Genome-wide prediction of transcription factor binding sites using an integrated model

Abstract We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory element...
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Gespeichert in:

Autor*in:	Won, Kyoung-Jae [verfasserIn] Ren, Bing Wang, Wei

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2010

Schlagwörter:	Hide Markov Model Histone Modification Histone Mark Hide Markov Model Model P300 Binding Site

Anmerkung:	© Won et al.; license BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (

Übergeordnetes Werk:	Enthalten in: Genome biology - London : BioMed Central, 2000, 11(2010), 1 vom: 22. Jan.
Übergeordnetes Werk:	volume:11 ; year:2010 ; number:1 ; day:22 ; month:01

Links:	Volltext

DOI / URN:	10.1186/gb-2010-11-1-r7

Katalog-ID:	SPR030007011

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allfields	10.1186/gb-2010-11-1-r7 doi (DE-627)SPR030007011 (SPR)gb-2010-11-1-r7-e DE-627 ger DE-627 rakwb eng Won, Kyoung-Jae verfasserin aut Genome-wide prediction of transcription factor binding sites using an integrated model 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Won et al.; license BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( Abstract We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments. Hide Markov Model (dpeaa)DE-He213 Histone Modification (dpeaa)DE-He213 Histone Mark (dpeaa)DE-He213 Hide Markov Model Model (dpeaa)DE-He213 P300 Binding Site (dpeaa)DE-He213 Ren, Bing aut Wang, Wei aut Enthalten in Genome biology London : BioMed Central, 2000 11(2010), 1 vom: 22. Jan. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:11 year:2010 number:1 day:22 month:01 https://dx.doi.org/10.1186/gb-2010-11-1-r7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 22 01
spelling	10.1186/gb-2010-11-1-r7 doi (DE-627)SPR030007011 (SPR)gb-2010-11-1-r7-e DE-627 ger DE-627 rakwb eng Won, Kyoung-Jae verfasserin aut Genome-wide prediction of transcription factor binding sites using an integrated model 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Won et al.; license BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( Abstract We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments. Hide Markov Model (dpeaa)DE-He213 Histone Modification (dpeaa)DE-He213 Histone Mark (dpeaa)DE-He213 Hide Markov Model Model (dpeaa)DE-He213 P300 Binding Site (dpeaa)DE-He213 Ren, Bing aut Wang, Wei aut Enthalten in Genome biology London : BioMed Central, 2000 11(2010), 1 vom: 22. Jan. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:11 year:2010 number:1 day:22 month:01 https://dx.doi.org/10.1186/gb-2010-11-1-r7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 22 01
allfields_unstemmed	10.1186/gb-2010-11-1-r7 doi (DE-627)SPR030007011 (SPR)gb-2010-11-1-r7-e DE-627 ger DE-627 rakwb eng Won, Kyoung-Jae verfasserin aut Genome-wide prediction of transcription factor binding sites using an integrated model 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Won et al.; license BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( Abstract We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments. Hide Markov Model (dpeaa)DE-He213 Histone Modification (dpeaa)DE-He213 Histone Mark (dpeaa)DE-He213 Hide Markov Model Model (dpeaa)DE-He213 P300 Binding Site (dpeaa)DE-He213 Ren, Bing aut Wang, Wei aut Enthalten in Genome biology London : BioMed Central, 2000 11(2010), 1 vom: 22. Jan. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:11 year:2010 number:1 day:22 month:01 https://dx.doi.org/10.1186/gb-2010-11-1-r7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 22 01
allfieldsGer	10.1186/gb-2010-11-1-r7 doi (DE-627)SPR030007011 (SPR)gb-2010-11-1-r7-e DE-627 ger DE-627 rakwb eng Won, Kyoung-Jae verfasserin aut Genome-wide prediction of transcription factor binding sites using an integrated model 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Won et al.; license BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( Abstract We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments. Hide Markov Model (dpeaa)DE-He213 Histone Modification (dpeaa)DE-He213 Histone Mark (dpeaa)DE-He213 Hide Markov Model Model (dpeaa)DE-He213 P300 Binding Site (dpeaa)DE-He213 Ren, Bing aut Wang, Wei aut Enthalten in Genome biology London : BioMed Central, 2000 11(2010), 1 vom: 22. Jan. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:11 year:2010 number:1 day:22 month:01 https://dx.doi.org/10.1186/gb-2010-11-1-r7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 22 01
allfieldsSound	10.1186/gb-2010-11-1-r7 doi (DE-627)SPR030007011 (SPR)gb-2010-11-1-r7-e DE-627 ger DE-627 rakwb eng Won, Kyoung-Jae verfasserin aut Genome-wide prediction of transcription factor binding sites using an integrated model 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Won et al.; license BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( Abstract We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments. Hide Markov Model (dpeaa)DE-He213 Histone Modification (dpeaa)DE-He213 Histone Mark (dpeaa)DE-He213 Hide Markov Model Model (dpeaa)DE-He213 P300 Binding Site (dpeaa)DE-He213 Ren, Bing aut Wang, Wei aut Enthalten in Genome biology London : BioMed Central, 2000 11(2010), 1 vom: 22. Jan. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:11 year:2010 number:1 day:22 month:01 https://dx.doi.org/10.1186/gb-2010-11-1-r7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 22 01
language	English
source	Enthalten in Genome biology 11(2010), 1 vom: 22. Jan. volume:11 year:2010 number:1 day:22 month:01
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topic_facet	Hide Markov Model Histone Modification Histone Mark Hide Markov Model Model P300 Binding Site
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authorswithroles_txt_mv	Won, Kyoung-Jae @@aut@@ Ren, Bing @@aut@@ Wang, Wei @@aut@@
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author	Won, Kyoung-Jae
spellingShingle	Won, Kyoung-Jae misc Hide Markov Model misc Histone Modification misc Histone Mark misc Hide Markov Model Model misc P300 Binding Site Genome-wide prediction of transcription factor binding sites using an integrated model
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topic_title	Genome-wide prediction of transcription factor binding sites using an integrated model Hide Markov Model (dpeaa)DE-He213 Histone Modification (dpeaa)DE-He213 Histone Mark (dpeaa)DE-He213 Hide Markov Model Model (dpeaa)DE-He213 P300 Binding Site (dpeaa)DE-He213
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title	Genome-wide prediction of transcription factor binding sites using an integrated model
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title_full	Genome-wide prediction of transcription factor binding sites using an integrated model
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title_sort	genome-wide prediction of transcription factor binding sites using an integrated model
title_auth	Genome-wide prediction of transcription factor binding sites using an integrated model
abstract	Abstract We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments. © Won et al.; license BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (
abstractGer	Abstract We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments. © Won et al.; license BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (
abstract_unstemmed	Abstract We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments. © Won et al.; license BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (
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title_short	Genome-wide prediction of transcription factor binding sites using an integrated model
url	https://dx.doi.org/10.1186/gb-2010-11-1-r7
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up_date	2024-07-04T02:57:17.189Z
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