{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T14:10:51Z","timestamp":1767276651124},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability and implementation: INSECT is freely available as a web server at http:\/\/bioinformatics.ibioba-mpsp-conicet.gov.ar\/INSECT<\/jats:p>\n               <jats:p>Contact: \u00a0cperezcastro@ibioba-mpsp-conicet.gov.ar or pyankilevich@ibioba-mpsp-conicet.gov.ar<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt506","type":"journal-article","created":{"date-parts":[[2013,9,6]],"date-time":"2013-09-06T00:39:36Z","timestamp":1378427976000},"page":"2852-2858","source":"Crossref","is-referenced-by-count":13,"title":["INSECT: IN-silico SEarch for Co-occurring Transcription factors"],"prefix":"10.1093","volume":"29","author":[{"given":"Cristian O.","family":"Rohr","sequence":"first","affiliation":[{"name":"1 Instituto de Ecolog\u00eda, Gen\u00e9tica y Evoluci\u00f3n (IEGEBA)-CONICET, 2Protein Physiology Laboratory, Departamento de Qu\u00edmica Biol\u00f3gica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, C1428EGA, Buenos Aires, Argentina and 3Instituto de Investigaci\u00f3n en Biomedicina de Buenos Aires (IBioBA) -CONICET- Partner Institute of the Max Planck Society, C1425FQD, Buenos Aires, Argentina"}]},{"given":"R. Gonzalo","family":"Parra","sequence":"additional","affiliation":[{"name":"1 Instituto de Ecolog\u00eda, Gen\u00e9tica y Evoluci\u00f3n (IEGEBA)-CONICET, 2Protein Physiology Laboratory, Departamento de Qu\u00edmica Biol\u00f3gica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, C1428EGA, Buenos Aires, Argentina and 3Instituto de Investigaci\u00f3n en Biomedicina de Buenos Aires (IBioBA) -CONICET- Partner Institute of the Max Planck Society, C1425FQD, Buenos Aires, Argentina"}]},{"given":"Patricio","family":"Yankilevich","sequence":"additional","affiliation":[{"name":"1 Instituto de Ecolog\u00eda, Gen\u00e9tica y Evoluci\u00f3n (IEGEBA)-CONICET, 2Protein Physiology Laboratory, Departamento de Qu\u00edmica Biol\u00f3gica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, C1428EGA, Buenos Aires, Argentina and 3Instituto de Investigaci\u00f3n en Biomedicina de Buenos Aires (IBioBA) -CONICET- Partner Institute of the Max Planck Society, C1425FQD, Buenos Aires, Argentina"}]},{"given":"Carolina","family":"Perez-Castro","sequence":"additional","affiliation":[{"name":"1 Instituto de Ecolog\u00eda, Gen\u00e9tica y Evoluci\u00f3n (IEGEBA)-CONICET, 2Protein Physiology Laboratory, Departamento de Qu\u00edmica Biol\u00f3gica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, C1428EGA, Buenos Aires, Argentina and 3Instituto de Investigaci\u00f3n en Biomedicina de Buenos Aires (IBioBA) -CONICET- Partner Institute of the Max Planck Society, C1425FQD, Buenos Aires, Argentina"}]}],"member":"286","published-online":{"date-parts":[[2013,9,4]]},"reference":[{"key":"2023012810470745200_btt506-B1","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1242\/dev.124.10.1851","article-title":"The hardwiring of development: organization and function of genomic regulatory systems","volume":"124","author":"Arnone","year":"1997","journal-title":"Development"},{"key":"2023012810470745200_btt506-B2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. 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