ArticleBMC bioinformatics2006
Predicting transcription factor binding sites using local over-representation and comparative genomics.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Perturbations of the Proteome and of Secreted Metabolites in Primary Astrocytes from the hSOD1(G93A) ALS Mouse Model.International journal of molecular sciences · 2021Article
- ETS1, ELK1, and ETV4 Transcription Factors Regulate Angiopoietin-1 Signaling and the Angiogenic Response in Endothelial Cells.Frontiers in physiology · 2021Article
- Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs.BMC genetics · 2017Article
- The Human Blood Metabolome-Transcriptome Interface.PLoS genetics · 2015Article
- In silico discovery of novel transcription factors regulated by mTOR-pathway activities.Frontiers in cell and developmental biology · 2014Article
- Selection of higher order regression models in the analysis of multi-factorial transcription data.PloS one · 2014Article
- A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.BMC bioinformatics · 2013Article
- oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.G3 (Bethesda, Md.) · 2012Article
- A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells.Genome research · 2012Article
- Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection.PLoS pathogens · 2012Article
- An information transmission model for transcription factor binding at regulatory DNA sites.Theoretical biology & medical modelling · 2012Article
- Genome-wide repression of NF-κB target genes by transcription factor MIBP1 and its modulation by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase.The Journal of biological chemistry · 2012Article
- MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences.BMC systems biology · 2012Article
- p38MAPK is a novel DNA damage response-independent regulator of the senescence-associated secretory phenotype.The EMBO journal · 2011Article
- Article
- Methods for transcriptomic analyses of the porcine host immune response: application to Salmonella infection using microarrays.Veterinary immunology and immunopathology · 2010Review
- Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.PloS one · 2010Article
- TFM-Explorer: mining cis-regulatory regions in genomes.Nucleic acids research · 2010Article
- Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data.Nucleic acids research · 2010Article
- TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.BMC genomics · 2010Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIdentifying cis-regulatory elements is crucial to understanding gene expression, which highlights the importance of the computational detection of overrepresented transcription factor binding sites (TFBSs) in coexpressed or coregulated genes. However, this is a challenging problem, especially when considering higher eukaryotic organisms.
resultsWe have developed a method, named TFM-Explorer, that searches for locally overrepresented TFBSs in a set of coregulated genes, which are modeled by profiles provided by a database of position weight matrices. The novelty of the method is that it takes advantage of spatial conservation in the sequence and supports multiple species. The efficiency of the underlying algorithm and its robustness to noise allow weak regulatory signals to be detected in large heterogeneous data sets.
conclusionTFM-Explorer provides an efficient way to predict TFBS overrepresentation in related sequences. Promising results were obtained in a variety of examples in human, mouse, and rat genomes. The software is publicly available at http://bioinfo.lifl.fr/TFM-Explorer.
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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.