Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny

Abstract

Background: The rabbit is an important model organism used in a wide range of biomedical research. However, the rabbit genome is still sparsely annotated, thus prohibiting extensive functional analysis of gene sets derived from whole-genome experiments. We developed a web-based application that provides augmented annotation and orthologue analysis for rabbit genes. Importantly, the application allows comprehensive functional analysis through the use of orthologous relationships.

Results: Using data extracted from several public bioinformatics repositories we created Better Bunny, a database and query tool that extensively augments the available functional annotation for rabbit genes. Using the complete set of target genes from a commercial rabbit gene expression microarray as our benchmark, we are able to obtain functional information for 88 % of the genes on the microarray. Previously, functional information was available for fewer than 10 % of the rabbit genes.

Conclusions: We have developed a freely available, web-accessible bioinformatics tool that enables investigators to quickly and easily perform extensive functional analysis of rabbit genes (http://cptweb.cpt.wayne.edu). The software application fills a critical void for a wide range of biomedical research that relies on the rabbit model and requires characterization of biological function for large sets of genes.

Figure 1

The Better Bunny query page. Better Bunny provides an easy to use interface that accepts several rabbit gene identifiers as input. The user can select from a range of available output, including ontology classification and putative orthologues in human, mouse, and rat.

Figure 2

Better Bunny architecture. Better Bunny integrates all available rabbit data from Ensembl, NCBI, and Agilent (gene expression microarray) for rabbit gene annotation and augmentation. Data sources are shown along with the number of records drawn from each source.

Figure 3

Example of Better Bunny output. Each row represents an input query gene, and each column provides a selected annotation element. Hyperlinks are available to Ensembl resources. Gene identifiers from selected orthologue species are provided, and the output gene sets can be seamlessly submitted to DAVID with one mouse click for extensive functional analysis.