PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]

Many biological studies of transcriptional control mechanisms produce lists of genes and non-coding genomic intervals from corresponding gene expression and epigenomic assays. In higher organisms, such as eukaryotes, genes may be regulated by distal elements, with these elements lying 10s–100s of ki...

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Autores principales:	Peter Briggs, A. Louise Hunter, Shen-hsi Yang, Andrew D. Sharrocks, Mudassar Iqbal
Formato:	article
Lenguaje:	EN
Publicado:	F1000 Research Ltd 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ca50e2425dbc43789366f412e4e6f37b
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spelling	oai:doaj.org-article:ca50e2425dbc43789366f412e4e6f37b2021-11-08T10:53:47ZPEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]2046-140210.12688/f1000research.53926.2https://doaj.org/article/ca50e2425dbc43789366f412e4e6f37b2021-11-01T00:00:00Zhttps://f1000research.com/articles/10-570/v2https://doaj.org/toc/2046-1402Many biological studies of transcriptional control mechanisms produce lists of genes and non-coding genomic intervals from corresponding gene expression and epigenomic assays. In higher organisms, such as eukaryotes, genes may be regulated by distal elements, with these elements lying 10s–100s of kilobases away from a gene transcription start site. To gain insight into these distal regulatory mechanisms, it is important to determine comparative enrichment of genes of interest in relation to genomic regions of interest, and to be able to do so at a range of distances. Existing bioinformatics tools can annotate genomic regions to nearest known genes, or look for transcription factor binding sites in relation to gene transcription start sites. Here, we present PEGS (Peak set Enrichment in Gene Sets). This tool efficiently provides an exploratory analysis by calculating enrichment of multiple gene sets, associated with multiple non-coding elements (peak sets), at multiple genomic distances, and within topologically associated domains. We apply PEGS to gene sets derived from gene expression studies, and genomic intervals from corresponding ChIP-seq and ATAC-seq experiments to derive biologically meaningful results. We also demonstrate an extended application to tissue-specific gene sets and publicly available GWAS data, to find enrichment of sleep trait associated SNPs in relation to tissue-specific gene expression profiles.Peter BriggsA. Louise HunterShen-hsi YangAndrew D. SharrocksMudassar IqbalF1000 Research LtdarticleMedicineRScienceQENF1000Research, Vol 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Peter Briggs A. Louise Hunter Shen-hsi Yang Andrew D. Sharrocks Mudassar Iqbal PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]
description	Many biological studies of transcriptional control mechanisms produce lists of genes and non-coding genomic intervals from corresponding gene expression and epigenomic assays. In higher organisms, such as eukaryotes, genes may be regulated by distal elements, with these elements lying 10s–100s of kilobases away from a gene transcription start site. To gain insight into these distal regulatory mechanisms, it is important to determine comparative enrichment of genes of interest in relation to genomic regions of interest, and to be able to do so at a range of distances. Existing bioinformatics tools can annotate genomic regions to nearest known genes, or look for transcription factor binding sites in relation to gene transcription start sites. Here, we present PEGS (Peak set Enrichment in Gene Sets). This tool efficiently provides an exploratory analysis by calculating enrichment of multiple gene sets, associated with multiple non-coding elements (peak sets), at multiple genomic distances, and within topologically associated domains. We apply PEGS to gene sets derived from gene expression studies, and genomic intervals from corresponding ChIP-seq and ATAC-seq experiments to derive biologically meaningful results. We also demonstrate an extended application to tissue-specific gene sets and publicly available GWAS data, to find enrichment of sleep trait associated SNPs in relation to tissue-specific gene expression profiles.
format	article
author	Peter Briggs A. Louise Hunter Shen-hsi Yang Andrew D. Sharrocks Mudassar Iqbal
author_facet	Peter Briggs A. Louise Hunter Shen-hsi Yang Andrew D. Sharrocks Mudassar Iqbal
author_sort	Peter Briggs
title	PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]
title_short	PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]
title_full	PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]
title_fullStr	PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]
title_full_unstemmed	PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]
title_sort	pegs: an efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]
publisher	F1000 Research Ltd
publishDate	2021
url	https://doaj.org/article/ca50e2425dbc43789366f412e4e6f37b
work_keys_str_mv	AT peterbriggs pegsanefficienttoolforgenesetenrichmentwithindefinedsetsofgenomicintervalsversion2peerreview2approved AT alouisehunter pegsanefficienttoolforgenesetenrichmentwithindefinedsetsofgenomicintervalsversion2peerreview2approved AT shenhsiyang pegsanefficienttoolforgenesetenrichmentwithindefinedsetsofgenomicintervalsversion2peerreview2approved AT andrewdsharrocks pegsanefficienttoolforgenesetenrichmentwithindefinedsetsofgenomicintervalsversion2peerreview2approved AT mudassariqbal pegsanefficienttoolforgenesetenrichmentwithindefinedsetsofgenomicintervalsversion2peerreview2approved
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PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals [version 2; peer review: 2 approved]

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