Visual Understanding of Metabolic Pathways Across Organisms Using Layout in Two and a Half Dimensions
Full article [PDF] (2,29 MB)
doi:10.2390/biecoll-jib-2004-2
October 03, 2003
January 16, 2004
Ulrik Brandes, Tim Dwyer, Falk Schreiber
Correspondence should be addressed to:
Falk Schreiber
Bioinformatics Center, Inst. of Plant Genetics and Crop Plant Research, Gatersleben, Germany
ed.nebelsretag-kpi@nullebierhcs
Abstract
We propose a method for visualizing a set of related metabolic pathways across organisms using 2 1/2 dimensional graph visualization. Interdependent, two-dimensional layouts of each pathway are stacked on top of each other so that biologists get a full picture of subtle and significant differences among the pathways. The (dis)similarities between pathways are expressed by the Hamming distances of the underlying graphs which are used to compute a stacking order for the pathways. Layouts are determined by a global layout of the union of all pathway graphs using a variant of the proven Sugiyama approach for layered graph drawing. Our variant layout approach allows edges to cross if they appear in different graphs.