Integrative Systems Approaches to Study Innate Immunity

Abstract

Essential human immunome is composed of about 900 genes and proteins. Primary immunodeficiencies (IDs) are a large and heterogenic group of inherited disorders of the immune system. Since defects in any part of the adaptive or innate immune system can cause disorders, numerous IDs have been detected. Immunodeficiency patients have increased susceptibility to recurrent and persistent, even life-threatening infections. Other symptoms vary greatly between IDs. To date, some 200 IDs and 150 affected genes have been identified. ID-related genes are distributed throughout the genome. Features of IDs and information sources for them are discussed. Genotype–phenotype correlations are rather rare for IDs. Those diseases in which mutation type has effect on disease phenotype are described. ImmunoDeficiency Resource (IDR) is a comprehensive knowledge base for all essential information about IDs. The service is freely available at http://bioinf.uta.fi/IDR. IDdiagnostics (http://bioinf.uta.fi/IDdiagnostics) is dedicated to health professionals looking for laboratories performing gene and clinical tests for IDs. ID mutation data can be accessed in locus-specific, patient-related mutation databases, IDbases (http://bioinf.uta.fi/IDbases). Mutations are described at DNA, mRNA, and protein levels, with links to reference sequences and reference articles. The mutation data have been collated into entries, along with some clinical information. Currently, we have databases for 123 ID genes with 5359 patient entries. Immunome genes and proteins, their evolution, mouse–human comparisons, phylogenetics trees and orthologs for Metazoan immunome entities are available in Immunome Database, ImmTree, and ImmunomeBase all of which can be accessed via Immunome Knowledge Base (IKB) (http://bioinf.uta.fi/IKB).