PathwayMatrix: visualizing binary relationships between proteins in biological pathways

BMC Proceedings

Research

Angus Graeme Forbes¹  Paul Murray¹  Tuan Nhon Dang¹ 

[1] Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, 60607-7053, Chicago, IL, USA;

关键词: Pathway visualization;    Biological networks;    Matrix visualization;    Binary Relationships;   

DOI  :  10.1186/1753-6561-9-S6-S3

来源: Springer

【 摘 要 】

BackgroundMolecular activation pathways are inherently complex, and understanding relations across many biochemical reactions and reaction types is difficult. Visualizing and analyzing a pathway is a challenge due to the network size and the diversity of relations between proteins and molecules.ResultsIn this paper, we introduce PathwayMatrix, a visualization tool that presents the binary relations between proteins in the pathway via the use of an interactive adjacency matrix. We provide filtering, lensing, clustering, and brushing and linking capabilities in order to present relevant details about proteins within a pathway.ConclusionsWe evaluated PathwayMatrix by conducting a series of in-depth interviews with domain experts who provided positive feedback, leading us to believe that our visualization technique could be helpful for the larger community of researchers utilizing pathway visualizations. PathwayMatrix is freely available at https://github.com/CreativeCodingLab/PathwayMatrix.

【 授权许可】

Unknown   
© Dang et al. 2015. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.