PathwayMatrix: visualizing binary relationships between proteins in biological pathways

BMC Proceedings

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, Chicago 60607-7053, IL, USA

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

Others  :  1222587
DOI  :  10.1186/1753-6561-9-S6-S3

【 摘 要 】

Background

Molecular 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.

Results

In 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.

Conclusions

We 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 webcite.

【 授权许可】

   
2015 Dang et al.

【 图 表 】

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