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PMC:7321036 / 40229-42525 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T323 59-67 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T324 110-115 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T325 166-170 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T326 191-200 Body_part denotes cytokines http://purl.org/sig/ont/fma/fma84050
T327 201-214 Body_part denotes interleukin-6 http://purl.org/sig/ont/fma/fma264829
T328 457-461 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T329 676-683 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T330 694-702 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T331 792-797 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T332 872-881 Body_part denotes cytokines http://purl.org/sig/ont/fma/fma84050
T333 889-896 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T334 1182-1190 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T335 1260-1264 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T336 1483-1487 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T337 1519-1523 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T338 1626-1634 Body_part denotes Cytokine http://purl.org/sig/ont/fma/fma84050
T339 1681-1685 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T340 1756-1760 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T341 1776-1781 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T342 2036-2045 Body_part denotes cytokines http://purl.org/sig/ont/fma/fma84050
T343 2070-2074 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T344 2101-2106 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T345 2172-2176 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T346 2195-2198 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T193 80-88 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T194 223-228 Disease denotes tumor http://purl.obolibrary.org/obo/MONDO_0005070
T195 288-297 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T196 435-443 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T197 663-671 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T198 1027-1035 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T199 1153-1161 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T200 1650-1659 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T201 1872-1881 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T202 1887-1895 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T203 2135-2143 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T204 2146-2155 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T449 105-109 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T450 105-109 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T451 105-109 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T452 105-109 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T453 105-109 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T454 105-109 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T455 105-109 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T456 105-109 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T457 110-115 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T458 201-214 http://purl.obolibrary.org/obo/PR_000001393 denotes interleukin-6
T459 223-250 http://purl.obolibrary.org/obo/PR_000000134 denotes tumor necrosis factor alpha
T460 338-339 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T461 530-532 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T462 610-615 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T463 690-692 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T464 723-725 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T465 736-740 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T466 736-740 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T467 792-797 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T468 996-997 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T469 1140-1148 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T470 1164-1169 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T471 1210-1212 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T472 1260-1264 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T473 1404-1406 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T474 1483-1493 http://purl.obolibrary.org/obo/CLO_0000031 denotes cell lines
T475 1495-1499 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T476 1495-1499 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T477 1495-1499 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T478 1495-1499 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T479 1495-1499 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T480 1495-1499 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T481 1495-1499 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T482 1495-1499 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T483 1509-1513 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T484 1509-1513 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T485 1519-1523 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T486 1681-1685 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T487 1723-1724 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T488 1766-1770 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T489 1766-1770 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T490 1766-1770 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T491 1766-1770 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T492 1766-1770 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T493 1766-1770 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T494 1766-1770 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T495 1766-1770 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T496 1776-1781 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T497 1924-1931 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test is
T498 1944-1948 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T499 1970-1971 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T500 1985-1986 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T501 1992-1993 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T502 2070-2074 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T503 2093-2106 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T504 2172-2176 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T505 2251-2258 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test is
T506 2272-2276 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T264 142-151 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T265 152-160 Chemical denotes SB203580 http://purl.obolibrary.org/obo/CHEBI_90705
T266 216-218 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T268 245-250 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T269 530-532 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T270 581-589 Chemical denotes SB203580 http://purl.obolibrary.org/obo/CHEBI_90705
T271 676-683 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T272 690-692 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T275 723-725 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T276 889-896 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T277 914-916 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T279 993-995 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T280 1071-1079 Chemical denotes SB203580 http://purl.obolibrary.org/obo/CHEBI_90705
T281 1210-1212 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T282 1340-1345 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T283 1404-1406 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T286 1623-1625 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T287 1803-1812 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T288 1813-1821 Chemical denotes SB203580 http://purl.obolibrary.org/obo/CHEBI_90705
T289 1965-1967 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T290 2062-2064 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T291 2190-2194 Chemical denotes DAPI http://purl.obolibrary.org/obo/CHEBI_51231
T292 2195-2198 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T293 2293-2295 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T283 43-47 http://purl.obolibrary.org/obo/GO_0004707 denotes MAPK
T284 59-78 http://purl.obolibrary.org/obo/GO_0001816 denotes cytokine production
T285 229-237 http://purl.obolibrary.org/obo/GO_0070265 denotes necrosis
T286 229-237 http://purl.obolibrary.org/obo/GO_0019835 denotes necrosis
T287 229-237 http://purl.obolibrary.org/obo/GO_0008219 denotes necrosis
T288 229-237 http://purl.obolibrary.org/obo/GO_0001906 denotes necrosis
T289 558-575 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T290 558-575 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T291 1127-1131 http://purl.obolibrary.org/obo/GO_0004707 denotes MAPK
T292 1182-1201 http://purl.obolibrary.org/obo/GO_0001816 denotes cytokine production
T293 1681-1691 http://purl.obolibrary.org/obo/GO_0007049 denotes Cell Cycle
T294 2070-2080 http://purl.obolibrary.org/obo/GO_0007049 denotes Cell cycle

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T9 223-228 Phenotype denotes tumor http://purl.obolibrary.org/obo/HP_0002664

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
793 1500-1504 Gene denotes ACE2 Gene:103231639
794 1495-1499 CellLine denotes A549 CVCL:0023
795 1514-1516 CellLine denotes E6 CVCL:4582
798 1661-1664 Gene denotes p38 Gene:5594
799 1650-1659 Disease denotes Infection MESH:D007239
808 1799-1802 Gene denotes p38 Gene:5594
809 1887-1897 Species denotes SARS-CoV-2 Tax:2697049
810 1813-1821 Chemical denotes SB203580 MESH:C093642
811 2190-2194 Chemical denotes DAPI MESH:C007293
812 1872-1881 Disease denotes infection MESH:D007239
813 2135-2155 Disease denotes SARS-CoV-2 infection MESH:C000657245
814 1766-1775 CellLine denotes A549-ACE2 CVCL:0023
815 2098-2100 CellLine denotes E6 CVCL:4582
844 39-42 Gene denotes p38 Gene:5594
845 100-104 Gene denotes ACE2 Gene:59272
846 138-141 Gene denotes p38 Gene:5594
847 201-214 Gene denotes interleukin-6 Gene:3569
848 216-220 Gene denotes IL-6 Gene:3569
849 223-250 Gene denotes tumor necrosis factor alpha Gene:7124
850 252-257 Gene denotes TNF-α Gene:7124
851 320-323 Gene denotes p38 Gene:5594
852 407-410 Gene denotes p38 Gene:5594
853 914-918 Gene denotes IL-6 Gene:3569
854 920-925 Gene denotes CXCL8 Gene:3576
855 927-932 Gene denotes CCL20 Gene:6364
856 938-942 Gene denotes CCL2 Gene:6347
857 970-973 Gene denotes p38 Gene:5594
858 1123-1126 Gene denotes p38 Gene:5594
859 674-675 Gene denotes N Gene:43740575
860 435-445 Species denotes SARS-CoV-2 Tax:2697049
861 1027-1037 Species denotes SARS-CoV-2 Tax:2697049
862 1153-1163 Species denotes SARS-CoV-2 Tax:2697049
863 663-673 Species denotes SARS-CoV-2 Tax:2697049
864 152-160 Chemical denotes SB203580 MESH:C093642
865 581-589 Chemical denotes SB203580 MESH:C093642
866 1071-1079 Chemical denotes SB203580 MESH:C093642
867 80-99 Disease denotes SARS-CoV-2-infected MESH:C000657245
868 288-297 Disease denotes infection MESH:D007239
869 513-521 Disease denotes toxicity MESH:D064420
870 105-109 CellLine denotes A549 CVCL:0023
871 741-743 CellLine denotes E6 CVCL:4582

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T263 0-161 Sentence denotes To investigate the contribution of the p38/MAPK pathway to cytokine production, SARS-CoV-2-infected ACE2-A549 cells were treated with the p38 inhibitor SB203580.
T264 162-391 Sentence denotes The mRNA of the inflammatory cytokines interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), and others increased during infection and were inhibited by p38 inhibition in a dose-dependent manner (Figures 6F, right, and S4A).
T265 392-576 Sentence denotes Interestingly, p38 inhibition also reduced SARS-CoV-2 subgenomic mRNA (Figure 6F, left) in the absence of major cellular toxicity (Figure S5 ), indicative of reduced viral replication.
T266 577-745 Sentence denotes The SB203580-induced decrease in virus production was further confirmed using an anti-SARS-CoV-2 N protein (anti-NP) antibody-based assay (Figure S5, New York Vero E6).
T267 746-1009 Sentence denotes Multiplexed ELISA analysis of supernatants of cells from the same experiment demonstrated strong upregulation of inflammatory cytokines at the protein level, including IL-6, CXCL8, CCL20, and CCL2, which were decreased upon p38 inhibition (Figure S4 B; Table S7).
T268 1010-1202 Sentence denotes However, because SARS-CoV-2 replication is also inhibited by SB203580, we cannot deconvolve the contributions of p38/MAPK pathway activity and SARS-CoV-2 virus presence on cytokine production.
T269 1203-1295 Sentence denotes Figure S5 Pharmacological Profiling for Viral Titers and Cell Viability, Related to Figure 7
T270 1296-1360 Sentence denotes Dose response of phosphoproteomics-informed drugs and compounds.
T271 1361-1518 Sentence denotes Assays performed in New York (N; red, anti-NP; blue TCID50) and Paris (P; red, RT-qPCR; purple, plaque assays) across two cell lines (A549-ACE2 and Vero E6).
T272 1519-1549 Sentence denotes Cell viability shown in black.
T273 1550-1595 Sentence denotes Mean of three biological replicates is shown.
T274 1596-1615 Sentence denotes Error bars are SEM.
T275 1616-1721 Sentence denotes Figure S4 Cytokine Profiling upon Infection, p38 Inhibition, and Cell Cycle Analysis, Related to Figure 6
T276 1722-1911 Sentence denotes (A) RT-qPCR analysis of indicated mRNA from A549-ACE2 cells pre-treated with p38 inhibitor SB203580 at indicated concentrations for one hour prior to infection with SARS-CoV-2 for 24 hours.
T277 1912-1949 Sentence denotes Statistical test is Student’s t test.
T278 1950-2046 Sentence denotes Error bars are SD. (B) Same as in (A) but a Luminex-based quantification of indicated cytokines.
T279 2047-2171 Sentence denotes Error bars are SD. (C) Cell cycle analysis of Vero E6 cells (same as in Figure 6I) upon SARS-CoV-2 infection at an MOI of 1.
T280 2172-2238 Sentence denotes Cell stained with DAPI DNA stain prior to flow cytometry analysis.
T281 2239-2277 Sentence denotes Statistical test is Mann-Whitney test.
T282 2278-2296 Sentence denotes Error bars are SD.