Predicting regulatory elements in repetitive sequences using transcription factor binding sites

Repeat sequences are the most abundant ones in the extragenic region of genomes. Biologists have already found a large number of regulatory elements in this region. These elements may profoundly impact the chromatin structure formation in nucleus and also contain important clues in genetic evolution...

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Autores principales:	Horng,Jorng-Tzong, Cho,Wen-Fu
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2000
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582000000300004
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spelling	oai:scielo:S0717-345820000003000042003-08-18Predicting regulatory elements in repetitive sequences using transcription factor binding sitesHorng,Jorng-TzongCho,Wen-Fu Repeat sequences are the most abundant ones in the extragenic region of genomes. Biologists have already found a large number of regulatory elements in this region. These elements may profoundly impact the chromatin structure formation in nucleus and also contain important clues in genetic evolution and phylogenic study. This study attempts to mine rules on how combinations of individual binding sites are distributed repeat sequences. The association rules mined would facilitate efforts to identify gene classes regulated by similar mechanisms and accurately predict regulatory elements. Herein, the combinations of transcription factor binding sites in the repeat sequences are obtained and, then, data mining techniques are applied to mine the association rules from the combinations of binding sites. In addition, the discovered associations are further pruned to remove those insignificant associations and obtain a set of discovered associations. Finally, the discovered association rules are used to partially classify the repeat sequences in our repeat database. Experiments on several genomes include C. elegans, human chromosome 22 and yeast. <A NAME="Article"></A>info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.3 n.3 20002000-12-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582000000300004en
institution	Scielo Chile
collection	Scielo Chile
language	English
description	Repeat sequences are the most abundant ones in the extragenic region of genomes. Biologists have already found a large number of regulatory elements in this region. These elements may profoundly impact the chromatin structure formation in nucleus and also contain important clues in genetic evolution and phylogenic study. This study attempts to mine rules on how combinations of individual binding sites are distributed repeat sequences. The association rules mined would facilitate efforts to identify gene classes regulated by similar mechanisms and accurately predict regulatory elements. Herein, the combinations of transcription factor binding sites in the repeat sequences are obtained and, then, data mining techniques are applied to mine the association rules from the combinations of binding sites. In addition, the discovered associations are further pruned to remove those insignificant associations and obtain a set of discovered associations. Finally, the discovered association rules are used to partially classify the repeat sequences in our repeat database. Experiments on several genomes include C. elegans, human chromosome 22 and yeast. <A NAME="Article"></A>
author	Horng,Jorng-Tzong Cho,Wen-Fu
spellingShingle	Horng,Jorng-Tzong Cho,Wen-Fu Predicting regulatory elements in repetitive sequences using transcription factor binding sites
author_facet	Horng,Jorng-Tzong Cho,Wen-Fu
author_sort	Horng,Jorng-Tzong
title	Predicting regulatory elements in repetitive sequences using transcription factor binding sites
title_short	Predicting regulatory elements in repetitive sequences using transcription factor binding sites
title_full	Predicting regulatory elements in repetitive sequences using transcription factor binding sites
title_fullStr	Predicting regulatory elements in repetitive sequences using transcription factor binding sites
title_full_unstemmed	Predicting regulatory elements in repetitive sequences using transcription factor binding sites
title_sort	predicting regulatory elements in repetitive sequences using transcription factor binding sites
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2000
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582000000300004
work_keys_str_mv	AT horngjorngtzong predictingregulatoryelementsinrepetitivesequencesusingtranscriptionfactorbindingsites AT chowenfu predictingregulatoryelementsinrepetitivesequencesusingtranscriptionfactorbindingsites
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Predicting regulatory elements in repetitive sequences using transcription factor binding sites

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