JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

Abstract

Background: Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community.

Results: Here we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria.

Conclusions: JContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.

Figure 1

Layout of JContextExplorer windows. (A) JContextExplorer operates via usage of an initial data-loading frame, followed by coordination of a main window and multi-genome browser context viewer window (top). These frames have several associated child windows (second row): from the main window, a scrollable list of gene annotations (Annotations) and a window to facilitate multiple loading and switching between alternative context sets (Add/Remove Context Sets); from the context viewer window, an alphabetized gene color legend (Color Legend), and pop-up window of information relating to a specific gene (Gene Information). An enlarged view of the context viewer window (B) reveals a scrollable viewing area, where genes are rendered as colors rectangles appearing above or below a centerline, depending on their strandedness. Genes are colored according to homology or associated annotation. The Gene Information panel (lower left-hand corner) describes information to be delivered upon click (Gene Information window). Toggling checkboxes in the Genome Display panel (lower center) modifies the display of all rendered genomic segments. The range of the displayed region may be easily changed in the Range Around Context Segment panel (lower right-hand corner).

Figure 2

JContextExplorer technical terminology. Technical terms relevant to the JContextExplorer program (column 1) are defined (column 2) and demonstrated via graphical representation (column 3).

Figure 3

hpxW and ggt context tree. Clusters of all homologous gene clusters in 22 alpha and gamma proteobacterial species were constructed using BLAST [33] and tribe-MCL [34]. All ggt and hpxW genes naturally grouped into the same homology cluster. Using JContextExplorer, we defined a context set, which we named “D75”, that placed all genes on the same strand within 75 nucleotides of each other into common gene groupings. We constructed a context tree of the ggt/hpxW homology cluster using the “Common Genes – Dice” dissimilarity metric and “Joint Between-Within” linkage function (above). The data segmented into two branches, one of which corresponded to the previously described hpxW context (green box), and the other into a combination of the ggt context (blue box) and an undetermined third group. Manual inspection of individual contexts in the third group might reveal that some members of this group belong with the ggt group, and some with the hpxW group. Additionally, some members in this third unknown group could represent “transitional” cases between the hpxW and ggt gene (a gene that performs the functions of both hpxW and ggt, for example). JContextExplorer’s context viewer tool proved helpful in manually interrogating this third group.