ArticleBMC bioinformatics2005
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers, 1 of them a synthesis that pooled it.
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Who cites it
107 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- 1,25DOncotarget · 2017Article
- A microRNA signature of response to erlotinib is descriptive of TGFβ behaviour in NSCLC.Scientific reports · 2017Article
- SNPs in microRNA target sites and their potential role in human disease.Open biology · 2017Review
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- The pseudokinase MLKL mediates programmed hepatocellular necrosis independently of RIPK3 during hepatitis.The Journal of clinical investigation · 2016Article
- Nuclear respiratory factor 2 induces SIRT3 expression.Aging cell · 2015Article
- Inhibition of ERRα suppresses epithelial mesenchymal transition of triple negative breast cancer cells by directly targeting fibronectin.Oncotarget · 2015Article
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- Mechanisms of interferon-γ production by neutrophils and its function during Streptococcus pneumoniae pneumonia.American journal of respiratory cell and molecular biology · 2015Article
- Chronic morphine-induced microRNA-124 promotes microglial immunosuppression by modulating P65 and TRAF6.Journal of immunology (Baltimore, Md. : 1950) · 2015Article
- Enhanced transgene expression from recombinant single-stranded D-sequence-substituted adeno-associated virus vectors in human cell lines in vitro and in murine hepatocytes in vivo.Journal of virology · 2015Article
- Sox17 inhibits hepatocellular carcinoma progression by downregulation of KIF14 expression.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2014Article
47 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundCis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity.
resultsWe describe the implementation of a search method for putative transcription factor binding sites (TFBSs) based on hidden Markov models built from alignments of known sites. We built 1,079 models of TFBSs using experimentally determined sequence alignments of sites provided by the TRANSFAC and JASPAR databases and used them to scan sequences of the human, mouse, fly, worm and yeast genomes. In several cases tested the method identified correctly experimentally characterized sites, with better specificity and sensitivity than other similar computational methods. Moreover, a large-scale comparison using synthetic data showed that in the majority of cases our method performed significantly better than a nucleotide weight matrix-based method.
conclusionThe search engine, available at http://mapper.chip.org, allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, fly, worm and yeast genomes. In addition it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. Due to its extensive database of models, powerful search engine and flexible interface, MAPPER represents an effective resource for the large-scale computational analysis of transcriptional regulation.
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