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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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Related in: MedlinePlus

All-to-all comparison of modules between human and mouse.The heat map (bi-clustered) displays a globally low similarity between the inter-species modules. The similarity between a pair of module is calculated by Eqs. (1).
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pone-0011730-g002: All-to-all comparison of modules between human and mouse.The heat map (bi-clustered) displays a globally low similarity between the inter-species modules. The similarity between a pair of module is calculated by Eqs. (1).

Mentions: In order to further examine the difference of modules between human and mouse, we compared the pair-wise modules derived from human and mouse with the use of similarity measurement calculated by Eqa. (1) (see Methods). As shown in Figure 2 and Figure S3, we can hardly find any pairs of modules with high similarity between species. Meanwhile, in order to further explore the relationship of modules between the two species, we conducted a hierarchical clustering of all the modules (Figure S4). The dendrograph indicated that all of the modules were separated into two “biggest” clusters, one harboring modules, the overwhelming majority of which are human-derived, and the other containing all but one mouse-derived modules. Taken together, the results suggested that the composition of the modules diverged extensively between the two species.


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

Yang R, Su B - PLoS ONE (2010)

All-to-all comparison of modules between human and mouse.The heat map (bi-clustered) displays a globally low similarity between the inter-species modules. The similarity between a pair of module is calculated by Eqs. (1).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0011730-g002: All-to-all comparison of modules between human and mouse.The heat map (bi-clustered) displays a globally low similarity between the inter-species modules. The similarity between a pair of module is calculated by Eqs. (1).
Mentions: In order to further examine the difference of modules between human and mouse, we compared the pair-wise modules derived from human and mouse with the use of similarity measurement calculated by Eqa. (1) (see Methods). As shown in Figure 2 and Figure S3, we can hardly find any pairs of modules with high similarity between species. Meanwhile, in order to further explore the relationship of modules between the two species, we conducted a hierarchical clustering of all the modules (Figure S4). The dendrograph indicated that all of the modules were separated into two “biggest” clusters, one harboring modules, the overwhelming majority of which are human-derived, and the other containing all but one mouse-derived modules. Taken together, the results suggested that the composition of the modules diverged extensively between the two species.

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
Related in: MedlinePlus