title: PathwayMatrix: visualizing binary relationships between proteins in biological pathways.
abstract: 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.
authors.affiliation: Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, Chicago 60607-7053, IL, USA.
authors.forename: Tuan Nhon
authors.initials: TN
authors.lastname: Dang
authors.affiliation: Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, Chicago 60607-7053, IL, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Murray
authors.affiliation: Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, Chicago 60607-7053, IL, USA.
authors.forename: Angus Graeme
authors.initials: AG
authors.lastname: Forbes
keywords: Binary Relationships; Biological networks; Matrix visualization; Pathway visualization