TY - JOUR
T1 - DES-Tcell is a knowledgebase for exploring immunology-related literature
AU - AlSaieedi, Ahdab
AU - Salhi, Adil
AU - Tifratene, Faroug
AU - Raies, Arwa Bin
AU - Hungler, Arnaud
AU - Uludag, Mahmut
AU - Van Neste, Christophe Marc
AU - Bajic, Vladimir B.
AU - Gojobori, Takashi
AU - Essack, Magbubah
N1 - KAUST Repository Item: Exported on 2021-07-14
Acknowledged KAUST grant number(s): BAS/1/1059-01-01, BAS/1/1606-01-01, FCC/1/1976-17-01
Acknowledgements: This 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.
PY - 2021/7/12
Y1 - 2021/7/12
N2 - AbstractT-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.
AB - AbstractT-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.
UR - http://hdl.handle.net/10754/670163
UR - http://www.nature.com/articles/s41598-021-93809-1
U2 - 10.1038/s41598-021-93809-1
DO - 10.1038/s41598-021-93809-1
M3 - Article
C2 - 34253812
SN - 2045-2322
VL - 11
JO - Scientific Reports
JF - Scientific Reports
IS - 1
ER -