Systems-Biology Approaches to Discover Anti-Viral Effectors of the Human Innate Immune Response
Abstract
:1. Introduction
2. Employing Systems-Biology Approaches for Unbiased Identification of Anti-Viral Effectors
3. Historical Perspective: Discovery of Restriction Factors through Conventional Screening Approaches
4. Genomics Technologies Enabled the Discovery of Genome-Wide Host-Pathogen Interactions
5. Systems-Based Approach to Detect ISGs as Novel Antiviral Effectors
6. Proteomics: The Innate Immune Interactome
7. The Advantage of Integrating Systems Approaches
8. Major Challenges in Systems-Biology Research on Host-Viral Interactions
Acknowledgments
Conflict of Interest
References and Notes
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Database | Website Link | Details | Reference | |
---|---|---|---|---|
Immune Databases | ISG Database | http://www.lerner.ccf.org/labs/williams/ | A database for Interferon-stimulated genes. Can be queried for functional categories | [52] |
Interferome Database | http://www.interferome.org/ | A database for Interferon-regulated genes | [55] | |
Innate Database | http://www.innatedb.ca/ | Innate immunity-relevant interactions and pathways | [64] | |
Reference Database of immune Cells (RefDIC) | http://refdic.rcai.riken.jp/welcome.cgi | Gene expression profiles at the mRNA and protein levels for Immune cells and tissues | [85] | |
Innate immune database | http://db.systemsbiology.net/cgibin/GLUE/U54/IIDBHome.cgi | Information on more than 2000 mouse genes related to immune responses | [86] | |
PRRDB | http://www.imtech.res.in/raghava/prrdb/ | Comprehensive database of pattern-recognition receptors and their ligands | [87] | |
Immunome | http://bioinf.uta.fi/immunome | Database for genes and proteins of the human immune system | [88] | |
Macrophages.com | http://www.macrophages.com/ | Broad repository for data and information about macrophages | - | |
Host-Pathogen interactions | Pathogen interaction gateway | http://molvis.vbi.vt.edu/pig/ | User interface for searching available data and tools to predict interactions between host and pathogen | [71] |
Virusmint | http://mint.bio.uniroma2.it/virusmint/Welcome.do | Collection of interactions between human and viral proteins and integration into human protein interaction network. | [72,73] | |
HIV-1, Human Protein Interaction Database | http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/ | HIV-1, human protein interaction data presented here are based on literature reports | [89,90,91] | |
Protein-Protein interactions | HPRD | http://www.hprd.org/ | Human proteome-wide database for domain architecture, post-translational modifications, interaction networks and disease association | [92] |
MINT | http://mint.bio.uniroma2.it/mint | Interaction database focused on experimentally verified protein-protein-interactions | [73] | |
BIND | http://bind.ca | Archive of biomolecular interaction, complex and pathway information. | [93] | |
BIOGRID | http://thebiogrid.org/ | Database for genetic and protein interaction data from human and model organisms | [94] | |
DIP | http://dip.doe-mbi.ucla.edu/dip/Main.cgi | Information on verified protein-protein interactions complied from diverse sources | [95] | |
STRING | http://string-db.org/ | Databank for known and predicted direct (physical) and indirect (functional) protein associations | [96] | |
Pathways | Reactome | http://www.reactome.org | Literature-curated database of human pathways, which contains51586 interactions among 1473 human proteins | [97,98] |
KEGG | http://www.genome.jp/kegg | Knowledge base containing genomic, chemical and systemic functional information | [99] | |
Pathguide | http://www.pathguide.org/ | Collection of biological pathway and molecular interaction related resources | [100] | |
PID | http://pid.nci.nih.gov/ | Molecular interactions and biological processes in biomolecular pathways | [101] | |
Other useful sites | BioGPS | http://biogps.gnf.org | Free customizable gene annotation portal | [102] |
Symatlas | http://symatlas.gnf.org | Gene expression atlas, integrated into BioGPS Portal | [103] | |
Gene Expression atlas | http://www.ebi.ac.uk/gxa/ | Curated gene expression archive | - | |
ArrayExpress Archive | http://www.ebi.ac.uk/arrayexpress/ | Database of functional genomics experiments | [104] | |
miRBase | http://www.mirbase.org/ | Database of published miRNA sequences and annotation | [105] | |
Cytoscape | http://www.cytoscape.org/ | Open source software platform for visualizing complex-networks | [106] |
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Münk, C.; Sommer, A.F.R.; König, R. Systems-Biology Approaches to Discover Anti-Viral Effectors of the Human Innate Immune Response. Viruses 2011, 3, 1112-1130. https://doi.org/10.3390/v3071112
Münk C, Sommer AFR, König R. Systems-Biology Approaches to Discover Anti-Viral Effectors of the Human Innate Immune Response. Viruses. 2011; 3(7):1112-1130. https://doi.org/10.3390/v3071112
Chicago/Turabian StyleMünk, Carsten, Andreas F.R. Sommer, and Renate König. 2011. "Systems-Biology Approaches to Discover Anti-Viral Effectors of the Human Innate Immune Response" Viruses 3, no. 7: 1112-1130. https://doi.org/10.3390/v3071112