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Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

Ryan A. Miller, Peter Woollard, Egon L. Willighagen, Daniela Digles, Martina Kutmon, Antonis Loizou, Andra Waagmeester, Stefan Senger, Chris T. Evelo
2018 F1000Research  
Having high quality biological interaction information in the Open PHACTS Discovery Platform is needed to answer multiple pathway related questions. PubMed Abstract | Publisher Full Text 2.  ...  Waagmeester A, Kutmon M, Riutta A, et al.: Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLoS Comput Biol. 2016; 12(6): e1004989.  ...  The API call can help aid drug discovery by taking a target, in this case AKT, and easily identify other connected proteins that could potentially be used as drug targets with a common downstream effect  ... 
doi:10.12688/f1000research.13197.1 fatcat:dfrlt4lsujaqzhu54je5ikrl5e

ReactionFlow: an interactive visualization tool for causality analysis in biological pathways

Tuan Dang, Paul Murray, Jillian Aurisano, Angus Forbes
2015 BMC Proceedings  
common downstream elements from two or more proteins.  ...  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  ...  Acknowledgements We thank Guang Yao and Ryan Gutenkunst who provided useful insight into biological pathways and emphasized the importance of representing causality when analyzing pathways.  ... 
doi:10.1186/1753-6561-9-s6-s6 pmid:26361502 pmcid:PMC4547159 fatcat:wyqwekeisbh7xkxrvanpcp62im

Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

Ryan A Miller, Peter Woollard, Egon L Willighagen, Daniela Digles, Martina Kutmon, Antonis Loizou, Andra Waagmeester, Stefan Senger, Chris T Evelo
2018 F1000Research  
Having high quality biological interaction information in the Open PHACTS Discovery Platform is needed to answer multiple pathway related questions.  ...  This data includes information about biological interactions, such as stimulation and inhibition.  ...  The API calls can help aid drug discovery by taking a target, in this case AKT, and easily identify other connected proteins that could potentially be used as drug targets with a common downstream effect  ... 
doi:10.12688/f1000research.13197.2 pmid:30416713 pmcid:PMC6206606 fatcat:swrjqaahk5brdhwwlu4w7su4ji

TRANSPATH(R): an integrated database on signal transduction and a tool for array analysis

M. Krull
2003 Nucleic Acids Research  
It uses the TRANSPATH data set to identify key regulators in pathways connected with up-or down-regulated genes of the respective array.  ...  TRANSPATH 1 is a database system about gene regulatory networks that combines encyclopedic information on signal transduction with tools for visualization and analysis.  ...  In most cases, reactions are directed and allow pathway upstream or downstream queries.  ... 
doi:10.1093/nar/gkg089 pmid:12519957 pmcid:PMC165536 fatcat:wh2xy6zm3jahpakgbatlcoq62m

Pathway Analysis for Drug Repositioning Based on Public Database Mining

Yongmei Pan, Tiejun Cheng, Yanli Wang, Stephen H. Bryant
2014 Journal of Chemical Information and Modeling  
Interestingly, some drugs identified pathways responsible for other diseases than their current therapeutic uses, and these pathways were verified retrospectively by in vitro tests, in vivo tests, or clinical  ...  Entrez E-Utilities were applied, and in-house Ruby scripts were developed for data retrieval and pathway analysis to identify and evaluate relevant pathways common to the retrieved drug targets.  ...  the retrieved target proteins or genes were not the direct targets of the drug but interacted with the drug in an indirect way as up or downstream proteins or by crosstalking with the primary pathways  ... 
doi:10.1021/ci4005354 pmid:24460210 pmcid:PMC3956470 fatcat:ha6nsnwribel5j3d4u22cngpwi

Target identification in biological systems using network connectivity information from literature mining databases

Ugur Guner, Jay H. Lee, Omar L. Francone, Dmitriy Leyfer
2010 IFAC Proceedings Volumes  
A gene downstream or upstream in the pathway can be a remedy, however, finding such an alternative target using existing in-silico or bench tools can be extremely labor-intensive.  ...  Recently, increasing amounts of information and observations have been compiled from different areas of biological research and deposited on databases.  ...  A gene downstream or upstream in the network might be a solution, however, not all pathways are known, and finding such an alternative target using existing in-silico or bench tools can be extremely laborintensive  ... 
doi:10.3182/20100705-3-be-2011.00016 fatcat:e6ixfdcea5fwtcbufppomrjv4u

Illuminating drug discovery with biological pathways

Gordana Apic, Tijana Ignjatovic, Scott Boyer, Robert B. Russell
2005 FEBS Letters  
A "systems" approach can help identify pathways related to a disease and can suggest secondary effects of drugs that might cause these problems and thus ultimately improve the drug discovery pipeline.  ...  Although this goal is a long way off, many useful insights can already come from currently available information and technology.  ...  Example of how drug-specificity problems might be predicted using pathway information.  ... 
doi:10.1016/j.febslet.2005.02.023 pmid:15763566 fatcat:be3pef5wgrco3cgtsiu6gn4d3y

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action

Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Yubo Zhou, Erica Bowton, Dan M. Roden, Joshua C. Denny, Melinda C. Aldrich, Hua Xu (+2 others)
2015 PLoS Computational Biology  
A drug exerts its effects typically through a signal transduction cascade, which is non-linear and involves intertwined networks of multiple signaling pathways.  ...  Construction of such a signaling pathway network (SPNetwork) can enable identification of novel drug targets and deep understanding of drug action.  ...  Furthermore, as the time and costs for developing novel drugs dramatically increased recently, many drug developers prefer to find new uses for existing drugs including the approved and non-approved drugs  ... 
doi:10.1371/journal.pcbi.1004202 pmid:26083494 pmcid:PMC4470683 fatcat:s22thhxti5ch3is7s77ijq5f54

Pathway-based drug repositioning using causal inference

Jiao Li, Zhiyong Lu
2013 BMC Bioinformatics  
Conclusions: We successfully developed a computational method for discovering new uses of existing drugs based on casual inference in a layered drug-target-pathway-gene-disease network.  ...  based on rich information in several expert-curated knowledge-bases.  ...  By taking advantage of the increasing amount of expert-curated biological knowledge in the public domain (e.g. pathway information in Pathway Commons [21] ), we built a multi-layer causal network (CauseNet  ... 
doi:10.1186/1471-2105-14-s16-s3 pmid:24564553 pmcid:PMC3853312 fatcat:sqkqsnsby5by3kzf24r4c4763y

Development of Molecularly Targeted Therapies to Treat Pediatric Malignancies

Clinton F. Stewart, Giles W. Robinson
2017 Clinical Pharmacology and Therapeutics  
Drugs and biologics developed to treat children with cancer have been historically developed in adults for adult indications.  ...  Although leading to many useful drugs and biologics to treat pediatric cancer, future development of molecularly targeted therapies (MTTs) should be directed toward pediatric tumors more specifically to  ...  As noted earlier, drugs and biologics developed first in adults have been subsequently used in children with cancer and found to provide clinical benefit.  ... 
doi:10.1002/cpt.785 pmid:28836264 pmcid:PMC5656826 fatcat:ybu6jvxmcbhkrbfn2xnolgzdl4

Systems biology visualization tools for drug target discovery

Tianxiao Huan, Xiaogang Wu, Jake Y Chen
2010 Expert Opinion on Drug Discovery  
phenotypes with pathway-level molecular changes to guide targeted therapy [78] Design drugs by modeling downstream signaling molecules inside a particular pathway [30] Examine side effects of drugs  ...  Systems biology provides a new paradigm for drug developers to understand the effects of drugs on targets, target-interacting proteins, regulatory control genes, in downstream metabolic pathways, and in  ... 
doi:10.1517/17460441003725102 pmid:22823128 fatcat:3gumecrgwjafrkgzxcn753sbhu

Biological substantiation of antipsychotic-associated pneumonia: Systematic literature review and computational analyses

Janet Sultana, Marco Calabró, Ricard Garcia-Serna, Carmen Ferrajolo, Concetta Crisafulli, Jordi Mestres, Gianluca Trifirò', Kenji Hashimoto
2017 PLoS ONE  
Cytoscape was then used to map biological pathways that could link AP targets and off-targets to pneumonia. Results The literature search yielded 200 articles; 41 were included in the review.  ...  Methods A search was conducted in Medline and Web of Science to identify studies exploring the association between pneumonia and antipsychotic use, from which information on hypothesized mechanism of action  ...  In the second approach, the "Pathway Commons" [31] database was used in order to identify nodes related to the function of the off-targets identified.  ... 
doi:10.1371/journal.pone.0187034 pmid:29077727 pmcid:PMC5659779 fatcat:otwq5mhldfgm3osmada4ajmfkm

Druggable Targets and Targeted Drugs: Enhancing the Development of New Therapeutics

Melvin L. Billingsley
2008 Pharmacology  
In spite of these advances, the gross measure of approvable drug output is declining, with only 17 new chemical entities approved by the FDA in 2007.  ...  The approaches that are needed to facilitate such convergence include merging computational methods, systems biology, and gene-linked categorization of diseases with the use of appropriate drug delivery  ...  Thus, pathway analysis can be useful as a biologic system to explore the relationships between casual and correlative effects of the target, the disease and drug treatment.  ... 
doi:10.1159/000157624 pmid:18802381 fatcat:dnenvnh3qnclfmawgarweqz2gm

Proteomics as a guiding tool for more effective personalized therapy

J.-m. Lee, E. C. Kohn
2010 Annals of Oncology  
, but 'is the pathway upregulated?' This will be successful if validated peptide biomarkers are applied for patient selection prospectively and with inclusion of preplanned biological correlates.  ...  This has given us insight into the perturbations of signaling pathways within tumor cells and has improved the discovery of new drug targets and possible prognostic indicators of outcome and disease response  ...  signaling pathway with a 'smart' drug selection approach.  ... 
doi:10.1093/annonc/mdq375 pmid:20943616 pmcid:PMC3018888 fatcat:ykfeoylkr5h2rly5riopmwaf6y

Molecular basis of mood and cognitive adverse events elucidated via a combination of pharmacovigilance data mining and functional enrichment analysis

Christos Andronis, João Pedro Silva, Eftychia Lekka, Vassilis Virvilis, Helena Carmo, Konstantina Bampali, Margot Ernst, Yang Hu, Irena Loryan, Jacques Richard, Félix Carvalho, Miroslav M. Savić
2020 Archives of Toxicology  
120 associated genes and common pathway nodes possibly underlying MCAEs.  ...  To fill some gaps in the understanding and elucidate potential biological mechanisms of action frequently associated with MCAEs, we present a unique workflow linking observational population data with  ...  , drugs, etc.), visualize biological interconnections and communicate findings with peers (https ://www.biovi sta.com/vizit /).  ... 
doi:10.1007/s00204-020-02788-1 pmid:32504122 fatcat:y76b3nl7dvct3laf4qkafsqxju
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