Immunome Knowledge Base (IKB)
Category Cross-Omics>Knowledge Bases/Databases/Tools
Abstract The Immunome Knowledge Base (IKB) is a dedicated resource for immunological information.
IKB contains information for human immunome genes and proteins, phylogenetic trees and evolutionary information for immunome orthologs, ortholog groups for metazoan immunome, and variation data on genomic, transcriptomic and proteomic level.
IKB integrates three (3) databases, Immunome, ImmTree and ImmunomeBase with additional data.
IKB contains information about immunity related proteins, their domain structure and the related ontology terms. Also, information can be found about the localization of the coding genes and their comparison with the existing mouse orthologs.
Phylogenetic trees are available for orthologs from 104 species. Orthologs for genes in metazoan organisms are available and clustered into two classes/levels.
Note: Vertebrate immunoglobulin’s (IG), T cell receptors (TR) and major histocompatibility complex (MHC) were excluded from Immunome Knowledge Base as they are specific for the 'adaptive immune response' and because they are well covered in IMGT®, the international ImMunoGeneTics information system®.
IKB search capabilities - In IKB you can perform searches using gene names, GenBank accession numbers, GI numbers or keywords as queries.
1) Immunome -- Database for genes and proteins of the Human Immune System -
The internet resource called Immunome was constructed for the characterization of the human immune system.
Immunome contains information about immunity related proteins, their domain structure and related ontology terms. Info can also be found about the localization of the coding genes and their comparison with existing mouse orthologs.
In addition, links to the ImmTree database are also included for phylogenetic trees for orthologs from 104 species.
Immunome search capabilities include:
- a) Search for a Group of genes -
- Search for genes by protein Domains; Search for genes by Ontology;
- Search for genes by Description of the gene; Search for genes by Categories; Search for genes where the Ka/Ks value is compared with the mouse ortholog; and Search for genes where the Z score is compared with the mouse ortholog.
- b) Search for a Single gene -
- Search for a human gene by gene name; Search for a human gene by GenBank GI number; Search for a human gene by GenBank accession number; Search for a human gene by UniProt accession number; and Search for a human gene by keyword.
2) ImmTree -- The database of evolutionary relationships of proteins and genes of the human immune system -
The human immune system is one of the most complex but widely investigated machinery both on the molecular and organ level, in normal state and in diseases.
Despite being of intense scientific interest, the evolutionary history of this system is Not well known.
There have been several studies related to the development and evolution of immunological processes, but a full scale genome and sequence based analysis has Not been carried out until now.
The manufacturer’s study includes 893 human genes involved in immune related processes.
This study carried out a 'data mining centered' analysis based on existing data from the NCBI's HomoloGene and TIGR's EGO databases.
Phylogenetic trees have been generated for all 893 gene groups together with the available orthologs from eukaryota genomes. Results of this analysis, is presented in the 'ImmTree database' which contains the trees and other related data for all 893 genes.
The main objective of the ImmTree database is the human immune system related genes and the corresponding phylogenetic trees which describe the evolutionary past of each ortholog group.
The genes and trees are presented in several groupings allowing useful search features for end-users.
Besides the trees, other data such as alignments of the sequences, statistics on nucleotide changes, domain and ontology data are also available.
This database can help researchers carry out further evolutionary studies of the immune system.
ImmTree search capabilities include:
- a) Search for Gene Groups - You can perform a complex search for groups of trees with similar characteristics, e.g. trees with species from the same taxon group or genes with similar ontology terms etc.
- b) Search for Single Genes - You can use this search page if you want to find a certain gene by BI or accession number or a keyword search in the description field.
3) ImmunomeBase -- A database of 'metazoan immunity genes' and orthologs -
These immunity genes were used as seeds to search for 'tentative orthologs' using reciprocal protein-protein Blast searches against proteins from the GenBank and RefSeq databases. The genes, both seeds and non-seeds were clustered into 2 classes or levels of ortholog groups.
These classes of ortholog groups were designated according to the order of 'reciprocal ortholog pairs' among the seed immunity genes.
Briefly, in the level 1 groups, the seed genes don’t necessarily all form orthologous relationships with each other and it is possible for a non- seed gene to belong to more than one group (i.e. if it forms an orthologous pair with more than one seed gene, and the seed genes aren’t in the same ortholog group).
In the level 2 groups, all the seed genes form orthologous pairs with each other and the non-seed genes are only allowed to belong to one group, the one containing the gene with which it has the closest sequence similarity.
The manufacturer's initial phylogenetic analysis suggests that this is a valid approach and attempt to collect a spectrum of immunity genes.
All the immunity genes and their evidence of immune function, orthologs and ortholog groups have been combined into the ImmunomeBase database and it is fully searchable by:
- a) Species (use the binomial);
- b) GeneID;
- c) GenBank Accession;
- d) Name or keyword;
- e) Gene Ontology ID;
- f) Ontology description; and
- g) Level 1 or 2 group ID (e.g. if known from a previous visit to the database).
System Requirements
Web-based.
Manufacturer
- Institute of Medical Technology, FI-33014
- University of Tampere, Finland
Manufacturer Web Site IKB
Price Contact manufacturer.
G6G Abstract Number 20412
G6G Manufacturer Number 104042