ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa.
Identifieur interne : 002326 ( Main/Exploration ); précédent : 002325; suivant : 002327ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa.
Auteurs : Sergiu Netotea ; David Sundell ; Nathaniel R. Street ; Torgeir R. Hvidsten [Suède]Source :
- BMC genomics [ 1471-2164 ] ; 2014.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Arabidopsis (génétique), Gènes de plante (MeSH), Interface utilisateur (MeSH), Internet (MeSH), Oryza (génétique), Populus (génétique), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH), Séquence conservée (MeSH), Séquence nucléotidique (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
BACKGROUND
Divergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regulation of genes.
RESULTS
We inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual information and context likelihood of relatedness, and conducted a comprehensive comparison of these networks across a range of co-expression thresholds. In addition to quantifying gene-gene link and network neighbourhood conservation, we also applied recent advancements in network analysis to do cross-species comparisons of network properties such as scale free characteristics and gene centrality as well as network motifs. We found that in all species the networks emerged as scale free only above a certain co-expression threshold, and that the high-centrality genes upholding this organization tended to be conserved. Network motifs, in particular the feed-forward loop, were found to be significantly enriched in specific functional subnetworks but where much less conserved across species than gene centrality. Although individual gene-gene co-expression had massively diverged, up to ~80% of the genes still had a significantly conserved network neighbourhood. For genes with multiple predicted orthologs, about half had one ortholog with conserved regulation and another ortholog with diverged or non-conserved regulation. Furthermore, the most sequence similar ortholog was not the one with the most conserved gene regulation in over half of the cases.
CONCLUSIONS
We have provided a comprehensive analysis of gene regulation evolution in plants and built a web tool for Comparative analysis of Plant co-Expression networks (ComPlEx, http://complex.plantgenie.org/). The tool can be particularly useful for identifying the ortholog with the most conserved regulation among several sequence-similar alternatives and can thus be of practical importance in e.g. finding candidate genes for perturbation experiments.
DOI: 10.1186/1471-2164-15-106
PubMed: 24498971
PubMed Central: PMC3925997
Affiliations:
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Street</name></author><author><name sortKey="Hvidsten, Torgeir R" sort="Hvidsten, Torgeir R" uniqKey="Hvidsten T" first="Torgeir R" last="Hvidsten">Torgeir R. Hvidsten</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden. torgeir.r.hvidsten@nmbu.no.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><term>Arabidopsis (genetics)</term><term>Base Sequence (MeSH)</term><term>Conserved Sequence (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Internet (MeSH)</term><term>Oryza (genetics)</term><term>Populus (genetics)</term><term>User-Computer Interface (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes (MeSH)</term><term>Arabidopsis (génétique)</term><term>Gènes de plante (MeSH)</term><term>Interface utilisateur (MeSH)</term><term>Internet (MeSH)</term><term>Oryza (génétique)</term><term>Populus (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>Séquence conservée (MeSH)</term><term>Séquence nucléotidique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Oryza</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Oryza</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Base Sequence</term><term>Conserved Sequence</term><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>Genes, Plant</term><term>Internet</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Gènes de plante</term><term>Interface utilisateur</term><term>Internet</term><term>Régulation de l'expression des gènes végétaux</term><term>Réseaux de régulation génique</term><term>Séquence conservée</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Divergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regulation of genes.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual information and context likelihood of relatedness, and conducted a comprehensive comparison of these networks across a range of co-expression thresholds. In addition to quantifying gene-gene link and network neighbourhood conservation, we also applied recent advancements in network analysis to do cross-species comparisons of network properties such as scale free characteristics and gene centrality as well as network motifs. We found that in all species the networks emerged as scale free only above a certain co-expression threshold, and that the high-centrality genes upholding this organization tended to be conserved. Network motifs, in particular the feed-forward loop, were found to be significantly enriched in specific functional subnetworks but where much less conserved across species than gene centrality. Although individual gene-gene co-expression had massively diverged, up to ~80% of the genes still had a significantly conserved network neighbourhood. For genes with multiple predicted orthologs, about half had one ortholog with conserved regulation and another ortholog with diverged or non-conserved regulation. Furthermore, the most sequence similar ortholog was not the one with the most conserved gene regulation in over half of the cases.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>We have provided a comprehensive analysis of gene regulation evolution in plants and built a web tool for Comparative analysis of Plant co-Expression networks (ComPlEx, http://complex.plantgenie.org/). The tool can be particularly useful for identifying the ortholog with the most conserved regulation among several sequence-similar alternatives and can thus be of practical importance in e.g. finding candidate genes for perturbation experiments.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24498971</PMID><DateCompleted><Year>2014</Year><Month>12</Month><Day>15</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><PubDate><Year>2014</Year><Month>Feb</Month><Day>06</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa.</ArticleTitle><Pagination><MedlinePgn>106</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-15-106</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Divergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regulation of genes.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual information and context likelihood of relatedness, and conducted a comprehensive comparison of these networks across a range of co-expression thresholds. In addition to quantifying gene-gene link and network neighbourhood conservation, we also applied recent advancements in network analysis to do cross-species comparisons of network properties such as scale free characteristics and gene centrality as well as network motifs. We found that in all species the networks emerged as scale free only above a certain co-expression threshold, and that the high-centrality genes upholding this organization tended to be conserved. Network motifs, in particular the feed-forward loop, were found to be significantly enriched in specific functional subnetworks but where much less conserved across species than gene centrality. Although individual gene-gene co-expression had massively diverged, up to ~80% of the genes still had a significantly conserved network neighbourhood. For genes with multiple predicted orthologs, about half had one ortholog with conserved regulation and another ortholog with diverged or non-conserved regulation. Furthermore, the most sequence similar ortholog was not the one with the most conserved gene regulation in over half of the cases.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">We have provided a comprehensive analysis of gene regulation evolution in plants and built a web tool for Comparative analysis of Plant co-Expression networks (ComPlEx, http://complex.plantgenie.org/). 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uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name><name sortKey="Sundell, David" sort="Sundell, David" uniqKey="Sundell D" first="David" last="Sundell">David Sundell</name></noCountry><country name="Suède"><noRegion><name sortKey="Hvidsten, Torgeir R" sort="Hvidsten, Torgeir R" uniqKey="Hvidsten T" first="Torgeir R" last="Hvidsten">Torgeir R. Hvidsten</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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