GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response.
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.
Affiliation: INRA, UnitÃ© de Recherche en GÃ©nomique VÃ©gÃ©tale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, UnitÃ© de Recherche en GÃ©nomique VÃ©gÃ©tale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France.Show MeSH
Related in: MedlinePlus
Mentions: The GEM2Net Web interface (http://urgv.evry.inra.fr/GEM2NET) allows users to query the database by stress category or to submit a list of genes of interest to retrieve the stress categories they are implicated in. It is possible to answer questions like â€˜are my genes of interest involved in the same co-expression unit?â€™ by exploring graphically the results of meta-data analyses. To identify at a glance and summarize the potential functional biases of each cluster, GEM2Net proposes an original representation and interactive visualization, using pie charts and graphs. For each stress category, cluster annotation analyses are divided into several tabs, one per meta-data type, which allow the organization of complex and abundant results. In such tabs, a central panel displays every cluster as a pie chart whose diameter is directly related to the total number of genes in the cluster. Colored sections within a pie chart materialize the numbers of genes of the corresponding meta-data when over-represented. For example, Figure 3 presents a view of clusters enrichment analyses for the GO Slim branch â€˜Biological Processâ€™ of the â€˜Virusâ€™ stress category. Complementary information related to each cluster is also available in a table nearby the central panel, which appears when moving the mouse over a given cluster. In Figure 4, a synthetic view of one cluster, the cluster_49 from the â€˜Virusâ€™ stress category, shows a summary of all the meta-data analyses done for this cluster. In each pie chart, significant enrichments are seen in color for few meta-data analyses, e.g. in the GO terms â€˜cell organization and biogenesisâ€™ and â€˜response to stressâ€™ of the â€˜Biological Processâ€™ ontology. The complete list of 213 genes of cluster_49 appears in a table sorted by gene roles in the selected meta-data type and highlights their implication in other biases by colored circles.
Affiliation: INRA, UnitÃ© de Recherche en GÃ©nomique VÃ©gÃ©tale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, UnitÃ© de Recherche en GÃ©nomique VÃ©gÃ©tale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France.