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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
Functional assignments and expression profiles of genes with the most and the least variable expression across multiple conditions. (A) 100 genes with the most variable expression (highest standard deviation of logE). (B) 100 genes with the most steady expression (lowest standard deviation of logE). The scale along Y axis (expression values) is the same for both plots to facilitate comparison of the expression profiles between them. Inlet shows a version of plot B with zoomed scale of expression values.
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Figure 7: Functional assignments and expression profiles of genes with the most and the least variable expression across multiple conditions. (A) 100 genes with the most variable expression (highest standard deviation of logE). (B) 100 genes with the most steady expression (lowest standard deviation of logE). The scale along Y axis (expression values) is the same for both plots to facilitate comparison of the expression profiles between them. Inlet shows a version of plot B with zoomed scale of expression values.

Mentions: We identified the genes with highly varied expression, little variation in expression, as well as those genes that had sub- or super- mean levels of expression, from the expression profiles of the 22,746 probes in the Arabidopsis ATH1 chip using the same 963-chips dataset. To evaluate whether the genes with extremes in expression patterns have any particular characteristics, the functions of the 100 genes with the most varied expression, the steadiest expression and also those with the highest and lowest expression were assigned to functional classes based on TAIR and GO annotations and manual curation (Figure 7 and Additional file 3).


Regulon organization of Arabidopsis.

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

Functional assignments and expression profiles of genes with the most and the least variable expression across multiple conditions. (A) 100 genes with the most variable expression (highest standard deviation of logE). (B) 100 genes with the most steady expression (lowest standard deviation of logE). The scale along Y axis (expression values) is the same for both plots to facilitate comparison of the expression profiles between them. Inlet shows a version of plot B with zoomed scale of expression values.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Functional assignments and expression profiles of genes with the most and the least variable expression across multiple conditions. (A) 100 genes with the most variable expression (highest standard deviation of logE). (B) 100 genes with the most steady expression (lowest standard deviation of logE). The scale along Y axis (expression values) is the same for both plots to facilitate comparison of the expression profiles between them. Inlet shows a version of plot B with zoomed scale of expression values.
Mentions: We identified the genes with highly varied expression, little variation in expression, as well as those genes that had sub- or super- mean levels of expression, from the expression profiles of the 22,746 probes in the Arabidopsis ATH1 chip using the same 963-chips dataset. To evaluate whether the genes with extremes in expression patterns have any particular characteristics, the functions of the 100 genes with the most varied expression, the steadiest expression and also those with the highest and lowest expression were assigned to functional classes based on TAIR and GO annotations and manual curation (Figure 7 and Additional file 3).

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