ArticleGenome biology2012
Computational discovery of regulatory elements in a continuous expression space.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.PLoS computational biology · 2021Article
- Statistical modelling of bacterial promoter sequences for regulatory motif discovery with the help of transcriptome data: application toJournal of the Royal Society, Interface · 2020Article
- Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA.BMC genomics · 2015Article
- Construction and validation of a gene co-expression network in grapevine (Vitis vinifera. L.).Horticulture research · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Approaches for regulatory element discovery from gene expression data usually rely on clustering algorithms to partition the data into clusters of co-expressed genes. Gene regulatory sequences are then mined to find overrepresented motifs in each cluster. However, this ad hoc partition rarely fits the biological reality. We propose a novel method called RED2 that avoids data clustering by estimating motif densities locally around each gene. We show that RED2 detects numerous motifs not detected by clustering-based approaches, and that most of these correspond to characterized motifs. RED2 can be accessed online through a user-friendly interface.
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Registered trials
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