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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2013
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v29_n22_p2852_Rohr http://hdl.handle.net/20.500.12110/paper_13674803_v29_n22_p2852_Rohr |
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paper:paper_13674803_v29_n22_p2852_Rohr2023-06-08T16:12:10Z INSECT: IN-silico SEarch for Co-occurring Transcription factors 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. 2013 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v29_n22_p2852_Rohr 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 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. |
| 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 |
| publishDate |
2013 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v29_n22_p2852_Rohr http://hdl.handle.net/20.500.12110/paper_13674803_v29_n22_p2852_Rohr |
| _version_ |
1768543527483998208 |