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EHFPI: a database and analysis resource of essential host factors for pathogenic infection.

Liu Y, Xie D, Han L, Bai H, Li F, Wang S, Bo X - Nucleic Acids Res. (2014)

Bottom Line: High-throughput screening and computational technology has greatly changed the face of microbiology in better understanding pathogen-host interactions.The EHFPI web interface provides appropriate tools that allow efficient query of EHF data and visualization of custom-made analysis results.EHFPI data and tools shall keep available without charge and serve the microbiology, biomedicine and pharmaceutics research communities, to finally facilitate the development of diagnostics, prophylactics and therapeutics for human pathogens.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R.China.

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Related in: MedlinePlus

(A) List of pathogen interacting protein (PIP) analysis result for EHFs of IAV. (B) Partial illustration of the human PPI network for EHF gene TP53 of IAV. An automatically generated graph can be used to view the interactions and topology properties (hubs and bottlenecks) of EHFs in the human PPI network. And for each interaction, brief information on annotations and external links to supporting evidence are provided. Further within-network search can be performed using gene symbol(s), with matched results highlighted in the viewer window.
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Figure 4: (A) List of pathogen interacting protein (PIP) analysis result for EHFs of IAV. (B) Partial illustration of the human PPI network for EHF gene TP53 of IAV. An automatically generated graph can be used to view the interactions and topology properties (hubs and bottlenecks) of EHFs in the human PPI network. And for each interaction, brief information on annotations and external links to supporting evidence are provided. Further within-network search can be performed using gene symbol(s), with matched results highlighted in the viewer window.

Mentions: For the current use case, the PIP analysis identified 260 out of 1213 EHF genes (21.43%) for IAV as PIPs (Figure 4A), which means the large proportion of EHF gene products (78.57%) are not direct interacting proteins for IAV. Meanwhile, a total of 876 interactions were observed for the 260 EHF gene products that are also PIPs for IAV. Of note, the most highly interconnected EHF gene products for IAV include TP53 (i.e. 272 interactions, Figure 4B), EP300 (i.e. 211 interactions), GRB2 (i.e. 195 interactions) and PRKCA (i.e. 174 interactions), these basic topological properties of which can be easily summarized in the csv file for user download (Supplementary Table S2). This result implies that dysregulation of these EHF genes upon infection may perturb multiple host cell functions of biological essentiality and thereby affect the consequences where infection may lead to. Further, users can refer to the Search result on the start page of PIP analysis for detailed PIP resource information on interested EHF(s), e.g. TP53 (cellular tumor antigen p53, Figure 4A). This highly interacted EHF gene product of IAV, is also the PIP for eight other virus types, including HIV-1, HCV, Simian virus 40, Human adenovirus 1 and 2, Human papillomavirus (type 11, 16, 18 and 31), Bovine papillomavirus type 1, Alphapapillomavirus 7 and JC polyomavirus. Together, this comparative analysis of EHF and PIP provides insights into the functional understanding of EHFs at translational level.


EHFPI: a database and analysis resource of essential host factors for pathogenic infection.

Liu Y, Xie D, Han L, Bai H, Li F, Wang S, Bo X - Nucleic Acids Res. (2014)

(A) List of pathogen interacting protein (PIP) analysis result for EHFs of IAV. (B) Partial illustration of the human PPI network for EHF gene TP53 of IAV. An automatically generated graph can be used to view the interactions and topology properties (hubs and bottlenecks) of EHFs in the human PPI network. And for each interaction, brief information on annotations and external links to supporting evidence are provided. Further within-network search can be performed using gene symbol(s), with matched results highlighted in the viewer window.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383917&req=5

Figure 4: (A) List of pathogen interacting protein (PIP) analysis result for EHFs of IAV. (B) Partial illustration of the human PPI network for EHF gene TP53 of IAV. An automatically generated graph can be used to view the interactions and topology properties (hubs and bottlenecks) of EHFs in the human PPI network. And for each interaction, brief information on annotations and external links to supporting evidence are provided. Further within-network search can be performed using gene symbol(s), with matched results highlighted in the viewer window.
Mentions: For the current use case, the PIP analysis identified 260 out of 1213 EHF genes (21.43%) for IAV as PIPs (Figure 4A), which means the large proportion of EHF gene products (78.57%) are not direct interacting proteins for IAV. Meanwhile, a total of 876 interactions were observed for the 260 EHF gene products that are also PIPs for IAV. Of note, the most highly interconnected EHF gene products for IAV include TP53 (i.e. 272 interactions, Figure 4B), EP300 (i.e. 211 interactions), GRB2 (i.e. 195 interactions) and PRKCA (i.e. 174 interactions), these basic topological properties of which can be easily summarized in the csv file for user download (Supplementary Table S2). This result implies that dysregulation of these EHF genes upon infection may perturb multiple host cell functions of biological essentiality and thereby affect the consequences where infection may lead to. Further, users can refer to the Search result on the start page of PIP analysis for detailed PIP resource information on interested EHF(s), e.g. TP53 (cellular tumor antigen p53, Figure 4A). This highly interacted EHF gene product of IAV, is also the PIP for eight other virus types, including HIV-1, HCV, Simian virus 40, Human adenovirus 1 and 2, Human papillomavirus (type 11, 16, 18 and 31), Bovine papillomavirus type 1, Alphapapillomavirus 7 and JC polyomavirus. Together, this comparative analysis of EHF and PIP provides insights into the functional understanding of EHFs at translational level.

Bottom Line: High-throughput screening and computational technology has greatly changed the face of microbiology in better understanding pathogen-host interactions.The EHFPI web interface provides appropriate tools that allow efficient query of EHF data and visualization of custom-made analysis results.EHFPI data and tools shall keep available without charge and serve the microbiology, biomedicine and pharmaceutics research communities, to finally facilitate the development of diagnostics, prophylactics and therapeutics for human pathogens.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R.China.

Show MeSH
Related in: MedlinePlus