TY - JOUR
T1 - ReactionFlow
T2 - An interactive visualization tool for causality analysis in biological pathways
AU - Dang, Tuan Nhon
AU - Murray, Paul
AU - Aurisano, Jillian
AU - Forbes, Angus Graeme
N1 - Funding Information:
We thank Guang Yao and Ryan Gutenkunst who provided useful insight into biological pathways and emphasized the importance of representing causality when analyzing pathways. We also thank Emek Demir and Tamara Munzner for providing useful feedback on our design choices during the development of this application. This work was funded by the DARPA Big Mechanism Program under ARO contract WF911NF-14-1-0395.
Publisher Copyright:
© 2015 Dang et al.
PY - 2015/8/13
Y1 - 2015/8/13
N2 - Background: Molecular and systems biologists are tasked with the comprehension and analysis of incredibly complex networks of biochemical interactions, called pathways, that occur within a cell. Through interviews with domain experts, we identified four common tasks that require an understanding of the causality within pathways, that is, the downstream and upstream relationships between proteins and biochemical reactions, including: visualizing downstream consequences of perturbing a protein; finding the shortest path between two proteins; detecting feedback loops within the pathway; and identifying common downstream elements from two or more proteins. Results: We introduce ReactionFlow, a visual analytics application for pathway analysis that emphasizes the structural and causal relationships amongst proteins, complexes, and biochemical reactions within a given pathway. To support the identified causality analysis tasks, user interactions allow an analyst to filter, cluster, and select pathway components across linked views. Animation is used to highlight the flow of activity through a pathway. Conclusions: We evaluated ReactionFlow by providing our application to two domain experts who have significant experience with biomolecular pathways, after which we conducted a series of in-depth interviews focused on each of the four causality analysis tasks. Their feedback leads us to believe that our techniques could be useful to researchers who must be able to understand and analyze the complex nature of biological pathways. ReactionFlow is available at https://github.com/CreativeCodingLab/ReactionFlow.
AB - Background: Molecular and systems biologists are tasked with the comprehension and analysis of incredibly complex networks of biochemical interactions, called pathways, that occur within a cell. Through interviews with domain experts, we identified four common tasks that require an understanding of the causality within pathways, that is, the downstream and upstream relationships between proteins and biochemical reactions, including: visualizing downstream consequences of perturbing a protein; finding the shortest path between two proteins; detecting feedback loops within the pathway; and identifying common downstream elements from two or more proteins. Results: We introduce ReactionFlow, a visual analytics application for pathway analysis that emphasizes the structural and causal relationships amongst proteins, complexes, and biochemical reactions within a given pathway. To support the identified causality analysis tasks, user interactions allow an analyst to filter, cluster, and select pathway components across linked views. Animation is used to highlight the flow of activity through a pathway. Conclusions: We evaluated ReactionFlow by providing our application to two domain experts who have significant experience with biomolecular pathways, after which we conducted a series of in-depth interviews focused on each of the four causality analysis tasks. Their feedback leads us to believe that our techniques could be useful to researchers who must be able to understand and analyze the complex nature of biological pathways. ReactionFlow is available at https://github.com/CreativeCodingLab/ReactionFlow.
KW - Biological networks
KW - Causality analysis
KW - Pathway visualization
KW - Topological ordering
UR - http://www.scopus.com/inward/record.url?scp=85018193387&partnerID=8YFLogxK
U2 - 10.1186/1753-6561-9-S6-S6
DO - 10.1186/1753-6561-9-S6-S6
M3 - Article
AN - SCOPUS:85018193387
VL - 9
JO - BMC Proceedings
JF - BMC Proceedings
SN - 1753-6561
M1 - S6
ER -