Cargando…

Comparative modular analysis of gene expression in vertebrate organs

BACKGROUND: The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level o...

Descripción completa

Detalles Bibliográficos
Autores principales: Piasecka, Barbara, Kutalik, Zoltán, Roux, Julien, Bergmann, Sven, Robinson-Rechavi, Marc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359279/
https://www.ncbi.nlm.nih.gov/pubmed/22458817
http://dx.doi.org/10.1186/1471-2164-13-124
_version_ 1782233852204285952
author Piasecka, Barbara
Kutalik, Zoltán
Roux, Julien
Bergmann, Sven
Robinson-Rechavi, Marc
author_facet Piasecka, Barbara
Kutalik, Zoltán
Roux, Julien
Bergmann, Sven
Robinson-Rechavi, Marc
author_sort Piasecka, Barbara
collection PubMed
description BACKGROUND: The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity. RESULTS: Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human. CONCLUSIONS: Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.
format Online
Article
Text
id pubmed-3359279
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-33592792012-06-01 Comparative modular analysis of gene expression in vertebrate organs Piasecka, Barbara Kutalik, Zoltán Roux, Julien Bergmann, Sven Robinson-Rechavi, Marc BMC Genomics Research Article BACKGROUND: The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity. RESULTS: Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human. CONCLUSIONS: Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species. BioMed Central 2012-03-29 /pmc/articles/PMC3359279/ /pubmed/22458817 http://dx.doi.org/10.1186/1471-2164-13-124 Text en Copyright ©2012 Piasecka et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Piasecka, Barbara
Kutalik, Zoltán
Roux, Julien
Bergmann, Sven
Robinson-Rechavi, Marc
Comparative modular analysis of gene expression in vertebrate organs
title Comparative modular analysis of gene expression in vertebrate organs
title_full Comparative modular analysis of gene expression in vertebrate organs
title_fullStr Comparative modular analysis of gene expression in vertebrate organs
title_full_unstemmed Comparative modular analysis of gene expression in vertebrate organs
title_short Comparative modular analysis of gene expression in vertebrate organs
title_sort comparative modular analysis of gene expression in vertebrate organs
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359279/
https://www.ncbi.nlm.nih.gov/pubmed/22458817
http://dx.doi.org/10.1186/1471-2164-13-124
work_keys_str_mv AT piaseckabarbara comparativemodularanalysisofgeneexpressioninvertebrateorgans
AT kutalikzoltan comparativemodularanalysisofgeneexpressioninvertebrateorgans
AT rouxjulien comparativemodularanalysisofgeneexpressioninvertebrateorgans
AT bergmannsven comparativemodularanalysisofgeneexpressioninvertebrateorgans
AT robinsonrechavimarc comparativemodularanalysisofgeneexpressioninvertebrateorgans