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Abstract:

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 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 gene(s) 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 TFBSs, by applying differing search schemes and restriction parameters. © The Author 2013. Published by Oxford University Press. All rights reserved.

Registro:

Documento: Artículo
Título:INSECT: IN-silico SEarch for Co-occurring Transcription factors
Autor:Rohr, C.O.; Parra, R.G.; Yankilevich, P.; Perez-Castro, C.
Filiación:Instituto de Ecología, Genética y Evolución (IEGEBA)-CONICET, UBA-CONICET-IQUIBICEN, C1428EGA, Buenos Aires, Argentina
Protein Physiology Laboratory, Departamento de Química Biológica, UBA-CONICET-IQUIBICEN, C1428EGA, Buenos Aires, Argentina
Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of Max Planck Society, C1425FQD, Buenos Aires, Argentina
Palabras clave:transcription factor; transcription factor; algorithm; binding site; chromatin immunoprecipitation; computer program; computer simulation; DNA sequence; Internet; metabolism; procedures; regulatory sequence; article; DNA sequence; metabolism; methodology; Algorithms; Binding Sites; Chromatin Immunoprecipitation; Computer Simulation; Internet; Regulatory Elements, Transcriptional; Sequence Analysis, DNA; Software; Transcription Factors; Algorithms; Binding Sites; Chromatin Immunoprecipitation; Computer Simulation; Internet; Regulatory Elements, Transcriptional; Sequence Analysis, DNA; Software; Transcription Factors
Año:2013
Volumen:29
Número:22
Página de inicio:2852
Página de fin:2858
DOI: http://dx.doi.org/10.1093/bioinformatics/btt506
Título revista:Bioinformatics
Título revista abreviado:Bioinformatics
ISSN:13674803
CODEN:BOINF
CAS:Transcription Factors; Transcription Factors
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v29_n22_p2852_Rohr

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Citas:

---------- APA ----------
Rohr, C.O., Parra, R.G., Yankilevich, P. & Perez-Castro, C. (2013) . INSECT: IN-silico SEarch for Co-occurring Transcription factors. Bioinformatics, 29(22), 2852-2858.
http://dx.doi.org/10.1093/bioinformatics/btt506
---------- CHICAGO ----------
Rohr, C.O., Parra, R.G., Yankilevich, P., Perez-Castro, C. "INSECT: IN-silico SEarch for Co-occurring Transcription factors" . Bioinformatics 29, no. 22 (2013) : 2852-2858.
http://dx.doi.org/10.1093/bioinformatics/btt506
---------- MLA ----------
Rohr, C.O., Parra, R.G., Yankilevich, P., Perez-Castro, C. "INSECT: IN-silico SEarch for Co-occurring Transcription factors" . Bioinformatics, vol. 29, no. 22, 2013, pp. 2852-2858.
http://dx.doi.org/10.1093/bioinformatics/btt506
---------- VANCOUVER ----------
Rohr, C.O., Parra, R.G., Yankilevich, P., Perez-Castro, C. INSECT: IN-silico SEarch for Co-occurring Transcription factors. Bioinformatics. 2013;29(22):2852-2858.
http://dx.doi.org/10.1093/bioinformatics/btt506