publication . Article . Other literature type . 2019

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

Blucher, Aurora S.; McWeeney, Shannon K.; Stein, Lincoln; Wu, Guanming;
Open Access English
  • Published: 01 Jun 2019 Journal: F1000Research (issn: 2046-1402, Copyright policy)
  • Publisher: F1000 Research Ltd
Abstract
<ns7:p>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 reaction...
Subjects
free text keywords: Medicine, R, Science, Q, Software Tool Article, Articles, targeted therapy, drug interaction visualization, Reactome, biological pathway, functional interaction network, Boolean network, constrained fuzzy logic modeling, systems pharmacology, Interaction network, Computational biology, Precision medicine, Interaction information, medicine.medical_treatment, Computer science, Visualization, Biological network
Funded by
NIH| Oregon Clinical and Translational Research Institute
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5UL1TR000128-10
  • Funding stream: NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES
,
NIH| Illuminating molecular targetable pathways in HNSCC
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01CA192405-04
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| TRAINING PROGRAM IN HEALTH INFORMATICS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T15LM007088-10
  • Funding stream: NATIONAL LIBRARY OF MEDICINE
,
NIH| Reactome: An Open Knowledgebase of Human Pathways
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U41HG003751-07
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
55 references, page 1 of 4

1 Senft D Leiserson MDM Ruppin E: Precision Oncology: The Road Ahead.Trends Mol Med.2017;23(10):874–98. 10.1016/j.molmed.2017.08.003 28887051 [OpenAIRE] [PubMed] [DOI]

2 Salgado R Moore H Martens JWM: Steps forward for cancer precision medicine.Nat Rev Drug Discov.2018;17(1):1–2. 10.1038/nrd.2017.218 29170471 [PubMed] [DOI]

3 Yap TA Omlin A de Bono JS: Development of therapeutic combinations targeting major cancer signaling pathways.J Clin Oncol.2013;31(12):1592–605. 10.1200/JCO.2011.37.6418 23509311 [OpenAIRE] [PubMed] [DOI]

4 Bild AH Yao G Chang JT: Oncogenic pathway signatures in human cancers as a guide to targeted therapies.Nature.2006;439(7074):353–7. 10.1038/nature04296 16273092 [OpenAIRE] [PubMed] [DOI]

5 Filipp FV: Precision medicine dri ven by cancer systems biology.Cancer Metastasis Rev.2017;36(1):91–108. 10.1007/s10555-017-9662-4 28265786 [OpenAIRE] [PubMed] [DOI]

6 Campillos M Kuhn M Gavin AC: Drug target identification using side-effect similarity.Science.2008;321(5886):263–6. 10.1126/science.1158140 18621671 [OpenAIRE] [PubMed] [DOI]

7 Xie L Li J Xie L: Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors.PLoS Comput Biol.2009;5(5):e1000387. 10.1371/journal.pcbi.1000387 194367 20 [OpenAIRE] [PubMed] [DOI]

8 Holohan C Van Schaeybroeck S Longley DB: Cancer drug resistance: an evolving paradigm.Nat Rev Cancer.2013;13(10):714–26. 10.1038/nrc3599 24060863 [OpenAIRE] [PubMed] [DOI]

9 Rotow J Bivona TG: Understanding and targeting resistance mechanisms in NSCLC.Nat Rev Cancer.2017;17(11):637–58. 10.1038/nrc.2017.84 29068003 [OpenAIRE] [PubMed] [DOI]

10 Kamburov A Pentchev K Galicka H: ConsensusPathDB: toward a more complete picture of cell biology.Nucleic Acids Res.20 11;39(Database issue):D712–7. 10.1093/nar/gkq1156 21071422 [OpenAIRE] [PubMed] [DOI]

11 Thorn CF Klein TE Altman RB: PharmGKB: the Pharmacogenomics Knowledge Base.Methods Mol Biol Clifton NJ.2013;1015:311–20. 10.1007/978-1-62703-435-7_20 23824865 [OpenAIRE] [PubMed] [DOI]

12 ElKalaawy N Wassal A: Methodologies for the modeling and simulation of biochemical networks, illustrated for signal transduction pathways: a primer.Biosystems.2015;129:1–18. 10.1016/j.biosystems.2015.01.008 25637875 [OpenAIRE] [PubMed] [DOI]

13 Heine r M Gilbert D Donaldson R: Petri Nets for Systems and Synthetic Biology. In: Bernardo M, Degano P, Zavattaro G, editors. Formal Methods for Computational Systems Biology Berlin, Heidelberg: Springer Berlin Heidelberg;2008;5016:215–64. 10.1007/978-3-540-68894-5_7 [OpenAIRE] [DOI]

14 Palsson B: Systems biology: constraint-based reconstruction and analysis. Cambridge, United Kingdom: Cambridge University Press;2015;531 10.1017/CBO9781139854610 [DOI]

15 Vaske CJ Benz SC Sanborn JZ: Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.Bioinformatics.2010;26(12):i237–45. 10.1093/bioinformatics/btq182 20529912 [OpenAIRE] [PubMed] [DOI]

55 references, page 1 of 4
Abstract
<ns7:p>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 reaction...
Subjects
free text keywords: Medicine, R, Science, Q, Software Tool Article, Articles, targeted therapy, drug interaction visualization, Reactome, biological pathway, functional interaction network, Boolean network, constrained fuzzy logic modeling, systems pharmacology, Interaction network, Computational biology, Precision medicine, Interaction information, medicine.medical_treatment, Computer science, Visualization, Biological network
Funded by
NIH| Oregon Clinical and Translational Research Institute
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5UL1TR000128-10
  • Funding stream: NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES
,
NIH| Illuminating molecular targetable pathways in HNSCC
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01CA192405-04
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| TRAINING PROGRAM IN HEALTH INFORMATICS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T15LM007088-10
  • Funding stream: NATIONAL LIBRARY OF MEDICINE
,
NIH| Reactome: An Open Knowledgebase of Human Pathways
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U41HG003751-07
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
55 references, page 1 of 4

1 Senft D Leiserson MDM Ruppin E: Precision Oncology: The Road Ahead.Trends Mol Med.2017;23(10):874–98. 10.1016/j.molmed.2017.08.003 28887051 [OpenAIRE] [PubMed] [DOI]

2 Salgado R Moore H Martens JWM: Steps forward for cancer precision medicine.Nat Rev Drug Discov.2018;17(1):1–2. 10.1038/nrd.2017.218 29170471 [PubMed] [DOI]

3 Yap TA Omlin A de Bono JS: Development of therapeutic combinations targeting major cancer signaling pathways.J Clin Oncol.2013;31(12):1592–605. 10.1200/JCO.2011.37.6418 23509311 [OpenAIRE] [PubMed] [DOI]

4 Bild AH Yao G Chang JT: Oncogenic pathway signatures in human cancers as a guide to targeted therapies.Nature.2006;439(7074):353–7. 10.1038/nature04296 16273092 [OpenAIRE] [PubMed] [DOI]

5 Filipp FV: Precision medicine dri ven by cancer systems biology.Cancer Metastasis Rev.2017;36(1):91–108. 10.1007/s10555-017-9662-4 28265786 [OpenAIRE] [PubMed] [DOI]

6 Campillos M Kuhn M Gavin AC: Drug target identification using side-effect similarity.Science.2008;321(5886):263–6. 10.1126/science.1158140 18621671 [OpenAIRE] [PubMed] [DOI]

7 Xie L Li J Xie L: Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors.PLoS Comput Biol.2009;5(5):e1000387. 10.1371/journal.pcbi.1000387 194367 20 [OpenAIRE] [PubMed] [DOI]

8 Holohan C Van Schaeybroeck S Longley DB: Cancer drug resistance: an evolving paradigm.Nat Rev Cancer.2013;13(10):714–26. 10.1038/nrc3599 24060863 [OpenAIRE] [PubMed] [DOI]

9 Rotow J Bivona TG: Understanding and targeting resistance mechanisms in NSCLC.Nat Rev Cancer.2017;17(11):637–58. 10.1038/nrc.2017.84 29068003 [OpenAIRE] [PubMed] [DOI]

10 Kamburov A Pentchev K Galicka H: ConsensusPathDB: toward a more complete picture of cell biology.Nucleic Acids Res.20 11;39(Database issue):D712–7. 10.1093/nar/gkq1156 21071422 [OpenAIRE] [PubMed] [DOI]

11 Thorn CF Klein TE Altman RB: PharmGKB: the Pharmacogenomics Knowledge Base.Methods Mol Biol Clifton NJ.2013;1015:311–20. 10.1007/978-1-62703-435-7_20 23824865 [OpenAIRE] [PubMed] [DOI]

12 ElKalaawy N Wassal A: Methodologies for the modeling and simulation of biochemical networks, illustrated for signal transduction pathways: a primer.Biosystems.2015;129:1–18. 10.1016/j.biosystems.2015.01.008 25637875 [OpenAIRE] [PubMed] [DOI]

13 Heine r M Gilbert D Donaldson R: Petri Nets for Systems and Synthetic Biology. In: Bernardo M, Degano P, Zavattaro G, editors. Formal Methods for Computational Systems Biology Berlin, Heidelberg: Springer Berlin Heidelberg;2008;5016:215–64. 10.1007/978-3-540-68894-5_7 [OpenAIRE] [DOI]

14 Palsson B: Systems biology: constraint-based reconstruction and analysis. Cambridge, United Kingdom: Cambridge University Press;2015;531 10.1017/CBO9781139854610 [DOI]

15 Vaske CJ Benz SC Sanborn JZ: Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.Bioinformatics.2010;26(12):i237–45. 10.1093/bioinformatics/btq182 20529912 [OpenAIRE] [PubMed] [DOI]

55 references, page 1 of 4
Powered by OpenAIRE Open Research Graph
Any information missing or wrong?Report an Issue
publication . Article . Other literature type . 2019

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

Blucher, Aurora S.; McWeeney, Shannon K.; Stein, Lincoln; Wu, Guanming;