2019Article
- Computational enhancer prediction: evaluation and improvements.BMC bioinformatics · 2019Article
- REDfly: the transcriptional regulatory element database for Drosophila.Nucleic acids research · 2019Article
- CRM Discovery Beyond Model Insects.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Enhancer identification and activity evaluation in the red flour beetle,Development (Cambridge, England) · 2018Article
- Perspectives on Gene Regulatory Network Evolution.Trends in genetics : TIG · 2017Review
- A novel method for predicting activity of cis-regulatory modules, based on a diverse training set.Bioinformatics (Oxford, England) · 2017Article
- Genome-wide measurement of spatial expression in patterning mutants ofF1000Research · 2017Article
- Redeployment of a conserved gene regulatory network during Aedes aegypti development.Developmental biology · 2016Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
We present new approaches to cis-regulatory module (CRM) discovery in the common scenario where relevant transcription factors and/or motifs are unknown. Beginning with a small list of CRMs mediating a common gene expression pattern, we search genome-wide for CRMs with similar functionality, using new statistical scores and without requiring known motifs or accurate motif discovery. We cross-validate our predictions on 31 regulatory networks in Drosophila and through correlations with gene expression data. Five predicted modules tested using an in vivo reporter gene assay all show tissue-specific regulatory activity. We also demonstrate our methods' ability to predict mammalian tissue-specific enhancers. Finally, we predict human CRMs that regulate early blood and cardiovascular development. In vivo transgenic mouse analysis of two predicted CRMs demonstrates that both have appropriate enhancer activity. Overall, 7/7 predictions were validated successfully in vivo, demonstrating the effectiveness of our approach for insect and mammalian genomes.
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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.