Concept

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:

Design

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.

Overview

The different functions of ImmunomeDB can be accessed via the navigation bar at the top of the page:

Evidence

Query where evidence has been seen for a given gene.

B10K

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.

Ensembl

Query transcript information for alternative splice variants.

UniProt

Query amino acid sequences, either reviewed (SwissProt) or unreviewed (TrEMBL).

Citations

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.