Table 1. Public databases and resources for innate immunity research.
Here we highlight key, publicly available, tools that facilitate systems biology approaches for the study of innate immunity. Note that some descriptions are quoted directly from the organization’s website. There are also many commercial sources for similar information and reagents. In addition, there are non-commercial sources that are not listed (e.g. JAX, ATCC and others).
| Database | link | details | |
|---|---|---|---|
| Immune Databases | Immunome | http://bioinf.uta.fi/Immunome/ | a database for genes and proteins of the human immune system |
| Innate Immunity Database | http://db.systemsbiology.net/IIDB | a repository of genomic annotations and experimental data for over 2000 genes associated with immune response behavior in the mouse genome, with particular emphasis on TLR genes. | |
| InnateDB | http://www.innatedb.ca/ | a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice. The database captures the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with integrated bioinformatics and visualization tools provided at the site. | |
| Macrophages.com | http://www.macrophages.com | an online resource for those interested in macrophages and their role as major effector cells in innate and adaptive immunity. This website is designed to act as a centralised resource for the worldwide community of scientists interested in different aspects of macrophage biology | |
| Reference Database of Immune Cells (RefDIC) | http://refdic.rcai.riken.jp | an open-access database of quantitative mRNA and protein profiles specifically for immune cells and tissues. | |
| The Immunological Genome Project | http://www.immgen.org/index_content.html | a collaborative innitiative between immunologists and computational biologists who are generating a complete expression signatures of cells of the immune system in the mouse under various developemental and effector states. | |
| The Immunology Database and Analysis Portal (ImmPort) | https://www.immport.org | provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by NIAID/DAIT. | |
| Pathways | Ingenuity Pathway Analysis (IPA) | http://www.ingenuity.com | a privately run company that provides self curated databases that allow researchers to explore, visualize, and analyze biological and chemical findings related to genes, proteins, and small molecules. |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) | http://www.genome.jp/kegg/ | A bioinformatics resource that aims to provide a comprehensive representation of the cellular processes gained from genomic and molecular information. Includes protein interaction database, metabolic and signaling pathways, as well as chemical and drug databases. | |
| miRBASE | http://www.mirbase.org/ | a searchable database of published miRNA sequences and annotation as well as aims to provide an extensive target prediction | |
| Pathguide | http://www.pathguide.org | contains information about 325 biological pathway related resources and molecular interaction related resources. | |
| Pathway Interaction Database | http://pid.nci.nih.gov | a database containing biomolecular interactions and cellular processes assembled into reliable human signaling pathways. Curently includes 114 human pathways manually curated by NCI-Nature and 322 human pathways imported from BioCarta/Reactome | |
| Human Genetics | National Human Genome Research Institute | http://www.genome.gov/gwastudies/ | Provides a list of all GWAS publications (and data) that assay at least 100,000 single nucleotide polymorphisms (SNPs). |
| The International HapMap Project | http://hapmap.ncbi.nlm.nih.gov/ | a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals. | |
| Protein-protein interaction databases | BioGRID | http://www.thebiogrid.org/ | an online interaction repository with data compiled through comprehensive curation efforts. The current index is version searches 23,755 publications for 355,947 raw protein and genetic interactions from major model organism species. All interaction data are freely provided through the search index and available via download in a wide variety of standardized formats. |
| Biomolecular Interaction Network Database (BIND) | http://bond.unleashedinformatics.com/ | a comprehensive biomolecular data repository that stores curated descriptions of molecular complexes, pathways and biomolecular interactions. | |
| Database of Interacting Proteins (DIP) | http://dip.doe-mbi.ucla.edu/dip/Main.cgi | catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. | |
| IntAct | http://www.ebi.ac.uk/intact/main.xhtml | provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. | |
| MINT | http://mint.bio.uniroma2.it/mint/Welcome.do | focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The full MINT dataset can be freely downloaded and viewed graphically within the ‘MINT Viewer’. | |
| Pathogen Interaction Gateway (PIG) | http://molvis.vbi.vt.edu/pig/ | a database dedicated to the study of host-pathogen PPIs. PIG provides a number of user interfaces for searching available data and tools for predicting interactions between host and pathogen proteins and between pathogen proteins. | |
| VirusMINT | http://mint.bio.uniroma2.it/virusmint/Welcome.do | aims at collecting and annotating in a structured format all the interactions between human and viral proteins and to integrate this information in the human protein interaction network. | |
| Reagents | The I.M.A.G.E. Consortium | http://image.hudsonalpha.org/ | Provide arrayed oligo dT-primed, directionally cloned plasmid cDNA libraries as part of several public EST projects, including clones from human, mouse, rat, zebrafish, Fugu, Xenopus (X. laevis and X. tropicalis), cow, and primate libraries. |
| The International Knockout Mouse Consortium (IKMC) | http://www.knockoutmouse.org/ | The members of the IKMC are working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. | |
| The Knockout Mouse Project (KOMP) | http://www.genome.gov/17515708 | a trans-National Institutes of Health (NIH) initiative that aims to generate a comprehensive and public resource comprised of mice containing a null mutation in every gene in the mouse genome. | |
| Addgene | http://www.addgene.org | public plasmid repository for the research community. | |
| Mammalian Gene Collection (MGC) | http://mgc.nci.nih.gov/ | Provides researchers with unrestricted access to sequence-validated full-length protein-coding (FL- CDS) cDNA clones for human, mouse, and rat genes. |