Seq2Net : a relational information visualization solution

Abstract

The advent of faster and more powerful personal computers has resulted in a tremendous amount of growth in fields involving data analysis and processing. The field of Bioinformatics is no different, with an increased focus on the development of new tools to better help research. The field of expression Quantitative Trait Loci (eQTL) analysis has the potential to create conclusive tests for increased propensity towards diseases caused by genetic abnormalities.

The purpose of the author’s project was to create a tool that facilitates the analysis of eQTL through systematic and clear information visualization. The tool is meant to allow interactivity with user and the visualization of the uncovered pathways connecting associated loci and their target genes with additional information to expedite further analysis.

The tool was designed as a plugin for the popular biological network visualization tool Cytoscape and is called Seq2Net. Developed using a modular approach with the segregation of functionalities and utilizing the GNU public licensed library JFreeChart, Seq2Net provides a multi-paneled GUI which isolates different data sets while maintaining a logical link between them. The user can search for the loci of expression networks while simultaneously viewing a representation of the average copy number variation for the same loci. This allows for a degree of analysis hitherto unavailable thought he use of previous plugins in the Cytoscape environment. The author also suggests further extensions to the project, with respect to inclusion of linkages with online databases. The author also highlights the future maintenance issues and other limitations the plugin may face.