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Characterization and comparison of the tissue-related modules in human and mouse.

Yang R, Su B - PLoS ONE (2010)

Bottom Line: Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes.In addition, we defined a novel quantity, "total constraint intensity," a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context.We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

ABSTRACT

Background: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches.

Results: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity," a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse.

Conclusions: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions.

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Sensitivity of the modules with respect to the size of the dataset.Shown in the plot are the mean and standard deviation of the similarity between the modules identified when a fraction of data is removed from the raw dataset and those identified with the full dataset.
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pone-0011730-g008: Sensitivity of the modules with respect to the size of the dataset.Shown in the plot are the mean and standard deviation of the similarity between the modules identified when a fraction of data is removed from the raw dataset and those identified with the full dataset.

Mentions: To address the concerns regarding the robustness of modules, we conducted a sensitivity test by leaving out 5%, 10%, 15% and 20% of the genes from the raw data. Our results demonstrated that the modules are robust. For example, even though we removed up to 20% of the data of the human and mouse expression matrixes, we can still recover modules with a mean similarity of 0.80, and 0.86 to those identified by using the full dataset, respectively (see Figure 8).


Characterization and comparison of the tissue-related modules in human and mouse.

Yang R, Su B - PLoS ONE (2010)

Sensitivity of the modules with respect to the size of the dataset.Shown in the plot are the mean and standard deviation of the similarity between the modules identified when a fraction of data is removed from the raw dataset and those identified with the full dataset.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2908688&req=5

pone-0011730-g008: Sensitivity of the modules with respect to the size of the dataset.Shown in the plot are the mean and standard deviation of the similarity between the modules identified when a fraction of data is removed from the raw dataset and those identified with the full dataset.
Mentions: To address the concerns regarding the robustness of modules, we conducted a sensitivity test by leaving out 5%, 10%, 15% and 20% of the genes from the raw data. Our results demonstrated that the modules are robust. For example, even though we removed up to 20% of the data of the human and mouse expression matrixes, we can still recover modules with a mean similarity of 0.80, and 0.86 to those identified by using the full dataset, respectively (see Figure 8).

Bottom Line: Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes.In addition, we defined a novel quantity, "total constraint intensity," a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context.We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

ABSTRACT

Background: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches.

Results: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity," a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse.

Conclusions: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions.

Show MeSH