Abstract
BackgroundComparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset.ResultsWe devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file.ConclusionsCPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in comparative genomics, its original purpose, the software can be used to visualize any dataset where entity occupancy is compared between different classes.AvailabilityCPG software is available at sourceforge http://sourceforge.net/projects/coulson and http://dl.dropbox.com/u/6701906/Web/Sites/Labsite/CPG.html
Highlights
Comparative analysis is an essential component to biology
Availability: Coulson plot generator (CPG) software is available at sourceforge http://sourceforge.net/projects/coulson and http://dl.dropbox. com/u/6701906/Web/Sites/Labsite/CPG.html
An array of gene product components from multiple species with each complex is displayed as a pie chart comprising a variable number of components, the number of which matches the number of protein subunits in a functional complex, process or other functional group
Summary
We developed the Coulson plot to display and compare data on gene representation grouped by gene product complex or pathway membership and to display this information across multiple taxa (Figure 1). Pie charts are arranged by phylogenetic hierarchy to allow evaluation of evolutionary trends and the rapid identification of gene losses, specializations or expansions. Several such systems may be compared, so that an array of systems is represented for each species. CPG allows pies to be set up that have only one subunit, for example mimicking the more standard dot blot format, or to subdivide the data into subcomplexes with biological relevance, to improve clarity or increase the amount of data that may be logically compared (Figure 4). The program is lightweight, making minimal impact on CPU resources and runs without issue on most major platforms
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