INSECT: IN-silico SEarch for Co-occurring Transcription factors

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 cellul...

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Autores principales:	Rohr, C.O., Parra, R.G., Yankilevich, P., Perez-Castro, C.
Formato:	JOUR
Materias:	transcription factor algorithm binding site chromatin immunoprecipitation computer program computer simulation DNA sequence Internet metabolism procedures regulatory sequence article methodology Algorithms Binding Sites Chromatin Immunoprecipitation Computer Simulation Regulatory Elements, Transcriptional Sequence Analysis, DNA Software Transcription Factors
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_13674803_v29_n22_p2852_Rohr
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_13674803_v29_n22_p2852_Rohr
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spelling	todo:paper_13674803_v29_n22_p2852_Rohr2023-10-03T16:11:32Z INSECT: IN-silico SEarch for Co-occurring Transcription factors Rohr, C.O. Parra, R.G. Yankilevich, P. Perez-Castro, C. 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 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. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_13674803_v29_n22_p2852_Rohr
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	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
spellingShingle	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 Rohr, C.O. Parra, R.G. Yankilevich, P. Perez-Castro, C. INSECT: IN-silico SEarch for Co-occurring Transcription factors
topic_facet	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
description	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.
format	JOUR
author	Rohr, C.O. Parra, R.G. Yankilevich, P. Perez-Castro, C.
author_facet	Rohr, C.O. Parra, R.G. Yankilevich, P. Perez-Castro, C.
author_sort	Rohr, C.O.
title	INSECT: IN-silico SEarch for Co-occurring Transcription factors
title_short	INSECT: IN-silico SEarch for Co-occurring Transcription factors
title_full	INSECT: IN-silico SEarch for Co-occurring Transcription factors
title_fullStr	INSECT: IN-silico SEarch for Co-occurring Transcription factors
title_full_unstemmed	INSECT: IN-silico SEarch for Co-occurring Transcription factors
title_sort	insect: in-silico search for co-occurring transcription factors
url	http://hdl.handle.net/20.500.12110/paper_13674803_v29_n22_p2852_Rohr
work_keys_str_mv	AT rohrco insectinsilicosearchforcooccurringtranscriptionfactors AT parrarg insectinsilicosearchforcooccurringtranscriptionfactors AT yankilevichp insectinsilicosearchforcooccurringtranscriptionfactors AT perezcastroc insectinsilicosearchforcooccurringtranscriptionfactors
_version_	1807324371994279936

INSECT: IN-silico SEarch for Co-occurring Transcription factors

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