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Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz

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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Autores principales: Blucher, Aurora S., McWeeney, Shannon K., Stein, Lincoln, Wu, Guanming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6644836/
https://www.ncbi.nlm.nih.gov/pubmed/31372215
http://dx.doi.org/10.12688/f1000research.19592.1
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author Blucher, Aurora S.
McWeeney, Shannon K.
Stein, Lincoln
Wu, Guanming
author_facet Blucher, Aurora S.
McWeeney, Shannon K.
Stein, Lincoln
Wu, Guanming
author_sort Blucher, Aurora S.
collection PubMed
description 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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spelling pubmed-66448362019-07-31 Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz Blucher, Aurora S. McWeeney, Shannon K. Stein, Lincoln Wu, Guanming F1000Res Software Tool Article 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. F1000 Research Limited 2019-06-20 /pmc/articles/PMC6644836/ /pubmed/31372215 http://dx.doi.org/10.12688/f1000research.19592.1 Text en Copyright: © 2019 Blucher AS et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Blucher, Aurora S.
McWeeney, Shannon K.
Stein, Lincoln
Wu, Guanming
Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
title Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
title_full Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
title_fullStr Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
title_full_unstemmed Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
title_short Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
title_sort visualization of drug target interactions in the contexts of pathways and networks with reactomefiviz
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6644836/
https://www.ncbi.nlm.nih.gov/pubmed/31372215
http://dx.doi.org/10.12688/f1000research.19592.1
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