INSECT: IN-silico SEarch for Co-occurring Transcription factors
| Autor: | Cristian Oscar Rohr, R. Gonzalo Parra, Carolina Perez-Castro, Patricio Yankilevich |
|---|---|
| Rok vydání: | 2013 |
| Předmět: |
Statistics and Probability
Chromatin Immunoprecipitation Web server Bioinformatics Sequence analysis In silico Computational biology Biology computer.software_genre Biochemistry Transcription (biology) Transcriptional regulation Computer Simulation Regulatory Elements Transcriptional Molecular Biology Transcription factor Gene Genetics Internet Binding Sites fungi Sequence Analysis DNA Computer Science Applications Motif finding Computational Mathematics Computational Theory and Mathematics Ciencias de la Computación e Información Sequence Analysis Ciencias de la Información y Bioinformática Chromatin immunoprecipitation computer Algorithms Software CIENCIAS NATURALES Y EXACTAS Transcription Factors |
| Zdroj: | Bioinformatics. 29:2852-2858 |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/btt506 |
| Popis: | P. Yankilevich & C Perez Castro both corresponding authors. Motivation: Transcriptional regulation occurs through the concerted actions of multiple transcription factors (TFs) that bind cooperatively to cis-regulatory modules (CRMs) of genes. These CRMs usually contain a variable number of transcription factor-binding sites(TFBSs) involved in related cellular and physiological processes. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been effective in detecting TFBSs and nucleosome location in order to identify potential CRMs in genome-wide studies. Although several attempts were previously reported to predict the potential binding of TFs at TFBSs within CRMs by comparing different ChIP-seq data, these have been hampered by excessive background, usually emerging as a consequence of experimental conditions. To understand these complex regulatory circuits, it would be helpful to have reliable and updated user-friendly tools to assist in the identification of TFBSs and CRMs for genes of interest. Results: Here we present INSECT (IN-silico SEarch for Co-occurring Transcription factors), a novel web server for identifying potential TFBSs and CRMs in gene sequences. By combining several strategies, INSECT provides flexible analysis of multiple co-occurring TF binding sites, by applying differing search schemes and restriction parameters. Availability: INSECT is freely available as a web server at http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT Fil: Rohr, Cristian Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina Fil: Gonzalo Parra, R.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina Fil: Yankilevich, Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación en Biomedicina de Buenos Aires; Argentina Fil: Perez Castro, Carolina Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación en Biomedicina de Buenos Aires; Argentina |
| Databáze: | OpenAIRE |
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