Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

Abstract

Background: Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the "correct" set of genes. In this article, we present and describe the Avian Immunome DB (AVIMM) for easy gene property extraction as exemplified by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes. It is a vital trait to study particularly in birds considering that they are a significant driver in spreading zoonotic diseases. With the completion of phase II of the B10K ("Bird 10,000 Genomes") consortium's whole-genome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for AVIMM.

Construction and content: A relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up. The foundation stone or the "seed" for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus). Gene annotations, different transcript isoforms, nucleotide sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. AVIMM is supplemented by a command-line interface and a web front-end to query the database.

Utility and discussion: The internal mapping of unique gene symbol identifiers to canonical gene symbols allows for an ambiguous gene property search. The database is organised within core and feature tables, which makes it straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 612 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with download functionality offers sophisticated search functionalities and tracks the origin for each record. AVIMM is publicly accessible at https://avimm.ab.mpg.de .

Keywords: Avian; B10K; Genomics; Immunogenomics; Immunology; Immunome; Trait database.

Fig. 1

Concept of Avimm, the Avian Immunome DB

Fig. 2

Logical data model (LDM) in Crow’s Foot Notation [42] of Avimm. Core tables represent the basic structure of the database and link the evidence-specific identifiers to Avimm’s unique identifiers (uid). Feature tables represent evidence-specific features like isoforms, nucleotide sequences, or amino acid sequences of the immune genes

Fig. 3

Flow chart, loading of Avimm. Uncoloured boxes show preparatory steps. Yellow boxes describe imports into core tables and green boxes imports into feature tables. The initial set of immune genes in chicken is derived from “biological process/immune system process” in AmiGo 2 filtered for chicken. Gene symbols were extracted from Ensembl’s website since Ensembl has the most current/complete chicken annotation. All steps are explained in detail on the project’s wiki page [41]

Fig. 4

Avimm landing page with links to the four function pages (upper box) and description for each function (lower box)

Fig. 5

Excerpt of evidence function page. Gene selection either by “mark-and-arrow” or free text (top left box). Species selection based on taxonomic ranks (centre box). Checkboxes to filter columns (right box) and download data option (bottom left box). Each section has an information button (circled “i”) to provide further details

Fig. 6

The gene evidence result list shows one record for each evidence of the gene IFNL3A in the selected species. The columns can be sorted (ascending or descending) by clicking on the corresponding column header. On top of the list are links to B10K, Ensembl, and UniProt result pages based on the same search criteria (upper box). If there are alternative gene symbols for the query gene in Avimm, then these are listed on the bottom of the page (lower box)

Fig. 7

Excerpts of the result pages for IFNL3A in B10K (a), Ensembl (b), and UniProt (c). Each result page offers additional filters and download options. The original identifiers of the source of evidence are retained and linked to the original entries on Ensembl (b, left box) or UniProt (c, left box). Additionally, links to NCBI nucleotide sequence BLAST (a, box), NCBI gene information (b, right box), and NCBI amino acid sequence BLAST (c, right box) are provided for each record

Fig. 8

Excerpt of the result page for MASP2 evidence across all 363 species in Avimm. There is evidence in all Galliformes (11/11) and almost all Anseriformes (5/7) but only in two Passeriformes (out of 173 in Avimm)