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GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response.

Zaag R, Tamby JP, Guichard C, Tariq Z, Rigaill G, Delannoy E, Renou JP, Balzergue S, Mary-Huard T, Aubourg S, Martin-Magniette ML, Brunaud V - Nucleic Acids Res. (2014)

Bottom Line: To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications.GEM2Net presents the analysis of the 18 stress categories, in which 17,264 genes are involved and organized within 681 co-expression clusters.The meta-data analyses were stored and organized to compose a dynamic Web resource.

View Article: PubMed Central - PubMed

Affiliation: INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France.

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Protein Interactome Network for Cluster_49 of the ‘Virus’ stress category. In the central panel, all PPI (edges) between gene accessions (nodes) within the cluster_49 are represented with dark blue lines, using the Cytoscape Web software tool. Functional annotation is superimposed on nodes by selecting the corresponding checkbox above, hormone families (in blue) and orphans (in red) here. On the right frame, filters on GO categories can be applied to the network to view only nodes of the selected annotation. In addition, a ‘Targets of Transcription Factors’ option is available to display this type of interaction in the same network.
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Figure 5: Protein Interactome Network for Cluster_49 of the ‘Virus’ stress category. In the central panel, all PPI (edges) between gene accessions (nodes) within the cluster_49 are represented with dark blue lines, using the Cytoscape Web software tool. Functional annotation is superimposed on nodes by selecting the corresponding checkbox above, hormone families (in blue) and orphans (in red) here. On the right frame, filters on GO categories can be applied to the network to view only nodes of the selected annotation. In addition, a ‘Targets of Transcription Factors’ option is available to display this type of interaction in the same network.

Mentions: GEM2Net integrates protein interactomes and targets of TF data from external resources (Supplementary Table S1), so gene clusters can be viewed as interactive biological networks (Figure 5), thanks to the embedded Cytoscape Web software tool (33). Adding gene annotation, e.g. TFs families, GO terms or choosing experimentally confirmed PPI, makes it easier to predict regulatory networks of biological relevance and to identify new functional partners. Therefore, by combining gene annotation corresponding to relevant meta-analyses with the available interaction networks in GEM2Net, it is possible to gather clues to infer the biological functions of some orphan genes in a co-expression unit.


GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response.

Zaag R, Tamby JP, Guichard C, Tariq Z, Rigaill G, Delannoy E, Renou JP, Balzergue S, Mary-Huard T, Aubourg S, Martin-Magniette ML, Brunaud V - Nucleic Acids Res. (2014)

Protein Interactome Network for Cluster_49 of the ‘Virus’ stress category. In the central panel, all PPI (edges) between gene accessions (nodes) within the cluster_49 are represented with dark blue lines, using the Cytoscape Web software tool. Functional annotation is superimposed on nodes by selecting the corresponding checkbox above, hormone families (in blue) and orphans (in red) here. On the right frame, filters on GO categories can be applied to the network to view only nodes of the selected annotation. In addition, a ‘Targets of Transcription Factors’ option is available to display this type of interaction in the same network.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383956&req=5

Figure 5: Protein Interactome Network for Cluster_49 of the ‘Virus’ stress category. In the central panel, all PPI (edges) between gene accessions (nodes) within the cluster_49 are represented with dark blue lines, using the Cytoscape Web software tool. Functional annotation is superimposed on nodes by selecting the corresponding checkbox above, hormone families (in blue) and orphans (in red) here. On the right frame, filters on GO categories can be applied to the network to view only nodes of the selected annotation. In addition, a ‘Targets of Transcription Factors’ option is available to display this type of interaction in the same network.
Mentions: GEM2Net integrates protein interactomes and targets of TF data from external resources (Supplementary Table S1), so gene clusters can be viewed as interactive biological networks (Figure 5), thanks to the embedded Cytoscape Web software tool (33). Adding gene annotation, e.g. TFs families, GO terms or choosing experimentally confirmed PPI, makes it easier to predict regulatory networks of biological relevance and to identify new functional partners. Therefore, by combining gene annotation corresponding to relevant meta-analyses with the available interaction networks in GEM2Net, it is possible to gather clues to infer the biological functions of some orphan genes in a co-expression unit.

Bottom Line: To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications.GEM2Net presents the analysis of the 18 stress categories, in which 17,264 genes are involved and organized within 681 co-expression clusters.The meta-data analyses were stored and organized to compose a dynamic Web resource.

View Article: PubMed Central - PubMed

Affiliation: INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France.

Show MeSH
Related in: MedlinePlus