Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.

In this paper we perform a genome-wide analysis of H. sapiens promoters. To this aim, we developed and combined two mathematical methods that allow us to (i) classify promoters into groups characterized by specific global structural features, and (ii) recover, in full generality, any regular sequenc...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Lucia Pettinato, Elisa Calistri, Francesca Di Patti, Roberto Livi, Stefano Luccioli
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/51fc08e8c6634f6a873edbb93b9d6fae
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:51fc08e8c6634f6a873edbb93b9d6fae
record_format	dspace
spelling	oai:doaj.org-article:51fc08e8c6634f6a873edbb93b9d6fae2021-11-18T08:36:38ZGenome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.1932-620310.1371/journal.pone.0085260https://doaj.org/article/51fc08e8c6634f6a873edbb93b9d6fae2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24465517/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203In this paper we perform a genome-wide analysis of H. sapiens promoters. To this aim, we developed and combined two mathematical methods that allow us to (i) classify promoters into groups characterized by specific global structural features, and (ii) recover, in full generality, any regular sequence in the different classes of promoters. One of the main findings of this analysis is that H. sapiens promoters can be classified into three main groups. Two of them are distinguished by the prevalence of weak or strong nucleotides and are characterized by short compositionally biased sequences, while the most frequent regular sequences in the third group are strongly correlated with transposons. Taking advantage of the generality of these mathematical procedures, we have compared the promoter database of H. sapiens with those of other species. We have found that the above-mentioned features characterize also the evolutionary content appearing in mammalian promoters, at variance with ancestral species in the phylogenetic tree, that exhibit a definitely lower level of differentiation among promoters.Lucia PettinatoElisa CalistriFrancesca Di PattiRoberto LiviStefano LuccioliPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e85260 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lucia Pettinato Elisa Calistri Francesca Di Patti Roberto Livi Stefano Luccioli Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.
description	In this paper we perform a genome-wide analysis of H. sapiens promoters. To this aim, we developed and combined two mathematical methods that allow us to (i) classify promoters into groups characterized by specific global structural features, and (ii) recover, in full generality, any regular sequence in the different classes of promoters. One of the main findings of this analysis is that H. sapiens promoters can be classified into three main groups. Two of them are distinguished by the prevalence of weak or strong nucleotides and are characterized by short compositionally biased sequences, while the most frequent regular sequences in the third group are strongly correlated with transposons. Taking advantage of the generality of these mathematical procedures, we have compared the promoter database of H. sapiens with those of other species. We have found that the above-mentioned features characterize also the evolutionary content appearing in mammalian promoters, at variance with ancestral species in the phylogenetic tree, that exhibit a definitely lower level of differentiation among promoters.
format	article
author	Lucia Pettinato Elisa Calistri Francesca Di Patti Roberto Livi Stefano Luccioli
author_facet	Lucia Pettinato Elisa Calistri Francesca Di Patti Roberto Livi Stefano Luccioli
author_sort	Lucia Pettinato
title	Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.
title_short	Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.
title_full	Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.
title_fullStr	Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.
title_full_unstemmed	Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.
title_sort	genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/51fc08e8c6634f6a873edbb93b9d6fae
work_keys_str_mv	AT luciapettinato genomewideanalysisofpromotersclusteringbyalignmentandanalysisofregularpatterns AT elisacalistri genomewideanalysisofpromotersclusteringbyalignmentandanalysisofregularpatterns AT francescadipatti genomewideanalysisofpromotersclusteringbyalignmentandanalysisofregularpatterns AT robertolivi genomewideanalysisofpromotersclusteringbyalignmentandanalysisofregularpatterns AT stefanoluccioli genomewideanalysisofpromotersclusteringbyalignmentandanalysisofregularpatterns
_version_	1718421560225693696

Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.

Ejemplares similares