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Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network.

Atias O, Chor B, Chamovitz DA - BMC Syst Biol (2009)

Bottom Line: We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations.The analysis reveals that part of the Arabidopsis transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules.Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Sciences, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel. dafniosn@post.tau.ac.il

ABSTRACT

Background: Analyses of gene expression data from microarray experiments has become a central tool for identifying co-regulated, functional gene modules. A crucial aspect of such analysis is the integration of data from different experiments and different laboratories. How to weigh the contribution of different experiments is an important point influencing the final outcomes. We have developed a novel method for this integration, and applied it to genome-wide data from multiple Arabidopsis microarray experiments performed under a variety of experimental conditions. The goal of this study is to identify functional globally co-regulated gene modules in the Arabidopsis genome.

Results: Following the analysis of 21,000 Arabidopsis genes in 43 datasets and about 2 x 10(8) gene pairs, we identified a globally co-expressed gene network. We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations. Two types of modules were identified in the regulatory network that differed in their sensitivity to the node-scoring parameter; we further showed these two pertain to general and specialized modules. Some of these modules were further investigated using the Genevestigator compendium of microarray experiments. Analyses of smaller subsets of data lead to the identification of condition-specific modules.

Conclusion: Our method for identification of gene clusters allows the integration of diverse microarray experiments from many sources. The analysis reveals that part of the Arabidopsis transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules. Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.

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Genevestigator analysis of a putative cell-cycle regulated cluster. Cluster 7 from the 0.3 network, detected using the 0.2 node score cutoff, (see gene list at Table 7, Figure 4) was analyzed using Genevestigator. (A) Graph showing the genes in the cluster and the edges that exist between them in the 0.3 network. Expression according to (B) anatomical tissues or (C) developmental stages, is shown. Expression levels in B and C are shown in heat maps, where dark blue indicates maximal expression. (D) Gene expression in different mutants. Expression levels are shown in a heat map in which intense green and red indicate down- or up-regulation in comparison to wild type, respectively. The red rectangle emphasizes the genes expression in the hub1 mutant (see text for details). Figures in B, C and D were generated using Genevestigator.
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Figure 6: Genevestigator analysis of a putative cell-cycle regulated cluster. Cluster 7 from the 0.3 network, detected using the 0.2 node score cutoff, (see gene list at Table 7, Figure 4) was analyzed using Genevestigator. (A) Graph showing the genes in the cluster and the edges that exist between them in the 0.3 network. Expression according to (B) anatomical tissues or (C) developmental stages, is shown. Expression levels in B and C are shown in heat maps, where dark blue indicates maximal expression. (D) Gene expression in different mutants. Expression levels are shown in a heat map in which intense green and red indicate down- or up-regulation in comparison to wild type, respectively. The red rectangle emphasizes the genes expression in the hub1 mutant (see text for details). Figures in B, C and D were generated using Genevestigator.

Mentions: We next examined clusters that had no detected GO enrichment. Careful manual curation of some of these clusters identified new regulation networks. For example, within the list of genes of cluster ID 7 in the 0.3 network using the 0.2 node score cutoff, we noticed several genes that appear to be related to cell cycle control, even though this cluster had no enriched GO term detected (see Table 4 and Table 8 for the list of genes in this cluster). This cluster was found to be co-expressed using the data from Genevestigator in different tissues (Figure 6B) and different developmental times (Figure 6C). In the former, high expression of module genes is detected primarily in highly dividing tissues. To further substantiate our hypothesis that this is a cell-cycle regulated module, we also examined the expression of the genes in the cluster in different mutants (Figure 6D). In support of our hypothesis, we found that all the genes in the cluster are highly down-regulated in the hub1 mutant. HUB1 (also known as ANG4) is a histone monoubiquitinase, and the hub1 mutant has increased cell cycle duration in young leaves [25].


Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network.

Atias O, Chor B, Chamovitz DA - BMC Syst Biol (2009)

Genevestigator analysis of a putative cell-cycle regulated cluster. Cluster 7 from the 0.3 network, detected using the 0.2 node score cutoff, (see gene list at Table 7, Figure 4) was analyzed using Genevestigator. (A) Graph showing the genes in the cluster and the edges that exist between them in the 0.3 network. Expression according to (B) anatomical tissues or (C) developmental stages, is shown. Expression levels in B and C are shown in heat maps, where dark blue indicates maximal expression. (D) Gene expression in different mutants. Expression levels are shown in a heat map in which intense green and red indicate down- or up-regulation in comparison to wild type, respectively. The red rectangle emphasizes the genes expression in the hub1 mutant (see text for details). Figures in B, C and D were generated using Genevestigator.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2944327&req=5

Figure 6: Genevestigator analysis of a putative cell-cycle regulated cluster. Cluster 7 from the 0.3 network, detected using the 0.2 node score cutoff, (see gene list at Table 7, Figure 4) was analyzed using Genevestigator. (A) Graph showing the genes in the cluster and the edges that exist between them in the 0.3 network. Expression according to (B) anatomical tissues or (C) developmental stages, is shown. Expression levels in B and C are shown in heat maps, where dark blue indicates maximal expression. (D) Gene expression in different mutants. Expression levels are shown in a heat map in which intense green and red indicate down- or up-regulation in comparison to wild type, respectively. The red rectangle emphasizes the genes expression in the hub1 mutant (see text for details). Figures in B, C and D were generated using Genevestigator.
Mentions: We next examined clusters that had no detected GO enrichment. Careful manual curation of some of these clusters identified new regulation networks. For example, within the list of genes of cluster ID 7 in the 0.3 network using the 0.2 node score cutoff, we noticed several genes that appear to be related to cell cycle control, even though this cluster had no enriched GO term detected (see Table 4 and Table 8 for the list of genes in this cluster). This cluster was found to be co-expressed using the data from Genevestigator in different tissues (Figure 6B) and different developmental times (Figure 6C). In the former, high expression of module genes is detected primarily in highly dividing tissues. To further substantiate our hypothesis that this is a cell-cycle regulated module, we also examined the expression of the genes in the cluster in different mutants (Figure 6D). In support of our hypothesis, we found that all the genes in the cluster are highly down-regulated in the hub1 mutant. HUB1 (also known as ANG4) is a histone monoubiquitinase, and the hub1 mutant has increased cell cycle duration in young leaves [25].

Bottom Line: We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations.The analysis reveals that part of the Arabidopsis transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules.Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Sciences, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel. dafniosn@post.tau.ac.il

ABSTRACT

Background: Analyses of gene expression data from microarray experiments has become a central tool for identifying co-regulated, functional gene modules. A crucial aspect of such analysis is the integration of data from different experiments and different laboratories. How to weigh the contribution of different experiments is an important point influencing the final outcomes. We have developed a novel method for this integration, and applied it to genome-wide data from multiple Arabidopsis microarray experiments performed under a variety of experimental conditions. The goal of this study is to identify functional globally co-regulated gene modules in the Arabidopsis genome.

Results: Following the analysis of 21,000 Arabidopsis genes in 43 datasets and about 2 x 10(8) gene pairs, we identified a globally co-expressed gene network. We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations. Two types of modules were identified in the regulatory network that differed in their sensitivity to the node-scoring parameter; we further showed these two pertain to general and specialized modules. Some of these modules were further investigated using the Genevestigator compendium of microarray experiments. Analyses of smaller subsets of data lead to the identification of condition-specific modules.

Conclusion: Our method for identification of gene clusters allows the integration of diverse microarray experiments from many sources. The analysis reveals that part of the Arabidopsis transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules. Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.

Show MeSH
Related in: MedlinePlus