Pathline: A Tool For Comparative Functional Genomics

Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a cellular process, and phylogenetic relationship data that describe the relatedness of species. No existing visualization tool can visually encode the biologically interesting relationships between multiple pathways, multiple genes, and multiple species. We tackle the challenge of visualizing all aspects of this comparative functional genomics dataset with a new interactive tool called Pathline. In addition to the overall characterization of the problem and design of Pathline, our contributions include two new visual encoding techniques. One is a new method for linearizing metabolic pathways that provides appropriate topological info...

• Type: Journal
• Year: 2010
• Where: CGF
• Authors: Miriah D. Meyer, Bang Wong, Mark P. Styczynski, Tamara Munzner, Hanspeter Pfister
• Keywords: CGF 2010, Comparative Functional Genomics, Gene Activity, Multiple Species