Limits...
Functional networking of human divergently paired genes (DPGs).

Xie B, Wang D, Duan Y, Yu J, Lei H - PLoS ONE (2013)

Bottom Line: Here we report a network-based comprehensive analysis on human DPGs and our results indicate that the two members of the DPGs tend to participate in different biological processes while enforcing related functions as modules.The functional network bridged by DPGs consists of three major modules.This module also shows low variation in expression in both CNS (central nervous system) and non-CNS tissues.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China ; University of Chinese Academy of Sciences, Beijing, China.

ABSTRACT
Divergently paired genes (DPGs), also known as bidirectional (head-to-head positioned) genes, are conserved across species and lineages, and thus deemed to be exceptional in genomic organization and functional regulation. Despite previous investigations on the features of their conservation and gene organization, the functional relationship among DPGs in a given species and lineage has not been thoroughly clarified. Here we report a network-based comprehensive analysis on human DPGs and our results indicate that the two members of the DPGs tend to participate in different biological processes while enforcing related functions as modules. Comparing to randomly paired genes as a control, the DPG pairs have a tendency to be clustered in similar "cellular components" and involved in similar "molecular functions". The functional network bridged by DPGs consists of three major modules. The largest module includes many house-keeping genes involved in core cellular activities. This module also shows low variation in expression in both CNS (central nervous system) and non-CNS tissues. Based on analyses of disease transcriptome data, we further suggest that this particular module may play crucial roles in HIV infection and its disease mechanism.

Show MeSH

Related in: MedlinePlus

The interaction map of functional sets that linked by DPGs.We name the functional sets that linked by DPGs as interacted sets, and the linkage is based on the situation that one gene of a DPG pair is annotated for one function and the other for another functions. The interaction rate is related to the linked DPGs number and the set size. Interaction rate >7% is chosen to cover more functional sets. The edge color depends on the DPGs number that linked two adjacent sets, and the edge width depends on the interaction rate between two sets. Module 1 is related to histone and DNA packaging. Module 2 is related to regulation of cell cycle, gene expression, energy and some other functions. Module 3 is related to cancer signaling.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3815023&req=5

pone-0078896-g003: The interaction map of functional sets that linked by DPGs.We name the functional sets that linked by DPGs as interacted sets, and the linkage is based on the situation that one gene of a DPG pair is annotated for one function and the other for another functions. The interaction rate is related to the linked DPGs number and the set size. Interaction rate >7% is chosen to cover more functional sets. The edge color depends on the DPGs number that linked two adjacent sets, and the edge width depends on the interaction rate between two sets. Module 1 is related to histone and DNA packaging. Module 2 is related to regulation of cell cycle, gene expression, energy and some other functions. Module 3 is related to cancer signaling.

Mentions: We organized the interaction map in a clear layout (Figure 3) by setting the interaction rate >0.07 to maximize the coverage of functional sets (90 functional sets, 1,262 DPGs, relative coverage 92.86%) and to demonstrate the functional connections. Since DPG gene pairs share the same promoter sequences, the adjacent nodes on the interaction map are most likely to have better correlated expression. Based on the pathway absolute score calculated from dataset GSE3526 (details in Methods), the top 10 correlated DPGs are highlighted on the interaction map (Figure S3), all of which reside in the densely connected regions.


Functional networking of human divergently paired genes (DPGs).

Xie B, Wang D, Duan Y, Yu J, Lei H - PLoS ONE (2013)

The interaction map of functional sets that linked by DPGs.We name the functional sets that linked by DPGs as interacted sets, and the linkage is based on the situation that one gene of a DPG pair is annotated for one function and the other for another functions. The interaction rate is related to the linked DPGs number and the set size. Interaction rate >7% is chosen to cover more functional sets. The edge color depends on the DPGs number that linked two adjacent sets, and the edge width depends on the interaction rate between two sets. Module 1 is related to histone and DNA packaging. Module 2 is related to regulation of cell cycle, gene expression, energy and some other functions. Module 3 is related to cancer signaling.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815023&req=5

pone-0078896-g003: The interaction map of functional sets that linked by DPGs.We name the functional sets that linked by DPGs as interacted sets, and the linkage is based on the situation that one gene of a DPG pair is annotated for one function and the other for another functions. The interaction rate is related to the linked DPGs number and the set size. Interaction rate >7% is chosen to cover more functional sets. The edge color depends on the DPGs number that linked two adjacent sets, and the edge width depends on the interaction rate between two sets. Module 1 is related to histone and DNA packaging. Module 2 is related to regulation of cell cycle, gene expression, energy and some other functions. Module 3 is related to cancer signaling.
Mentions: We organized the interaction map in a clear layout (Figure 3) by setting the interaction rate >0.07 to maximize the coverage of functional sets (90 functional sets, 1,262 DPGs, relative coverage 92.86%) and to demonstrate the functional connections. Since DPG gene pairs share the same promoter sequences, the adjacent nodes on the interaction map are most likely to have better correlated expression. Based on the pathway absolute score calculated from dataset GSE3526 (details in Methods), the top 10 correlated DPGs are highlighted on the interaction map (Figure S3), all of which reside in the densely connected regions.

Bottom Line: Here we report a network-based comprehensive analysis on human DPGs and our results indicate that the two members of the DPGs tend to participate in different biological processes while enforcing related functions as modules.The functional network bridged by DPGs consists of three major modules.This module also shows low variation in expression in both CNS (central nervous system) and non-CNS tissues.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China ; University of Chinese Academy of Sciences, Beijing, China.

ABSTRACT
Divergently paired genes (DPGs), also known as bidirectional (head-to-head positioned) genes, are conserved across species and lineages, and thus deemed to be exceptional in genomic organization and functional regulation. Despite previous investigations on the features of their conservation and gene organization, the functional relationship among DPGs in a given species and lineage has not been thoroughly clarified. Here we report a network-based comprehensive analysis on human DPGs and our results indicate that the two members of the DPGs tend to participate in different biological processes while enforcing related functions as modules. Comparing to randomly paired genes as a control, the DPG pairs have a tendency to be clustered in similar "cellular components" and involved in similar "molecular functions". The functional network bridged by DPGs consists of three major modules. The largest module includes many house-keeping genes involved in core cellular activities. This module also shows low variation in expression in both CNS (central nervous system) and non-CNS tissues. Based on analyses of disease transcriptome data, we further suggest that this particular module may play crucial roles in HIV infection and its disease mechanism.

Show MeSH
Related in: MedlinePlus