PathwayMatrix: Visualizing binary relationships between proteins in biological pathways

Tuan Nhon Dang, Paul Murray, Angus Graeme Forbes

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


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

Original languageEnglish
Article numberS3
JournalBMC Proceedings
StatePublished - Aug 13 2015


  • Binary Relationships
  • Biological networks
  • Matrix visualization
  • Pathway visualization


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