Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.

Although most genes share their chromosomal neighbourhood with other genes, distribution of genes has not been explored in the context of individual organ development; the common focus of developmental biology studies. Because developmental processes are often associated with initially subtle change...

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Autores principales:	Rishi Das Roy, Outi Hallikas, Mona M Christensen, Elodie Renvoisé, Jukka Jernvall
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/abd8028eef474f2b9853a1fd277cb7e7
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spelling	oai:doaj.org-article:abd8028eef474f2b9853a1fd277cb7e72021-12-02T19:57:49ZChromosomal neighbourhoods allow identification of organ specific changes in gene expression.1553-734X1553-735810.1371/journal.pcbi.1008947https://doaj.org/article/abd8028eef474f2b9853a1fd277cb7e72021-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1008947https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Although most genes share their chromosomal neighbourhood with other genes, distribution of genes has not been explored in the context of individual organ development; the common focus of developmental biology studies. Because developmental processes are often associated with initially subtle changes in gene expression, here we explored whether neighbouring genes are informative in the identification of differentially expressed genes. First, we quantified the chromosomal neighbourhood patterns of genes having related functional roles in the mammalian genome. Although the majority of protein coding genes have at least five neighbours within 1 Mb window around each gene, very few of these neighbours regulate development of the same organ. Analyses of transcriptomes of developing mouse molar teeth revealed that whereas expression of genes regulating tooth development changes, their neighbouring genes show no marked changes, irrespective of their level of expression. Finally, we test whether inclusion of gene neighbourhood in the analyses of differential expression could provide additional benefits. For the analyses, we developed an algorithm, called DELocal that identifies differentially expressed genes by comparing their expression changes to changes in adjacent genes in their chromosomal regions. Our results show that DELocal removes detection bias towards large changes in expression, thereby allowing identification of even subtle changes in development. Future studies, including the detection of differential expression, may benefit from, and further characterize the significance of gene-gene neighbour relationships.Rishi Das RoyOuti HallikasMona M ChristensenElodie RenvoiséJukka JernvallPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 9, p e1008947 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Rishi Das Roy Outi Hallikas Mona M Christensen Elodie Renvoisé Jukka Jernvall Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.
description	Although most genes share their chromosomal neighbourhood with other genes, distribution of genes has not been explored in the context of individual organ development; the common focus of developmental biology studies. Because developmental processes are often associated with initially subtle changes in gene expression, here we explored whether neighbouring genes are informative in the identification of differentially expressed genes. First, we quantified the chromosomal neighbourhood patterns of genes having related functional roles in the mammalian genome. Although the majority of protein coding genes have at least five neighbours within 1 Mb window around each gene, very few of these neighbours regulate development of the same organ. Analyses of transcriptomes of developing mouse molar teeth revealed that whereas expression of genes regulating tooth development changes, their neighbouring genes show no marked changes, irrespective of their level of expression. Finally, we test whether inclusion of gene neighbourhood in the analyses of differential expression could provide additional benefits. For the analyses, we developed an algorithm, called DELocal that identifies differentially expressed genes by comparing their expression changes to changes in adjacent genes in their chromosomal regions. Our results show that DELocal removes detection bias towards large changes in expression, thereby allowing identification of even subtle changes in development. Future studies, including the detection of differential expression, may benefit from, and further characterize the significance of gene-gene neighbour relationships.
format	article
author	Rishi Das Roy Outi Hallikas Mona M Christensen Elodie Renvoisé Jukka Jernvall
author_facet	Rishi Das Roy Outi Hallikas Mona M Christensen Elodie Renvoisé Jukka Jernvall
author_sort	Rishi Das Roy
title	Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.
title_short	Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.
title_full	Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.
title_fullStr	Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.
title_full_unstemmed	Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.
title_sort	chromosomal neighbourhoods allow identification of organ specific changes in gene expression.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/abd8028eef474f2b9853a1fd277cb7e7
work_keys_str_mv	AT rishidasroy chromosomalneighbourhoodsallowidentificationoforganspecificchangesingeneexpression AT outihallikas chromosomalneighbourhoodsallowidentificationoforganspecificchangesingeneexpression AT monamchristensen chromosomalneighbourhoodsallowidentificationoforganspecificchangesingeneexpression AT elodierenvoise chromosomalneighbourhoodsallowidentificationoforganspecificchangesingeneexpression AT jukkajernvall chromosomalneighbourhoodsallowidentificationoforganspecificchangesingeneexpression
_version_	1718375794793775104

Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.

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