Cristian O Rohr1, R Gonzalo Parra, Patricio Yankilevich, Carolina Perez-Castro. 1. Instituto de Ecología, Genética y Evolución (IEGEBA)-CONICET, Protein Physiology Laboratory, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, C1428EGA, Buenos Aires, Argentina and Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) -CONICET- Partner Institute of the Max Planck Society, C1425FQD, Buenos Aires, Argentina.
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. availability and implementation: INSECT is freely available as a web server at http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT .
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. availability and implementation: INSECT is freely available as a web server at http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT .
Authors: Nazarena E Ferreyra Solari; Fiorella S Belforte; Lucía Canedo; Guillermo A Videla-Richardson; Joaquín M Espinosa; Mario Rossi; Eva Serna; Miguel A Riudavets; Horacio Martinetto; Gustavo Sevlever; Carolina Perez-Castro Journal: Cancer Res Date: 2016-07-12 Impact factor: 12.701
Authors: Carmen Navarro; Francisco J Lopez; Carlos Cano; Fernando Garcia-Alcalde; Armando Blanco Journal: PLoS One Date: 2014-09-30 Impact factor: 3.240