The JAX Synteny Browser for mouse-human comparative genomics

Abstract

Visualizing regions of conserved synteny between two genomes is supported by numerous software applications. However, none of the current applications allow researchers to select genome features to display or highlight in blocks of synteny based on the annotated biological properties of the features (e.g., type, function, and/or phenotype association). To address this usability gap, we developed an interactive web-based conserved synteny browser, The Jackson Laboratory (JAX) Synteny Browser. The browser allows researchers to highlight or selectively display genome features in the reference and/or the comparison genome according to the biological attributes of the features. Although the current implementation for the browser is limited to the reference genomes for the laboratory mouse and human, the software platform is intentionally genome agnostic. The JAX Synteny Browser software can be deployed for any two genomes where genome coordinates for syntenic blocks are defined and for which biological attributes of the features in one or both genomes are available in widely used standard bioinformatics file formats. The JAX Synteny Browser is available at: http://syntenybrowser.jax.org/. The code base is available from GitHub: https://github.com/TheJacksonLaboratory/syntenybrowser and is distributed under the Creative Commons Attribution license (CC BY).

Keywords: Bioinformatics; Candidate gene analysis; Comparative genomics; Conserved synteny.

Fig. 1

The JAX Synteny Browser is organized as four main panels: a the Feature Search panel allows users to search the reference species by genome features of interest or mapped phenotypes. b The Genome View panel presents a circos plot to display a genome level view for both the reference genome (outer ring) and comparison genome (inner ring). c The Syntenic Block Detail View allows users to browse and focus on features in both the reference (top track) and comparison (bottom track) species at the chromosome and block levels. d The Syntenic Block Feature Display Filters panel allows users to search for and highlight genome features based on different biological attributes such as feature type and function. Genome features that match the search criteria can be displayed selectively

Fig. 2

Screenshot of the Syntenic Block Detail View for genes annotated to the GO term, positive regulation of cell death: a the dialog box in the Syntenic Block Feature Display Filters panel set to search both genomes for genes annotated to the GO term of interest. b Search results displayed in the Syntenic Block Detail View using the option to turn off all genome features except for features that match the search criteria. The red lines indicate that the regions of synteny are in opposite orientations in the mouse and human genomes. They are displayed in the same orientation to simply the interface. This option can be turned off in the Settings menu

Fig. 3

Screenshot of the Syntenic Block Detail View for genes annotated to the DO term, type 2 diabetes mellitus: a the dialog box in the Syntenic Block Feature Display Filters panel with settings to search only the human genome for the DO term of interest. b Results displayed in the syntenic block region. The graphic at the top is the overview of the Reference genome (mouse, in this case). The colors correspond to the locations of the regions of synteny in the human genome. The black horizontal line indicates the chromosomal region corresponding to the syntenic block details displayed. The vertical tick marks indicate the locations of the genome features that matched the user’s search criteria shown in panel (a). Selecting a genome feature opens a dialog box with links to external resources for more information (MGI for mouse; NCBI Gene for human)