Literature-Based Enrichment Insights into Redox Control of Vascular Biology
Bin Res, Arwa A.
Van Neste, Christophe Marc
Bajic, Vladan P.
Bajic, Vladimir B.
Isenovic, Esma R.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Applied Mathematics and Computational Science Program
Computer Science Program
Permanent link to this recordhttp://hdl.handle.net/10754/652931
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AbstractIn cellular physiology and signaling, reactive oxygen species (ROS) play one of the most critical roles. ROS overproduction leads to cellular oxidative stress. This may lead to an irrecoverable imbalance of redox (oxidation-reduction reaction) function that deregulates redox homeostasis, which itself could lead to several diseases including neurodegenerative disease, cardiovascular disease, and cancers. In this study, we focus on the redox effects related to vascular systems in mammals. To support research in this domain, we developed an online knowledge base, DES-RedoxVasc, which enables exploration of information contained in the biomedical scientific literature. The DES-RedoxVasc system analyzed 233399 documents consisting of PubMed abstracts and PubMed Central full-text articles related to different aspects of redox biology in vascular systems. It allows researchers to explore enriched concepts from 28 curated thematic dictionaries, as well as literature-derived potential associations of pairs of such enriched concepts, where associations themselves are statistically enriched. For example, the system allows exploration of associations of pathways, diseases, mutations, genes/proteins, miRNAs, long ncRNAs, toxins, drugs, biological processes, molecular functions, etc. that allow for insights about different aspects of redox effects and control of processes related to the vascular system. Moreover, we deliver case studies about some existing or possibly novel knowledge regarding redox of vascular biology demonstrating the usefulness of DES-RedoxVasc. DES-RedoxVasc is the first compiled knowledge base using text mining for the exploration of this topic.
CitationEssack M, Salhi A, Stanimirovic J, Tifratene F, Bin Raies A, et al. (2019) Literature-Based Enrichment Insights into Redox Control of Vascular Biology. Oxidative Medicine and Cellular Longevity 2019: 1–16. Available: http://dx.doi.org/10.1155/2019/1769437.
SponsorsThis work has been supported by grant no. 173033 (ERI) and no. 173034 (BSP) from the Ministry of Education, Science and Technological Development, Republic of Serbia. VBB has been supported by the King Abdullah University of Science and Technology (KAUST) Base Research Fund (BAS/1/1606-01-01), and ME has been supported by KAUST Office of Sponsored Research (OSR) Award no. FCC/1/1976-24-01.
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