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Improving the Understanding of Pathogenesis of Human Papillomavirus 16 via Mapping Protein-Protein Interaction Network.

Dong Y, Kuang Q, Dai X, Li R, Wu Y, Leng W, Li Y, Li M - Biomed Res Int (2015)

Bottom Line: Furthermore, not only was HPV16 highly prone to interact with hub proteins and bottleneck proteins, but also it could effectively affect a breadth of signaling pathways.In addition, we found that the HPV16 evolved into high carcinogenicity on the condition that its own reproduction had been ensured.Meanwhile, this work will contribute to providing potential new targets for antiviral therapeutics and help experimental research in the future.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Sichuan University, Chengdu 610064, China.

ABSTRACT
The human papillomavirus 16 (HPV16) has high risk to lead various cancers and afflictions, especially, the cervical cancer. Therefore, investigating the pathogenesis of HPV16 is very important for public health. Protein-protein interaction (PPI) network between HPV16 and human was used as a measure to improve our understanding of its pathogenesis. By adopting sequence and topological features, a support vector machine (SVM) model was built to predict new interactions between HPV16 and human proteins. All interactions were comprehensively investigated and analyzed. The analysis indicated that HPV16 enlarged its scope of influence by interacting with human proteins as much as possible. These interactions alter a broad array of cell cycle progression. Furthermore, not only was HPV16 highly prone to interact with hub proteins and bottleneck proteins, but also it could effectively affect a breadth of signaling pathways. In addition, we found that the HPV16 evolved into high carcinogenicity on the condition that its own reproduction had been ensured. Meanwhile, this work will contribute to providing potential new targets for antiviral therapeutics and help experimental research in the future.

No MeSH data available.


Related in: MedlinePlus

Flowchart to integrate and analyze PPI network between HPV16 and human proteins. A candidate interaction was found, if the human protein had homologs in the human PPI network. This method provided 3,022 candidate interactions. An SVM model was employed to evaluate candidate interactions and 1,121 interactions were left. Subsequently, these interactions were filtered if human proteins with targeted human proteins had the same as cellular component. 1,015 interactions were obtained; positive training set and test set were further filtered by tissue specificity. Finally, 877 interactions were obtained and analyzed. Solid lines delineate validated interactions between virus and human proteins, and dotted lines delineate candidate interactions which would be validated. Homologous proteins are surrounded by ellipse.
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fig1: Flowchart to integrate and analyze PPI network between HPV16 and human proteins. A candidate interaction was found, if the human protein had homologs in the human PPI network. This method provided 3,022 candidate interactions. An SVM model was employed to evaluate candidate interactions and 1,121 interactions were left. Subsequently, these interactions were filtered if human proteins with targeted human proteins had the same as cellular component. 1,015 interactions were obtained; positive training set and test set were further filtered by tissue specificity. Finally, 877 interactions were obtained and analyzed. Solid lines delineate validated interactions between virus and human proteins, and dotted lines delineate candidate interactions which would be validated. Homologous proteins are surrounded by ellipse.

Mentions: We extracted 174 interactions between HPV16 and human proteins and integrated a human PPI network including 193,801 interactions. A flowchart of the whole experiment is shown in Figure 1.


Improving the Understanding of Pathogenesis of Human Papillomavirus 16 via Mapping Protein-Protein Interaction Network.

Dong Y, Kuang Q, Dai X, Li R, Wu Y, Leng W, Li Y, Li M - Biomed Res Int (2015)

Flowchart to integrate and analyze PPI network between HPV16 and human proteins. A candidate interaction was found, if the human protein had homologs in the human PPI network. This method provided 3,022 candidate interactions. An SVM model was employed to evaluate candidate interactions and 1,121 interactions were left. Subsequently, these interactions were filtered if human proteins with targeted human proteins had the same as cellular component. 1,015 interactions were obtained; positive training set and test set were further filtered by tissue specificity. Finally, 877 interactions were obtained and analyzed. Solid lines delineate validated interactions between virus and human proteins, and dotted lines delineate candidate interactions which would be validated. Homologous proteins are surrounded by ellipse.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4414230&req=5

fig1: Flowchart to integrate and analyze PPI network between HPV16 and human proteins. A candidate interaction was found, if the human protein had homologs in the human PPI network. This method provided 3,022 candidate interactions. An SVM model was employed to evaluate candidate interactions and 1,121 interactions were left. Subsequently, these interactions were filtered if human proteins with targeted human proteins had the same as cellular component. 1,015 interactions were obtained; positive training set and test set were further filtered by tissue specificity. Finally, 877 interactions were obtained and analyzed. Solid lines delineate validated interactions between virus and human proteins, and dotted lines delineate candidate interactions which would be validated. Homologous proteins are surrounded by ellipse.
Mentions: We extracted 174 interactions between HPV16 and human proteins and integrated a human PPI network including 193,801 interactions. A flowchart of the whole experiment is shown in Figure 1.

Bottom Line: Furthermore, not only was HPV16 highly prone to interact with hub proteins and bottleneck proteins, but also it could effectively affect a breadth of signaling pathways.In addition, we found that the HPV16 evolved into high carcinogenicity on the condition that its own reproduction had been ensured.Meanwhile, this work will contribute to providing potential new targets for antiviral therapeutics and help experimental research in the future.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Sichuan University, Chengdu 610064, China.

ABSTRACT
The human papillomavirus 16 (HPV16) has high risk to lead various cancers and afflictions, especially, the cervical cancer. Therefore, investigating the pathogenesis of HPV16 is very important for public health. Protein-protein interaction (PPI) network between HPV16 and human was used as a measure to improve our understanding of its pathogenesis. By adopting sequence and topological features, a support vector machine (SVM) model was built to predict new interactions between HPV16 and human proteins. All interactions were comprehensively investigated and analyzed. The analysis indicated that HPV16 enlarged its scope of influence by interacting with human proteins as much as possible. These interactions alter a broad array of cell cycle progression. Furthermore, not only was HPV16 highly prone to interact with hub proteins and bottleneck proteins, but also it could effectively affect a breadth of signaling pathways. In addition, we found that the HPV16 evolved into high carcinogenicity on the condition that its own reproduction had been ensured. Meanwhile, this work will contribute to providing potential new targets for antiviral therapeutics and help experimental research in the future.

No MeSH data available.


Related in: MedlinePlus