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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.

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Regulons with organelle-specific functions and organelle-encoded genes. Regulon 2, photosynthesis (for clarity, representative expression profiles of 200 randomly chosen genes from this regulon are shown) (A); Regulon 49, plastid-encoded genes (B); Regulon 29, mitochondrial respiration (C); Regulon 34, mitochondrion-encoded genes (D). The plots on the right side show expression profiles of the genes in respective regulon (each gene depicted with different color) across the 424 samples in the dataset. The samples have been arranged according to plant tissue. Pie charts are based on manual annotations from published data. RNA profiles plotted using MetaOmGraph [24,124].
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Figure 4: Regulons with organelle-specific functions and organelle-encoded genes. Regulon 2, photosynthesis (for clarity, representative expression profiles of 200 randomly chosen genes from this regulon are shown) (A); Regulon 49, plastid-encoded genes (B); Regulon 29, mitochondrial respiration (C); Regulon 34, mitochondrion-encoded genes (D). The plots on the right side show expression profiles of the genes in respective regulon (each gene depicted with different color) across the 424 samples in the dataset. The samples have been arranged according to plant tissue. Pie charts are based on manual annotations from published data. RNA profiles plotted using MetaOmGraph [24,124].

Mentions: Regulon 2, the second biggest cluster, contains 971 mainly nuclear-encoded genes involved in chloroplast biogenesis and photosynthesis (overrepresented GO terms: chloroplast: p-value < 10-85, thylakoid: p-value = 1.02 × 10-28, photosynthesis: p-value = 1.68 × 10-15) (Figure 4A). Nineteen genes are involved in the formation and development of plastid organelle: its biogenesis, organization, fission and relocation. An example of these genes is thylakoid formation 1 (PSB29), required for thylakoid membrane organization [62]. Transporters of sodium, calcium and other metals are represented. Two hundreds and eighteen genes in Regulon 2 have a photosynthesis-related activity. Of these, 36 encode enzymes required for synthesis of the photosynthetic apparatus metabolome (porphyrin pigments, tetrahydrofolate, chlorophyll, carotenoids, and other plastidic isoprenoids). Seventy five genes encode plastidic ribosome constituents and related functions. Twenty genes from the Calvin cycle, 16 genes from photorespiration, 14 genes representing a subset of plastidic glycolysis enzymes, and 11 genes involved in starch metabolism are also present, reflecting the coupling of these metabolic activities with the light reactions of photosynthesis. In addition, enzymes for plastidic metabolism of amino acids and nucleotides are represented.


Regulon organization of Arabidopsis.

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

Regulons with organelle-specific functions and organelle-encoded genes. Regulon 2, photosynthesis (for clarity, representative expression profiles of 200 randomly chosen genes from this regulon are shown) (A); Regulon 49, plastid-encoded genes (B); Regulon 29, mitochondrial respiration (C); Regulon 34, mitochondrion-encoded genes (D). The plots on the right side show expression profiles of the genes in respective regulon (each gene depicted with different color) across the 424 samples in the dataset. The samples have been arranged according to plant tissue. Pie charts are based on manual annotations from published data. RNA profiles plotted using MetaOmGraph [24,124].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Regulons with organelle-specific functions and organelle-encoded genes. Regulon 2, photosynthesis (for clarity, representative expression profiles of 200 randomly chosen genes from this regulon are shown) (A); Regulon 49, plastid-encoded genes (B); Regulon 29, mitochondrial respiration (C); Regulon 34, mitochondrion-encoded genes (D). The plots on the right side show expression profiles of the genes in respective regulon (each gene depicted with different color) across the 424 samples in the dataset. The samples have been arranged according to plant tissue. Pie charts are based on manual annotations from published data. RNA profiles plotted using MetaOmGraph [24,124].
Mentions: Regulon 2, the second biggest cluster, contains 971 mainly nuclear-encoded genes involved in chloroplast biogenesis and photosynthesis (overrepresented GO terms: chloroplast: p-value < 10-85, thylakoid: p-value = 1.02 × 10-28, photosynthesis: p-value = 1.68 × 10-15) (Figure 4A). Nineteen genes are involved in the formation and development of plastid organelle: its biogenesis, organization, fission and relocation. An example of these genes is thylakoid formation 1 (PSB29), required for thylakoid membrane organization [62]. Transporters of sodium, calcium and other metals are represented. Two hundreds and eighteen genes in Regulon 2 have a photosynthesis-related activity. Of these, 36 encode enzymes required for synthesis of the photosynthetic apparatus metabolome (porphyrin pigments, tetrahydrofolate, chlorophyll, carotenoids, and other plastidic isoprenoids). Seventy five genes encode plastidic ribosome constituents and related functions. Twenty genes from the Calvin cycle, 16 genes from photorespiration, 14 genes representing a subset of plastidic glycolysis enzymes, and 11 genes involved in starch metabolism are also present, reflecting the coupling of these metabolic activities with the light reactions of photosynthesis. In addition, enzymes for plastidic metabolism of amino acids and nucleotides are represented.

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