2.5D Visualisation of Overlapping Biological Networks

Abstract Biological data is often structured in the form of complex interconnected networks such as protein interaction and metabolic networks. In this paper, we investigate a new problem of visualising such overlapping biological networks. Two networks overlap if they share some nodes and edges. We present an approach for constructing visualisations of two overlapping networks, based on a restricted three dimensional representation. More specifically, we use three parallel two dimensional planes placed in three dimensions to represent overlapping networks: one for each network (the top and the bottom planes) and one for the overlapping part (in the middle plane). Our method aims to achieve both drawing aesthetics (or conventions) for each individual network, and highlighting the intersection part by them. Using three biological datasets, we evaluate our visualisation design with the aim to test whether overlapping networks can support the visual analysis of heterogeneous and yet interconnected networks.

[1]  Emek Demir,et al.  PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways , 2002, Bioinform..

[2]  Ralf Mrowka,et al.  A Java applet for visualizing protein-protein interaction , 2001, Bioinform..

[3]  Bernhard O Palsson,et al.  The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Chia-Hung Liu,et al.  Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online) , 2007, BMC Bioinformatics.

[5]  Chrystala Constantinidou,et al.  Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. , 2004, Nucleic acids research.

[6]  Kyungsook Han,et al.  A fast layout algorithm for protein interaction networks , 2003, Bioinform..

[7]  Karen Eilbeck,et al.  Straight-Line Drawings of Protein Interactions , 1999, Graph Drawing.

[8]  Isabel Rojas,et al.  A graph layout algorithm for drawing metabolic pathways , 2001, Bioinform..

[9]  Martin Vingron,et al.  A joint model of regulatory and metabolic networks , 2006, BMC Bioinformatics.

[10]  Falk Schreiber,et al.  High quality visualization of biochemical pathways in BioPath , 2002, Silico Biol..

[11]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[12]  Peter D. Karp,et al.  The Pathway Tools software , 2002, ISMB.

[13]  Ulrik Brandes,et al.  Visual triangulation of network-based phylogenetic trees , 2004, VISSYM'04.

[14]  Satoru Kawai,et al.  An Algorithm for Drawing General Undirected Graphs , 1989, Inf. Process. Lett..

[15]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[16]  Carsten Friedrich,et al.  Visualisation and navigation methods for typed protein-protein interaction networks. , 2003, Applied bioinformatics.

[17]  Ulrik Brandes,et al.  Visual Understanding of Metabolic Pathways Across Organisms Using Layout in Two and a Half Dimensions , 2004 .

[18]  Simo V. Zhang,et al.  A map of human cancer signaling , 2007, Molecular systems biology.

[19]  Ching-Lung Lai,et al.  Natural history of hepatitis-related hepatocellular carcinoma. , 2008, World journal of gastroenterology.

[20]  Tim Dwyer,et al.  GEOMI: GEOmetry for Maximum Insight , 2005, GD.