Protein (PSLT028/Q93GR5) Annotation. Expression Localizations Functions Interactions. RC Portal. Organism. Project. Experiment. Data Type. Master Protein Directory (PIR). Gene(s)/Protein(s). Data are made available to researchers in community standard formats.
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Master Protein Directory (PIR)
Data are made available to researchers in community standard formats
An Integrated Post-Genomic Data Resource for Host-Pathogen Interaction Profiles
Resource Center for
Biodefense Proteomics Research
C. Zhang1, S. Cammer1, O. Crasta1, R. Will1, M. Moore2, P. Mcgarvey3, C. Wu3, B. Sobral1
1- Virginia Bioinformatics Institute, 2- Social & Scientific Systems, Inc., 3- Georgetown University Medical Center
Example of Proteomics Resource Application
Visualization and Analysis Tools
High-throughput functional technologies that measure dynamic responses of living cells have generated massive amount of data. Storing and disseminating such data are critical to facilitating the exchange and integration of data and further analysis. To enable the application of the data from pathogen, host, and their interactions toward identification of targets for countermeasures, a Biodefense Proteomics Initiative has been established by NIAID through contracts with the seven proteomic research centers (PRCs) that generate data and reagents, and a Resource Center (RC) to manage the data and make it publicly accessible. The goals of RC are to: 1) provide data in standard formats; 2) enable data applications; 3) facilitate data visualization; and 4) link data to analysis tools.
Data Sets: Mass spectrometry, microarray, protein 3D structure and protein-protein interaction (Y2H ) and genomic clones.
Organisms: Bacillus anthracis, Mus musculus, Salmonella typhimurium, SARS-CoV, Vibrio cholerae, Yersinia pestis
Tools:Visualization and analysis are facilitated by web-based tools, such as gene ontology term analysis, cluster analysis, and 2D gel couple mass spectrometry data visualization.
The data at the Proteomics Resource Center at VBI has been integrated with the Protein Information Resource (PIR).
Web based protein-protein interaction visualization
Choose MS data set for log phase growth condition
Protein-protein interaction list
Select data for organism of interest (S. typhimurium)
Select a protein and explore its annotation
Select GO annotation for further study
Gene ontology frequency distribution
Visualization and analysis of expression profiles (e.g., clustering)
Key SARS proteins are visualized in interactive 3-D displays
An example of the interactive SARS protein structure annotations we are developing for the Data Center is shown in the figure. The figure highlights one of the views available for the nsp3 ADP-ribose-1’-phosphate phosphatase. In the view the interface between the two subunits in the assymetric crystal unit are shown. Hydrophobic residues contributing to the monomer-monomer interface are illustrated, along with two loops that contact between the monomers. Interactive 3-D structure presentations will enable researchers using the site to better understand the relevance of features illustrated in the manuscript related to this structure deposition. These view allow researchers to better use the structural information in design of therapeutics and vaccines.
GO analysis hierarchical visualization
Web-based navigation between the various components enables diverse analyses
2D Gel coupled MS data visualization (sample data)
Data/Annotations from PIR
Keyword(s) based search
Funded through NIAID/NIH Contract HHSN266200400061C (PI. M. Moore)
The authors would like to thank KJ. Stemple, RC Project Officer at NIAID; the Cyberinfrastructure Group at VBI; the Resource Center team at VBI, GU and SSS; and the researchers at the Proteomics Research Centers for critical comments and feedback.
Searching gene/protein(s) based on the UniProtKB accession number and protein function keywords across all the experiments and organisms is supported