ArticlePLoS computational biology2010
Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 38 citations in OpenAlex.
- TransPilot: mining key transcription factors by correlating binding sites with differentially expressed genes.Bioinformatics advances · 2026Article
- A transcriptomic atlas of acute stress response to low pH in multipleMicrobiology spectrum · 2024Article
- Predicting the impact of sequence motifs on gene regulation using single-cell data.Genome biology · 2023Article
- Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics.PLoS computational biology · 2022Article
- Article
- Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution.Nature communications · 2018Article
- Diet and endocrine effects on behavioral maturation-related gene expression in the pars intercerebralis of the honey bee brain.The Journal of experimental biology · 2015Article
- Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism.Nucleic acids research · 2015Article
- Bidirectional promoters of insects: genome-wide comparison, evolutionary implication and influence on gene expression.Journal of molecular biology · 2015Article
- Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions.BMC genomics · 2014Article
- Core and region-enriched networks of behaviorally regulated genes and the singing genome.Science (New York, N.Y.) · 2014Article
- Motif enrichment tool.Nucleic acids research · 2014Article
- Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes.PLoS genetics · 2014Article
- Causes and consequences of genetic background effects illuminated by integrative genomic analysis.Genetics · 2014Article
- Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization.Genome biology · 2013Article
- Spatial promoter recognition signatures may enhance transcription factor specificity in yeast.PloS one · 2013Article
- i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.Nucleic acids research · 2012Article
- Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Automatic annotation of spatial expression patterns via sparse Bayesian factor models.PLoS computational biology · 2011Article
- Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor.Genome biology and evolution · 2011Article
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Authors and funding
11 authors at 5 institutions in 3 countries.
Funding
Abstract
We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif-function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations.
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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.