1 Introduction
To understand the function of genes, it is necessary to study their biological context. In which biological processes is a gene involved? Is it involved in multiple similar processes? Pathways, representations of such processes, are consulted to provide answers to these questions. Pathway data can either be presented as a large, complex network with an automated layout, or as small functional graphs, handcrafted by experts. These small pathways frequently encode meta-knowledge, such as cell localization, in the layout. Widely used pathway databases are KEGG [11] and BioCarta
http://www.biocarta.com
, which together contain about 600 pathways. Screenshot of Caleydo with open Bucket view, a parallel coordinates view, a heat map and some meta-information. The Bucket concept is an integral part of Caleydo and allows us to place views for pathway and gene expression analysis in a 2.5D setup. Relations between views are shown by means of visual links.