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dc.contributor.authorAlSaieedi, Ahdab
dc.contributor.authorSalhi, Adil
dc.contributor.authorTifratene, Faroug
dc.contributor.authorRaies, Arwa Bin
dc.contributor.authorHungler, Arnaud
dc.contributor.authorUludag, Mahmut
dc.contributor.authorVan Neste, Christophe Marc
dc.contributor.authorBajic, Vladimir B.
dc.contributor.authorGojobori, Takashi
dc.contributor.authorEssack, Magbubah
dc.date.accessioned2021-07-13T05:38:31Z
dc.date.available2021-07-13T05:38:31Z
dc.date.issued2021-07-12
dc.date.submitted2021-02-08
dc.identifier.citationAlSaieedi, A., Salhi, A., Tifratene, F., Raies, A. B., Hungler, A., Uludag, M., … Essack, M. (2021). DES-Tcell is a knowledgebase for exploring immunology-related literature. Scientific Reports, 11(1). doi:10.1038/s41598-021-93809-1
dc.identifier.issn2045-2322
dc.identifier.doi10.1038/s41598-021-93809-1
dc.identifier.urihttp://hdl.handle.net/10754/670163
dc.description.abstractAbstractT-cells are a subtype of white blood cells circulating throughout the body, searching for infected and abnormal cells. They have multifaceted functions that include scanning for and directly killing cells infected with intracellular pathogens, eradicating abnormal cells, orchestrating immune response by activating and helping other immune cells, memorizing encountered pathogens, and providing long-lasting protection upon recurrent infections. However, T-cells are also involved in immune responses that result in organ transplant rejection, autoimmune diseases, and some allergic diseases. To support T-cell research, we developed the DES-Tcell knowledgebase (KB). This KB incorporates text- and data-mined information that can expedite retrieval and exploration of T-cell relevant information from the large volume of published T-cell-related research. This KB enables exploration of data through concepts from 15 topic-specific dictionaries, including immunology-related genes, mutations, pathogens, and pathways. We developed three case studies using DES-Tcell, one of which validates effective retrieval of known associations by DES-Tcell. The second and third case studies focuses on concepts that are common to Grave’s disease (GD) and Hashimoto’s thyroiditis (HT). Several reports have shown that up to 20% of GD patients treated with antithyroid medication develop HT, thus suggesting a possible conversion or shift from GD to HT disease. DES-Tcell found miR-4442 links to both GD and HT, and that miR-4442 possibly targets the autoimmune disease risk factor CD6, which provides potential new knowledge derived through the use of DES-Tcell. According to our understanding, DES-Tcell is the first KB dedicated to exploring T-cell-relevant information via literature-mining, data-mining, and topic-specific dictionaries.
dc.description.sponsorshipThis work has been supported by the King Abdullah University of Science and Technology (KAUST) Base Research Fund BAS/1/1059-01-01 and BAS/1/1606-01-01 awarded to T.G. and VBB, respectively. M.E. was supported by KAUST Office of Sponsored Research (OSR) Awards No. FCC/1/1976-17-01.
dc.publisherSpringer Science and Business Media LLC
dc.relation.urlhttp://www.nature.com/articles/s41598-021-93809-1
dc.rightsThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleDES-Tcell is a knowledgebase for exploring immunology-related literature
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentComputer, Electrical, and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955‑6900, Saudi Arabia.
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentApplied Mathematics and Computational Science Program
dc.contributor.departmentBioscience Program
dc.identifier.journalScientific Reports
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDepartment of Medical Laboratory Technology (MLT), Faculty of Applied Medical Sciences (FAMS), King Abdulaziz University (KAU), Jeddah 21589‑80324, Saudi Arabia.
dc.identifier.volume11
dc.identifier.issue1
kaust.personSalhi, Adil
kaust.personTifratene, Faroug
kaust.personRaies, Arwa Bin
kaust.personHungler, Arnaud
kaust.personUludag, Mahmut
kaust.personVan Neste, Christophe Marc
kaust.personBajic, Vladimir B.
kaust.personGojobori, Takashi
kaust.personEssack, Magbubah
kaust.grant.numberBAS/1/1059-01-01
kaust.grant.numberBAS/1/1606-01-01
kaust.grant.numberFCC/1/1976-17-01
dc.date.accepted2021-06-24
refterms.dateFOA2021-07-13T05:39:37Z
kaust.acknowledged.supportUnitBAS
kaust.acknowledged.supportUnitBase Research Fund
kaust.acknowledged.supportUnitKAUST Office of Sponsored Research (OSR)
dc.date.published-online2021-07-12
dc.date.published-print2021-12


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This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
Except where otherwise noted, this item's license is described as This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.