Victors: a web-based knowledge base of virulence factors in human and animal pathogens - PubMed (original) (raw)

. 2019 Jan 8;47(D1):D693-D700.

doi: 10.1093/nar/gky999.

Li Li 2, Edison Ong 1, Shunzhou Deng 1 3, Guanghua Fu 1 4, Yu Lin 1, Brian Yang 1, Shelley Zhang 1, Zhenzong Fa 5, Bin Zhao 1, Zuoshuang Xiang 1, Yongqing Li 6, Xing-Ming Zhao 7, Michal A Olszewski 5, Luonan Chen 2 8 9, Yongqun He 1

Affiliations

Victors: a web-based knowledge base of virulence factors in human and animal pathogens

Samantha Sayers et al. Nucleic Acids Res. 2019.

Abstract

Virulence factors (VFs) are molecules that allow microbial pathogens to overcome host defense mechanisms and cause disease in a host. It is critical to study VFs for better understanding microbial pathogenesis and host defense mechanisms. Victors (http://www.phidias.us/victors) is a novel, manually curated, web-based integrative knowledge base and analysis resource for VFs of pathogens that cause infectious diseases in human and animals. Currently, Victors contains 5296 VFs obtained via manual annotation from peer-reviewed publications, with 4648, 179, 105 and 364 VFs originating from 51 bacterial, 54 viral, 13 parasitic and 8 fungal species, respectively. Our data analysis identified many VF-specific patterns. Within the global VF pool, cytoplasmic proteins were more common, while adhesins were less common compared to findings on protective vaccine antigens. Many VFs showed homology with host proteins and the human proteins interacting with VFs represented the hubs of human-pathogen interactions. All Victors data are queriable with a user-friendly web interface. The VFs can also be searched by a customized BLAST sequence similarity searching program. These VFs and their interactions with the host are represented in a machine-readable Ontology of Host-Pathogen Interactions. Victors supports the 'One Health' research as a vital source of VFs in human and animal pathogens.

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Figures

Figure 1.

Figure 1.

The workflow of the Victors virulence factor annotation and analysis. .

Figure 2.

Figure 2.

Landscapes of predicted bacteria pathogen–human PPIs. (A) All 15 334 PPIs. (B) This figure shows that two pathogen proteins (GPT pyrophosphokinase rsh) from Brucella suis (Q8CY42) and Brucella melitensis (Q8YG65) interact with a group of human proteins (blue dots) on tRNA level, such as t-RNA editing proteins, tRNA ligase proteins. The GO enrichment analysis reveals that this group of proteins is enriched in tRNA aminoacylation (A2RTX5|Q9BW92|Q5JTZ9|P49588|P26639), corrected _P_-value 9.5487E-12. (C) This figure shows that two human proteins lengsin (Q5TDP6) and Glutamine synthetase (P15104) interact with a group of pathogen proteins from different species, such as Streptococcus pneumonia and Brucella suis, Brucella melitensis. Interestingly, all pathogen proteins are Glutamine synthetase. Nodes in red color are pathogen proteins, and nodes in blue are human proteins.

Figure 3.

Figure 3.

Example of Victors data query and BLAST sequence similarity analysis. In this example, a user selected ‘_Mycobacterium tuberculosis_’ in the ‘Pathogen or Disease’ menu bar and typed ‘transcriptional regulatory protein’. After clicking the ‘Search’ button, a list of 19 genes was shown up in the results page. A click on the Victors ID ‘110’ (the forth on the list) led to another page providing details about the VF (e.g. the gene mutation phenotype information and predicted interacting host proteins). A BLAST search was initiated by clicking ‘BLAST’.

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