Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz [version 1; peer review: 3 approved]

The precision medicine paradigm is centered on therapies targeted to particular molecular entities that will elicit an anticipated and controlled therapeutic response. However, genetic alterations in the drug targets themselves or in genes whose products interact with the targets can affect how well...

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Bibliographic Details
Published in:F1000 research Vol. 8; p. 908
Main Authors: Blucher, Aurora S, McWeeney, Shannon K, Stein, Lincoln, Wu, Guanming
Format: Journal Article
Language:English
Published: England Faculty of 1000 Ltd 2019
F1000 Research Limited
F1000 Research Ltd
Subjects:
Cancer therapies
Drug resistance
Fuzzy logic
Genes
Genomes
Metabolism
Mutation
Ordinary differential equations
Ovarian cancer
Patients
Precision medicine
Signal transduction
Software Tool
Variables
Visualization
Oregon
Canada
United States > US
targeted therapy
functional interaction network
drug interaction visualization
biological pathway
systems pharmacology
Boolean network
constrained fuzzy logic modeling
Reactome
ISSN:2046-1402, 2046-1402
Online Access:Get full text
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Summary:The precision medicine paradigm is centered on therapies targeted to particular molecular entities that will elicit an anticipated and controlled therapeutic response. However, genetic alterations in the drug targets themselves or in genes whose products interact with the targets can affect how well a drug actually works for an individual patient. To better understand the effects of targeted therapies in patients, we need software tools capable of simultaneously visualizing patient-specific variations and drug targets in their biological context. This context can be provided using pathways, which are process-oriented representations of biological reactions, or biological networks, which represent pathway-spanning interactions among genes, proteins, and other biological entities. To address this need, we have recently enhanced the Reactome Cytoscape app, ReactomeFIViz, to assist researchers in visualizing and modeling drug and target interactions. ReactomeFIViz integrates drug-target interaction information with high quality manually curated pathways and a genome-wide human functional interaction network. Both the pathways and the functional interaction network are provided by Reactome, the most comprehensive open source biological pathway knowledgebase. We describe several examples demonstrating the application of these new features to the visualization of drugs in the contexts of pathways and networks. Complementing previous features in ReactomeFIViz, these new features enable researchers to ask focused questions about targeted therapies, such as drug sensitivity for patients with different mutation profiles, using a pathway or network perspective.
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No competing interests were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.19592.1