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. 2007;8(7):R150.
doi: 10.1186/gb-2007-8-7-r150.

PHIDIAS: a pathogen-host interaction data integration and analysis system

Zuoshuang Xiang  1 , Yuying Tian, Yongqun He
Affiliations

PHIDIAS: a pathogen-host interaction data integration and analysis system

Zuoshuang Xiang et al. Genome Biol. 2007.

Abstract

The Pathogen-Host Interaction Data Integration and Analysis System (PHIDIAS) is a web-based database system that serves as a centralized source to search, compare, and analyze integrated genome sequences, conserved domains, and gene expression data related to pathogen-host interactions (PHIs) for pathogen species designated as high priority agents for public health and biological security. In addition, PHIDIAS allows submission, search and analysis of PHI genes and molecular networks curated from peer-reviewed literature. PHIDIAS is publicly available at http://www.phidias.us.

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Figures

Figure 1
Figure 1
PHIDIAS data flow. (a) The PHIDIAS system architecture. (b) PhiDB data flow among key elements of different PhiDB database modules. The relationships among these elements are represented by the following signs: *, zero or more; 1, one; and 2...*, two or more. For example, the labeling of a pathway with '1' and '2...*' indicates that one pathway includes two or more interactions.
Figure 2
Figure 2
Comparison and analyses of sodC genes in the PGBrowser. Thirty two sodC genes are found in 32 genomes from 11 bacteria species (a), including sodC from B. abortus strain 9-941 (b).
Figure 3
Figure 3
Integrative pathogen gene information in PHIDIAS.
Figure 4
Figure 4
Example of Pacodom applications. (a) Pacodom search of 'phagocytosis'. (b) There are 42 Nramp protein matches from 42 pathogen genomes of 15 microbial species available in Pacodom.
Figure 5
Figure 5
PhiDB Topic Search. The PhiDB Topic Search web interface is shown on the left and a comparison of immunoassays for diagnosis of B. melitensis and B. anthracis is shown on the right.
Figure 6
Figure 6
Gene search web interface in Phigen.
Figure 7
Figure 7
Visualization of an E. coli pathogenesis network in Phinet. A click on each node provides detailed information about a biological object in the bottom frame. When a mouse cursor moves over a node, a brief description of the biological object will appear. An interaction between biological objects is represented by a centered gray ball and arrows between nodes. Once the centered gray ball is clicked, details about the specific interaction appear in the bottom frame. Subcellular locations of biological objects are differentiated by the node border colors. The biological object types (for example, protein or gene) are represented by a combination of the node background colors and shapes. The program also displays different interactions, such as inhibition (solid T sign), activation (solid arrow), and indirect effects (dashed line).
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