ArticleGenome biology2008
ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Trial
- Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network.International journal of molecular sciences · 2019Article
- Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia.Genome biology and evolution · 2017Article
- Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells.Frontiers in genetics · 2016Review
- Identification and computational analysis of gene regulatory elements.Cold Spring Harbor protocols · 2015Review
- iRegulon: from a gene list to a gene regulatory network using large motif and track collections.PLoS computational biology · 2014Article
- Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana.BMC systems biology · 2013Article
- Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome.Genesis (New York, N.Y. : 2000) · 2013Review
- Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions.Genome research · 2013Article
- i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.Nucleic acids research · 2012Article
- Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection.Nucleic acids research · 2012Article
- Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors.Genome biology · 2011Article
- Selective genomic targeting by FRA-2/FOSL2 transcription factor: regulation of the Rgs4 gene is mediated by a variant activator protein 1 (AP-1) promoter sequence/CREB-binding protein (CBP) mechanism.The Journal of biological chemistry · 2011Article
- Assessing computational methods of cis-regulatory module prediction.PLoS computational biology · 2010Article
- Article
- Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification.PLoS biology · 2010Article
- Genome-wide prediction of transcription factor binding sites using an integrated model.Genome biology · 2010Article
- Modeling tissue-specific structural patterns in human and mouse promoters.Nucleic acids research · 2010Article
- Systems biology of embryogenesis.Reproduction, fertility, and development · 2010Article
- Identifying regulatory elements in eukaryotic genomes.Briefings in functional genomics & proteomics · 2009Review
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present ModuleMiner, a novel algorithm for computationally detecting cis-regulatory modules (CRMs) in a set of co-expressed genes. ModuleMiner outperforms other methods for CRM detection on benchmark data, and successfully detects CRMs in tissue-specific microarray clusters and in embryonic development gene sets. Interestingly, CRM predictions for differentiated tissues exhibit strong enrichment close to the transcription start site, whereas CRM predictions for embryonic development gene sets are depleted in this region.
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