ArticleGenome research2005
De novo discovery of a tissue-specific gene regulatory module in a chordate.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
- NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- regCNN: identifyingComputational and structural biotechnology journal · 2022Article
- Review
- Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.Genome research · 2016Article
- Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.PLoS genetics · 2015Article
- Initial deployment of the cardiogenic gene regulatory network in the basal chordate, Ciona intestinalis.Developmental biology · 2012Article
- Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs.BMC bioinformatics · 2012Article
- Assessing computational methods of cis-regulatory module prediction.PLoS computational biology · 2010Article
- Sequence features that drive human promoter function and tissue specificity.Genome research · 2010Article
- Markov chain-based promoter structure modeling for tissue-specific expression pattern prediction.DNA research : an international journal for rapid publication of reports on genes and genomes · 2008Article
- Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs.Genome biology · 2008Article
- Muscle development in Ciona intestinalis requires the b-HLH myogenic regulatory factor gene Ci-MRF.Developmental biology · 2007Article
- Statistical significance of cis-regulatory modules.BMC bioinformatics · 2007Article
- Experimental validation of predicted mammalian erythroid cis-regulatory modules.Genome research · 2006Article
- Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.BMC bioinformatics · 2006Article
- Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics.Genome biology · 2006Article
- Surfing with the tunicates into the post-genome era.Genes & development · 2005Review
- Identifying transcriptional cis-regulatory modules in animal genomes.Wiley interdisciplinary reviews. Developmental biologyReview
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We engage the experimental and computational challenges of de novo regulatory module discovery in a complex and largely unstudied metazoan genome. Our analysis is based on the comprehensive characterization of regulatory elements of 20 muscle genes in the chordate, Ciona savignyi. Three independent types of data we generate contribute to the characterization of a muscle-specific regulatory module: (1) Positive elements (PEs), short sequences sufficient for strong muscle expression that are identified in a high-resolution in vivo analysis; (2) CisModules (CMs), candidate regulatory modules defined by clusters of overrepresented motifs predicted de novo; and (3) Conserved elements (CEs), short noncoding sequences of strong conservation between C. savignyi and C. intestinalis. We estimate the accuracy of the computational predictions by an analysis of the intersection of these data. As final biological validation of the discovered muscle regulatory module, we implement a novel algorithm to search the genome for instances of the module and identify seven novel enhancers.
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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.