|Avimm size [gigabyte]||7.3|
|immune gene symbols||1 782|
|distinct immune genes||1 170|
|immune gene records per species [avg]||709|
|B10k exons per mRNA [avg]||8.2|
|Ensembl transcripts||41 595|
|UniProt amino acid sequences||9 422|
The aim of this project is to aggregate information about the avian immunome and at the same time, disentangle gene name (gene symbol) ambiguities by linking genes with different names (symbols) to the same unique gene identifier (gene_id) in the database. Currently, the database contains pieces of evidence for avian immune genes from Ensembl, UniProt and The Bird 10,000 Genomes (B10K) Project:
The database design is flexible and can be applied to any group of species or trait of interest. The basic idea is to get a seed of genes with associated gene symbols based on a biological process from Gene Ontology. Here, genes that fall into the category immune system process in the chicken (Gallus gallus) are used. Based on this seed, other pieces of evidence and other bird species are incorporated step-by-step. Details can be found on the project's wiki page.
The different functions of ImmunomeDB can be accessed via the navigation bar at the top of the page:
- Query where evidence has been seen for a given gene.
- Query nucleotide sequences of one/many species, families, orders. For type CDS, bin multiple CDS per species in corresponding bin. Download nucleotide sequences as FASTA files.
- Query transcript information for alternative splice variants.
- Query amino acid sequences, either reviewed (SwissProt) or unreviewed (TrEMBL).
Currently, most of the data come from
The Bird 10,000 Genomes (B10K) Project. Any publications utilising data from this site must cite
Mueller et al., 2020. Avian Immunome DB: an example of a user-friendly interface for extracting genetic information. BMC Bioinformatics 21.
and Feng et al.,2020. Dense sampling of bird diversity increases power of comparative genomics. Nature.