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PMC:7111504 / 12361-16550 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
181 44-47 Gene denotes CD8 Gene:925
182 49-52 Gene denotes TCR Gene:6962
183 18-27 Species denotes 2019-nCoV Tax:2697049
185 318-321 Gene denotes TCR Gene:6962
192 531-534 Gene denotes CD8 Gene:925
193 606-611 Gene denotes HLA-A Gene:3105
194 751-754 Gene denotes TCR Gene:6962
195 536-539 Gene denotes TCR Gene:6962
196 762-771 Species denotes 2019-nCoV Tax:2697049
197 406-411 Disease denotes tumor MESH:D009369
203 1374-1379 Gene denotes HLA-A Gene:3105
204 818-827 Species denotes 2019-nCoV Tax:2697049
205 1254-1263 Species denotes 2019-nCoV Tax:2697049
206 1300-1308 Chemical denotes peptides MESH:D010455
207 1408-1417 Chemical denotes NetMHCpan
210 1476-1479 Gene denotes TCR Gene:6962
211 1516-1525 Species denotes 2019-nCoV Tax:2697049
214 1661-1664 Gene denotes TCR Gene:6962
215 1622-1631 Species denotes 2019-nCoV Tax:2697049
221 1816-1821 Gene denotes HLA-A Gene:3105
222 1756-1759 Gene denotes TCR Gene:6962
223 1698-1707 Species denotes 2019-nCoV Tax:2697049
224 1831-1840 Chemical denotes NetMHCpan
225 1853-1862 Chemical denotes NetMHCpan
235 2809-2812 Gene denotes MHC Gene:3107
236 3400-3403 Gene denotes TCR Gene:6962
237 3218-3227 Species denotes 2019-nCoV Tax:2697049
238 2887-2896 Chemical denotes NetMHCpan
239 2914-2921 Chemical denotes leucine MESH:D007930
240 2923-2924 Chemical denotes L MESH:D007930
241 2930-2936 Chemical denotes valine MESH:D014633
242 3086-3093 Chemical denotes leucine MESH:D007930
243 3104-3110 Chemical denotes valine MESH:D014633
246 3466-3475 Species denotes 2019-nCoV Tax:2697049
247 3498-3505 Chemical denotes leucine MESH:D007930
252 3678-3683 Gene denotes HLA-A Gene:3105
253 3622-3625 Gene denotes TCR Gene:6962
254 3701-3710 Chemical denotes NetMHCpan
255 3723-3732 Chemical denotes NetMHCpan

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T149 0-14 BV_15 denotes Immunogenicity
T150 18-27 SP_7 denotes 2019-nCoV
T151 53-61 CHEBI:36357;CHEBI:36357 denotes molecule
T152 199-205 CL:0000084 denotes T cell
T153 323-329 CL:0000084 denotes T cell
T154 377-383 CL:0000084 denotes T cell
T155 412-420 CHEBI:59132;CHEBI:59132 denotes antigens
T156 473-480 CL:0000084 denotes T cells
T157 606-611 PR:000002009 denotes HLA-A
T158 762-771 SP_7 denotes 2019-nCoV
T159 804-808 SP_9 denotes mers
T160 818-827 SP_7 denotes 2019-nCoV
T161 1035-1049 BV_15 denotes immunogenicity
T162 1254-1263 SP_7 denotes 2019-nCoV
T163 1374-1379 PR:000002009 denotes HLA-A
T164 1516-1525 SP_7 denotes 2019-nCoV
T165 1599-1603 SP_9 denotes mers
T166 1622-1631 SP_7 denotes 2019-nCoV
T167 1632-1636 SO:0000236 denotes ORFs
T168 1698-1707 SP_7 denotes 2019-nCoV
T169 1816-1821 PR:000002009 denotes HLA-A
T170 2809-2812 GO:0042611 denotes MHC
T171 3030-3033 GO:0042611 denotes MHC
T172 3036-3043 PR:000002009 denotes HLA-A02
T173 3160-3167 PR:000002009 denotes HLA-A02
T174 3218-3227 SP_7 denotes 2019-nCoV
T175 3261-3275 BV_15 denotes immunogenicity
T176 3434-3441 PR:000002009 denotes HLA-A02
T177 3445-3454 SO:0001024 denotes haplotype
T178 3466-3475 SP_7 denotes 2019-nCoV
T179 3678-3683 PR:000002009 denotes HLA-A
T59205 0-14 BV_15 denotes Immunogenicity
T33056 18-27 SP_7 denotes 2019-nCoV
T536 53-61 CHEBI:36357;CHEBI:36357 denotes molecule
T9906 199-205 CL:0000084 denotes T cell
T69209 323-329 CL:0000084 denotes T cell
T36975 377-383 CL:0000084 denotes T cell
T33303 412-420 CHEBI:59132;CHEBI:59132 denotes antigens
T36223 473-480 CL:0000084 denotes T cells
T80986 606-611 PR:000002009 denotes HLA-A
T35114 762-771 SP_7 denotes 2019-nCoV
T99554 804-808 SP_9 denotes mers
T68802 818-827 SP_7 denotes 2019-nCoV
T66664 1035-1049 BV_15 denotes immunogenicity
T22144 1254-1263 SP_7 denotes 2019-nCoV
T48296 1374-1379 PR:000002009 denotes HLA-A
T18213 1516-1525 SP_7 denotes 2019-nCoV
T15461 1599-1603 SP_9 denotes mers
T62919 1622-1631 SP_7 denotes 2019-nCoV
T15838 1632-1636 SO:0000236 denotes ORFs
T241 1698-1707 SP_7 denotes 2019-nCoV
T1071 1816-1821 PR:000002009 denotes HLA-A
T4757 2809-2812 GO:0042611 denotes MHC
T28172 3030-3033 GO:0042611 denotes MHC
T77140 3036-3043 PR:000002009 denotes HLA-A02
T91368 3160-3167 PR:000002009 denotes HLA-A02
T69195 3218-3227 SP_7 denotes 2019-nCoV
T26868 3261-3275 BV_15 denotes immunogenicity
T24626 3434-3441 PR:000002009 denotes HLA-A02
T89323 3445-3454 SO:0001024 denotes haplotype
T65632 3466-3475 SP_7 denotes 2019-nCoV
T76744 3678-3683 PR:000002009 denotes HLA-A

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T78 201-205 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T79 325-329 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T80 379-383 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T81 475-480 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T82 606-609 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T83 1374-1377 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T84 1816-1819 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T85 2809-2812 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T86 2914-2921 Body_part denotes leucine http://purl.org/sig/ont/fma/fma82757
T87 2930-2936 Body_part denotes valine http://purl.org/sig/ont/fma/fma82766
T88 3030-3033 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T89 3036-3039 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T90 3086-3093 Body_part denotes leucine http://purl.org/sig/ont/fma/fma82757
T91 3104-3110 Body_part denotes valine http://purl.org/sig/ont/fma/fma82766
T92 3160-3163 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T93 3434-3437 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T94 3498-3505 Body_part denotes leucine http://purl.org/sig/ont/fma/fma82757
T95 3506-3512 Body_part denotes valine http://purl.org/sig/ont/fma/fma82766
T96 3678-3681 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T19 406-411 Disease denotes tumor http://purl.obolibrary.org/obo/MONDO_0005070

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T168 28-36 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T169 44-47 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T170 199-205 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T171 323-329 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T172 347-350 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T173 356-368 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrumental
T174 377-383 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T175 461-462 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T176 473-480 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T177 531-534 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T178 585-592 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T179 610-611 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T180 666-667 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 772-779 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T182 843-851 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T183 867-877 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activating
T184 965-972 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T185 1022-1023 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T186 1098-1108 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T187 1264-1272 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T188 1278-1279 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T189 1300-1308 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T190 1326-1334 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T191 1378-1379 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T192 1526-1534 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T193 1714-1722 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T194 1820-1821 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T195 1870-1877 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptide
T196 1894-1904 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activation
T197 2847-2855 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T198 2964-2966 http://purl.obolibrary.org/obo/CLO_0008307 denotes P2
T199 2975-2977 http://purl.obolibrary.org/obo/CLO_0008343 denotes P9
T200 3056-3064 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T201 3072-3080 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T202 3097-3099 http://purl.obolibrary.org/obo/CLO_0008307 denotes P2
T203 3114-3116 http://purl.obolibrary.org/obo/CLO_0008343 denotes P9
T204 3192-3199 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T205 3228-3236 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T206 3248-3256 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T207 3295-3303 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T208 3356-3364 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T209 3482-3490 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T210 3534-3542 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptides
T211 3682-3683 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T212 3740-3747 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptide
T213 3764-3774 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activation

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T86 28-36 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T87 53-61 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T88 412-420 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T89 585-592 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T90 772-779 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T91 843-851 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T92 965-972 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T93 1264-1272 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T94 1300-1308 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T95 1326-1334 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T96 1526-1534 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T97 1714-1722 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T98 1870-1877 Chemical denotes Peptide http://purl.obolibrary.org/obo/CHEBI_16670
T99 2847-2855 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T100 2914-2921 Chemical denotes leucine http://purl.obolibrary.org/obo/CHEBI_25017
T101 2930-2936 Chemical denotes valine http://purl.obolibrary.org/obo/CHEBI_27266
T102 2964-2966 Chemical denotes P2 http://purl.obolibrary.org/obo/CHEBI_33472
T103 3056-3064 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T104 3072-3080 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T105 3086-3093 Chemical denotes leucine http://purl.obolibrary.org/obo/CHEBI_25017
T106 3097-3099 Chemical denotes P2 http://purl.obolibrary.org/obo/CHEBI_33472
T107 3104-3110 Chemical denotes valine http://purl.obolibrary.org/obo/CHEBI_27266
T108 3189-3191 Chemical denotes LV http://purl.obolibrary.org/obo/CHEBI_73579
T109 3192-3199 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T110 3228-3236 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T111 3248-3256 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T112 3295-3303 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T113 3356-3364 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T114 3482-3490 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T115 3498-3505 Chemical denotes leucine http://purl.obolibrary.org/obo/CHEBI_25017
T116 3506-3512 Chemical denotes valine http://purl.obolibrary.org/obo/CHEBI_27266
T117 3740-3747 Chemical denotes Peptide http://purl.obolibrary.org/obo/CHEBI_16670

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 406-411 Phenotype denotes tumor http://purl.obolibrary.org/obo/HP_0002664

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T143 0-61 Sentence denotes Immunogenicity of 2019-nCoV peptides to 1G4 CD8+ TCR molecule
T144 62-223 Sentence denotes While our de novo candidates are appealing shortlisted targets for experimental validation, it does not provide information about target T cell receptors (TCRs).
T145 224-322 Sentence denotes We therefore set out to interrogate the possibility of cross reactivity with one well-studied TCR.
T146 323-444 Sentence denotes T cell cross-reactivity has been instrumental for the T cell immunity against both tumor antigens and external pathogens.
T147 445-618 Sentence denotes In that regard, a number of T cells have been extensively characterized including 1G4 CD8+ TCR, which is known to recognize the ‘SLLMWITQC’ peptide presented by HLA-A*02:01.
T148 619-780 Sentence denotes We therefore set out to leverage the data from a recently published study 7 and exploit the possibility of cross reactivity of this TCR to any 2019-nCoV peptide.
T149 781-1067 Sentence denotes Here, we scanned all 9-mers from the 2019-nCoV proteome (9613 peptides) with Binding, Activating and Killing Position Weight Matrices (PWM, see the method section) and associated each peptide with the geometric mean of these three assays as a measure of immunogenicity (Data Table 4 4).
T150 1068-1213 Sentence denotes The distributions of binding, activation and killing scores along with their multiplicative score and geometric mean are illustrated in Figure 4.
T151 1214-1315 Sentence denotes Based on geometric mean, we observed 20 2019-nCoV peptides with a score > 0.8 and 516 peptides > 0.7.
T152 1316-1444 Sentence denotes The 9-mer peptides with geometric mean > 0.7 and positive HLA-A*02:01 binding prediction by NetMHCpan 4.0 are listed in Table 4.
T153 1445-1454 Sentence denotes Figure 4.
T154 1456-1535 Sentence denotes Distribution of 1G4 TCR positional weight matrix scores for 2019-nCoV peptides.
T155 1536-1687 Sentence denotes The positional weight matrices were obtained from 7 and 9613 9-mers generated from 10 2019-nCoV ORFs were computed for their TCR recognition potential.
T156 1688-1696 Sentence denotes Table 4.
T157 1698-1869 Sentence denotes 2019-nCoV 9-mer peptides with geometric mean ≥ 0.7 by 1G4 TCR positional weight matrix and predicted positive to bind HLA-A*02:01 by NetMHCpan 4.0 (Rank = NetMHCpan rank).
T158 1870-1948 Sentence denotes Peptide Binding score Activation score Killing score geoMean Rank Binder
T159 1949-2013 Sentence denotes RIMTWLDMV 0.866377428 0.853995 0.776303 0.831249 0.3481 SB
T160 2014-2077 Sentence denotes ALNTLVKQL 0.802453741 0.75073 0.785957 0.779413 0.6159 WB
T161 2078-2140 Sentence denotes LLLDRLNQL 0.809895414 0.7752 0.741096 0.774888 0.0423 SB
T162 2141-2205 Sentence denotes MIAQYTSAL 0.766262499 0.789511 0.749477 0.768242 0.9238 WB
T163 2206-2269 Sentence denotes VLSTFISAA 0.799672451 0.756117 0.687278 0.746239 0.536 WB
T164 2270-2334 Sentence denotes NVLAWLYAA 0.761297552 0.686117 0.739944 0.728423 1.4457 WB
T165 2335-2399 Sentence denotes RLANECAQV 0.783161706 0.719705 0.680504 0.726572 0.2049 SB
T166 2400-2464 Sentence denotes KLLKSIAAT 0.748896679 0.708996 0.697463 0.718118 1.0923 WB
T167 2465-2528 Sentence denotes QLSLPVLQV 0.70128376 0.715259 0.708405 0.708293 0.4768 SB
T168 2529-2593 Sentence denotes VQMAPISAM 0.729320768 0.698514 0.689612 0.705612 1.4677 WB
T169 2594-2656 Sentence denotes LLLTILTSL 0.7131709 0.715194 0.680064 0.702623 0.2712 SB
T170 2657-2720 Sentence denotes SVLLFLAFV 0.736972762 0.690855 0.679534 0.70202 1.1449 WB
T171 2721-2992 Sentence denotes LMWLIINLV 0.727847374 0.681119 0.694007 0.700717 1.304 WB We further analysed the MHC binding propensities and gathered peptides not only predicted positive by NetMHCpan but also to have leucine (L) and valine (V) in anchor positions 2 (P2) and 9 (P9) respectively.
T172 2993-3173 Sentence denotes Previous studies have shown that for MHC-I HLA-A02:01 specific peptides, 9-mer peptides with leucine at P2 and valine at P9 are preferably presented on the surface of HLA-A02:01 8.
T173 3174-3321 Sentence denotes Looking at the LV peptide, we identified 44 2019-nCoV peptides of which 2 peptides had immunogenicity score > 0.7 and 12 peptides > 0.6 ( Table 5).
T174 3322-3455 Sentence denotes Thus, here we provide the list of peptides that are potential targets for 1G4 TCR recognition for subjects with HLA-A02:01 haplotype.
T175 3456-3464 Sentence denotes Table 5.
T176 3466-3533 Sentence denotes 2019-nCoV 9-mer peptides having leucine-valine in anchor positions.
T177 3534-3739 Sentence denotes Peptides have geometric mean ≥ 0.6 and ≤ 0.7 (for those ≥ 0.7, refer to Table 4) by 1G4 TCR positional weight matrix and predicted positive for HLA-A*02:01 binding by NetMHCpan 4.0 (Rank = NetMHCpan rank).
T178 3740-3818 Sentence denotes Peptide Binding score Activation score Killing score geoMean Rank Binder
T179 3819-3880 Sentence denotes TLMNVLTLV 0.723687 0.658986 0.652178 0.677534 0.0444 SB
T180 3881-3942 Sentence denotes QLEMELTPV 0.711291 0.651003 0.608605 0.655625 1.6769 WB
T181 3943-4003 Sentence denotes MLAKALRKV 0.668756 0.610664 0.65968 0.645854 0.3524 SB
T182 4004-4065 Sentence denotes GLFKDCSKV 0.675952 0.632375 0.594753 0.633494 0.2677 SB
T183 4066-4127 Sentence denotes ALSKGVHFV 0.652549 0.604952 0.586236 0.613954 0.0425 SB
T184 4128-4189 Sentence denotes YLNTLTLAV 0.624147 0.610826 0.575445 0.603119 0.0453 SB

MyTest

Id Subject Object Predicate Lexical cue
32269766-31695703-30420973 693-695 31695703 denotes 7
32269766-31695703-30420974 1586-1588 31695703 denotes 7
32269766-1709722-30420975 3171-3172 1709722 denotes 8

2_test

Id Subject Object Predicate Lexical cue
32269766-31695703-30420973 693-694 31695703 denotes 7
32269766-31695703-30420974 1586-1587 31695703 denotes 7
32269766-1709722-30420975 3171-3172 1709722 denotes 8