Limits...
Regulon organization of Arabidopsis.

Mentzen WI, Wurtele ES - BMC Plant Biol. (2008)

Bottom Line: To assess the significance of the clustering results, the statistical over-representation of GO terms is averaged over this set of regulons and compared to the analogous values for 100 randomly-generated sets of clusters.The set of regulons derived from the experimental data scores significantly better than any of the randomly-generated sets.This analysis creates a framework for generation of experimentally testable hypotheses, gives insight into the concerted functions of Arabidopsis at the transcript level, and provides a test bed for comparative systems analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: CRS4 Bioinformatics Laboratory, Parco Scientifico e Technologico POLARIS, 09010 Pula (CA), Italy. wimentzen@gmail.com

ABSTRACT

Background: Despite the mounting research on Arabidopsis transcriptome and the powerful tools to explore biology of this model plant, the organization of expression of Arabidopsis genome is only partially understood. Here, we create a coexpression network from a 22,746 Affymetrix probes dataset derived from 963 microarray chips that query the transcriptome in response to a wide variety of environmentally, genetically, and developmentally induced perturbations.

Results: Markov chain graph clustering of the coexpression network delineates 998 regulons ranging from one to 1623 genes in size. To assess the significance of the clustering results, the statistical over-representation of GO terms is averaged over this set of regulons and compared to the analogous values for 100 randomly-generated sets of clusters. The set of regulons derived from the experimental data scores significantly better than any of the randomly-generated sets. Most regulons correspond to identifiable biological processes and include a combination of genes encoding related developmental, metabolic pathway, and regulatory functions. In addition, nearly 3000 genes of unknown molecular function or process are assigned to a regulon. Only five regulons contain plastomic genes; four of these are exclusively plastomic. In contrast, expression of the mitochondrial genome is highly integrated with that of nuclear genes; each of the seven regulons containing mitochondrial genes also incorporates nuclear genes. The network of regulons reveals a higher-level organization, with dense local neighborhoods articulated for photosynthetic function, genetic information processing, and stress response.

Conclusion: This analysis creates a framework for generation of experimentally testable hypotheses, gives insight into the concerted functions of Arabidopsis at the transcript level, and provides a test bed for comparative systems analysis.

Show MeSH
Higher-order structure in the coexpression network. All regulons containing at least 20 genes are depicted; these comprise a total of 9,436 genes. Regulons are represented by ovals numbered 1 through 69. A linkage between two clusters means that one or more genes in one of the clusters are correlated with one or more genes in the other cluster. As observed from the proximity of regulons with similar broader functional category, three super-clusters of regulons are revealed: regulons related to information-related functions (purple), plastidic functions (green) and defense response-related functions (yellow). The predominant functionality of each regulon is defined in Table 1. Network was visualized using the GraphExplore tool [118].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2567982&req=5

Figure 3: Higher-order structure in the coexpression network. All regulons containing at least 20 genes are depicted; these comprise a total of 9,436 genes. Regulons are represented by ovals numbered 1 through 69. A linkage between two clusters means that one or more genes in one of the clusters are correlated with one or more genes in the other cluster. As observed from the proximity of regulons with similar broader functional category, three super-clusters of regulons are revealed: regulons related to information-related functions (purple), plastidic functions (green) and defense response-related functions (yellow). The predominant functionality of each regulon is defined in Table 1. Network was visualized using the GraphExplore tool [118].

Mentions: A simplified view of the coexpression network formed by 69 largest regulons is shown in Figure 3. A link between two regulons means that there are genes in one regulon that are correlated with genes in the second regulon. It is interesting to note the higher-order grouping of the regulons that predominantly contain genes with genetic information-related, photosynthetic/plastidic, and stress response functions.


Regulon organization of Arabidopsis.

Mentzen WI, Wurtele ES - BMC Plant Biol. (2008)

Higher-order structure in the coexpression network. All regulons containing at least 20 genes are depicted; these comprise a total of 9,436 genes. Regulons are represented by ovals numbered 1 through 69. A linkage between two clusters means that one or more genes in one of the clusters are correlated with one or more genes in the other cluster. As observed from the proximity of regulons with similar broader functional category, three super-clusters of regulons are revealed: regulons related to information-related functions (purple), plastidic functions (green) and defense response-related functions (yellow). The predominant functionality of each regulon is defined in Table 1. Network was visualized using the GraphExplore tool [118].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2567982&req=5

Figure 3: Higher-order structure in the coexpression network. All regulons containing at least 20 genes are depicted; these comprise a total of 9,436 genes. Regulons are represented by ovals numbered 1 through 69. A linkage between two clusters means that one or more genes in one of the clusters are correlated with one or more genes in the other cluster. As observed from the proximity of regulons with similar broader functional category, three super-clusters of regulons are revealed: regulons related to information-related functions (purple), plastidic functions (green) and defense response-related functions (yellow). The predominant functionality of each regulon is defined in Table 1. Network was visualized using the GraphExplore tool [118].
Mentions: A simplified view of the coexpression network formed by 69 largest regulons is shown in Figure 3. A link between two regulons means that there are genes in one regulon that are correlated with genes in the second regulon. It is interesting to note the higher-order grouping of the regulons that predominantly contain genes with genetic information-related, photosynthetic/plastidic, and stress response functions.

Bottom Line: To assess the significance of the clustering results, the statistical over-representation of GO terms is averaged over this set of regulons and compared to the analogous values for 100 randomly-generated sets of clusters.The set of regulons derived from the experimental data scores significantly better than any of the randomly-generated sets.This analysis creates a framework for generation of experimentally testable hypotheses, gives insight into the concerted functions of Arabidopsis at the transcript level, and provides a test bed for comparative systems analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: CRS4 Bioinformatics Laboratory, Parco Scientifico e Technologico POLARIS, 09010 Pula (CA), Italy. wimentzen@gmail.com

ABSTRACT

Background: Despite the mounting research on Arabidopsis transcriptome and the powerful tools to explore biology of this model plant, the organization of expression of Arabidopsis genome is only partially understood. Here, we create a coexpression network from a 22,746 Affymetrix probes dataset derived from 963 microarray chips that query the transcriptome in response to a wide variety of environmentally, genetically, and developmentally induced perturbations.

Results: Markov chain graph clustering of the coexpression network delineates 998 regulons ranging from one to 1623 genes in size. To assess the significance of the clustering results, the statistical over-representation of GO terms is averaged over this set of regulons and compared to the analogous values for 100 randomly-generated sets of clusters. The set of regulons derived from the experimental data scores significantly better than any of the randomly-generated sets. Most regulons correspond to identifiable biological processes and include a combination of genes encoding related developmental, metabolic pathway, and regulatory functions. In addition, nearly 3000 genes of unknown molecular function or process are assigned to a regulon. Only five regulons contain plastomic genes; four of these are exclusively plastomic. In contrast, expression of the mitochondrial genome is highly integrated with that of nuclear genes; each of the seven regulons containing mitochondrial genes also incorporates nuclear genes. The network of regulons reveals a higher-level organization, with dense local neighborhoods articulated for photosynthetic function, genetic information processing, and stress response.

Conclusion: This analysis creates a framework for generation of experimentally testable hypotheses, gives insight into the concerted functions of Arabidopsis at the transcript level, and provides a test bed for comparative systems analysis.

Show MeSH