PMC:7321036 / 122397-125869 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T216 999-1153 GO:0065007 denotes richment.Abundance tab), and phosphorylation dynamics clusters (from Figure 4A) upon SARS-CoV-2 infection (Enrichment.Ph_Clusters tab). Column description
T217 1893-1902 GO:0065007 denotes regulated
T243 1930-1940 SP_7 denotes SARS-CoV-2
T247 1947-1948 NCBITaxon:10239 denotes i
T250 1955-1956 NCBITaxon:10239 denotes r
T261 2005-2006 PG_3 denotes P
T263 2011-2012 NCBITaxon:11118 denotes a
T264 2015-2017 SO:0000417 denotes as
T265 2019-2020 PG_4 denotes o
T267 2033-2034 SP_7 denotes a
T299 2118-2119 SP_10 denotes o
T300 2119-2120 PG_4 denotes r
T312 2133-2134 PG_4 denotes p
T314 2149-2150 SP_7 denotes s
T322 2167-2168 GO:0018995 denotes h
T332 2216-2224 SP_7 denotes RS-CoV-2
T334 2226-2227 SP_7 denotes a
T336 2227-2228 GO:0018995 denotes t
T337 2228-2229 SP_6;NCBITaxon:9606 denotes h
T342 2269-2270 PG_4 denotes i
T343 2272-2274 GO:0006396 denotes on
T350 2284-2285 SO:0000203 denotes g
T354 2290-2291 SP_7 denotes o
T356 2291-2292 NCBITaxon:10239 denotes l
T363 2293-2294 MOP:0000780 denotes g
T364 2299-2301 GO:0005643 denotes co
T365 2301-2302 PR:000011526 denotes n
T382 2318-2319 GO:0006260 denotes P
T383 2319-2320 NCBITaxon:10239 denotes r
T384 2320-2321 SO:0001026 denotes e
T390 2336-2341 GO:0039703 denotes ption
T396 2350-2351 GO:0030532 denotes c
T397 2351-2353 GO:0005840 denotes ti
T402 2354-2358 PR:000000045 denotes itie
T406 2363-2368 GO:0065007 denotes lated
T408 2374-2376 GO:0065007 denotes gu
T419 2406-2407 GO:0006915 denotes t
T420 2412-2414 GO:0006260 denotes ri
T421 2414-2420 SO:0001811 denotes ption
T426 2439-2441 GO:0008150 denotes ro
T428 2445-2447 SP_7 denotes A-
T430 2467-2473 SP_7 denotes -CoV-2
T431 2474-2475 NCBITaxon:10239 denotes i
T453 2527-2528 GO:0000165 denotes l
T466 2555-2556 GO:0051235 denotes E
T495 2583-2584 PR:000008800 denotes 9
T498 2587-2588 CHEBI:23888;CHEBI:23888 denotes G
T510 2602-2603 GO:0006338 denotes E
T511 2603-2604 GO:0032991 denotes S
T514 2608-2610 GO:0065007 denotes re
T516 2622-2623 SO:0005836;GO:0065007 denotes l
T517 2625-2627 SO:0005836 denotes es
T518 2634-2635 PR:000008800 denotes p
T521 2636-2637 GO:0005680 denotes c
T523 2637-2638 GO:0065007 denotes t
T524 2638-2639 GO:0005856 denotes e
T539 2649-2650 PR:000000125 denotes 7
T554 2680-2682 CL:0011108;UBERON:0002424 denotes te
T577 2705-2706 GO:0065007 denotes r
T578 2706-2707 SP_7 denotes o
T591 2717-2720 PG_4 denotes pro
T596 2730-2740 SP_7 denotes SARS-CoV-2
T597 2744-2745 CL_6 denotes e
T599 2750-2752 CL_1 denotes AC
T601 2753-2754 SP_7 denotes 2
T604 2754-2755 SP_7 denotes -
T636 2783-2786 PR:000008220 denotes p38
T637 2787-2796 CHEBI:35222;CHEBI:35222 denotes inhibitor
T638 2811-2812 SP_7 denotes r
T640 2821-2823 CL_6 denotes ro
T641 2829-2830 SP_7 denotes c
T643 2846-2847 SP_7 denotes v
T650 2887-2888 GO:0031941 denotes t
T657 2907-2908 PR:000005952 denotes S
T670 2956-2958 CHEBI:51461;CHEBI:51461 denotes S5
T673 2981-2982 CL_6 denotes r
T674 2984-2985 SP_7 denotes s
T679 3011-3012 PR:000001245 denotes o
T680 3028-3029 GO:0010467 denotes i
T687 3073-3074 GO:0010467 denotes n
T693 3095-3096 GO:0065007 denotes u
T697 3107-3108 GO:0007050 denotes e
T707 3131-3132 BV_13 denotes g
T710 3134-3135 CHEBI:32958;CHEBI:32958 denotes s
T712 3138-3140 CHEBI:32958;CHEBI:32958 denotes pp
T717 3151-3152 SP_7 denotes s
T726 3162-3163 PR:000008814 denotes s
T728 3163-3166 PR:000002087 denotes upp
T730 3166-3168 GO:0065007 denotes li
T731 3176-3177 NCBITaxon:10239 denotes l
T735 3180-3181 GO:0000165 denotes n
T740 3193-3195 BV_27 denotes bl
T742 3202-3204 GO:0000165 denotes nn
T746 3220-3221 SP_7 denotes s
T747 3223-3224 CL_6 denotes e
T749 3229-3230 PR:000004986;CL_2 denotes c
T756 3244-3245 CHEBI:35222;CHEBI:35222 denotes i
T758 3250-3251 SP_7 denotes s
T763 3276-3277 SP_7 denotes v
T764 3278-3279 CL_6 denotes r
T791 3333-3335 SP_7 denotes ar
T796 3366-3367 SP_7 denotes R
T798 3375-3376 SP_7 denotes a
T801 3392-3393 CHEBI:35224;CHEBI:35224 denotes e
T804 3425-3426 SP_6;NCBITaxon:9606 denotes u
T805 3426-3427 UBERON:0002048 denotes g
T806 3433-3434 SP_6;NCBITaxon:9606 denotes n
T807 3434-3435 UBERON:0000483 denotes i
T808 3435-3437 UBERON:0002048 denotes ng
T811 3445-3446 UBERON:0002031;CL:0002328 denotes e
T812 3450-3451 GO:0065007 denotes d
T813 3452-3453 PR:000008220 denotes p
T43 2980-2985 CHEBI:36044;CHEBI:36044 denotes Drugs
T44 2990-2999 CHEBI:36357;CHEBI:36357 denotes compounds

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T50 100-105 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T51 260-267 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T52 509-516 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T53 543-548 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T54 729-737 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T55 848-852 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T56 978-985 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T57 1380-1387 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T58 2443-2446 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T59 2489-2493 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T60 2494-2498 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T61 2587-2591 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T62 2617-2621 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T63 2651-2659 Body_part denotes Cytokine http://purl.org/sig/ont/fma/fma84050
T64 2760-2765 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T65 2834-2839 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T66 2862-2871 Body_part denotes cytokines http://purl.org/sig/ont/fma/fma84050
T67 2872-2882 Body_part denotes chemokines http://purl.org/sig/ont/fma/fma241981
T68 3120-3127 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T69 3229-3233 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T70 3304-3308 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T34 2489-2493 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T395 111-119 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T396 122-131 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T397 203-211 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T398 214-223 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T399 1084-1092 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T400 1095-1104 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T401 1314-1323 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T402 1329-1337 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T403 1353-1368 Disease denotes Viral Infection http://purl.obolibrary.org/obo/MONDO_0005108
T404 1359-1368 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T405 1930-1938 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T406 1941-1950 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T407 2214-2222 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T408 2463-2471 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T409 2730-2738 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T161 6-8 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T162 92-105 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T163 535-548 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T164 641-643 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T165 641-643 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T166 845-847 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T167 848-852 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T168 1213-1223 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activities
T169 1278-1288 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T170 1446-1456 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T171 1473-1474 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T172 1496-1500 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T173 1664-1674 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T174 1802-1804 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T175 2033-2034 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T176 2349-2359 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activities
T177 2427-2437 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T178 2483-2488 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T179 2489-2493 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T180 2489-2493 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T181 2494-2504 http://purl.obolibrary.org/obo/CLO_0000031 denotes cell lines
T182 2587-2591 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T183 2617-2627 http://purl.obolibrary.org/obo/CLO_0000031 denotes cell lines
T184 2755-2759 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T185 2755-2759 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T186 2755-2759 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T187 2755-2759 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T188 2755-2759 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T189 2755-2759 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T190 2755-2759 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T191 2755-2759 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T192 2760-2765 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T193 2834-2839 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T194 2859-2861 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T195 2894-2896 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T196 2956-2958 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T197 2977-2979 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T198 3021-3031 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T199 3088-3090 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T200 3215-3219 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T201 3229-3238 http://purl.obolibrary.org/obo/CLO_0000031 denotes cell line
T202 3248-3253 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T203 3304-3308 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T204 3469-3471 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T78468 260-267 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T91318 509-516 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T26822 641-643 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T72017 729-737 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T77191 800-802 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T37437 978-985 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T65490 1193-1195 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T61100 1380-1387 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T43215 1802-1804 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T649 1876-1878 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T57781 2787-2796 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T84757 2797-2805 Chemical denotes SB203580 http://purl.obolibrary.org/obo/CHEBI_90705
T22546 2907-2909 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T40458 2956-2958 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T92142 2970-2972 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T29633 2977-2979 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T32084 3039-3041 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T81403 3088-3090 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T98259 3120-3127 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T51993 3423-3427 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T91938 3469-3471 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T41 9-24 http://purl.obolibrary.org/obo/GO_0016310 denotes Phosphorylation
T42 166-181 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T43 350-365 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T44 480-495 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T45 650-665 http://purl.obolibrary.org/obo/GO_0016310 denotes Phosphorylation
T46 900-915 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T47 1028-1043 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T48 1271-1288 http://purl.obolibrary.org/obo/GO_0016301 denotes kinase activities
T49 1353-1368 http://purl.obolibrary.org/obo/GO_0016032 denotes Viral Infection
T50 1439-1456 http://purl.obolibrary.org/obo/GO_0016301 denotes Kinase activities
T51 1657-1674 http://purl.obolibrary.org/obo/GO_0016301 denotes Kinase activities
T52 1817-1832 http://purl.obolibrary.org/obo/GO_0016310 denotes Phosphorylation
T53 1893-1918 http://purl.obolibrary.org/obo/GO_0042325 denotes regulated phosphorylation
T54 1903-1918 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T55 2133-2148 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T56 2225-2237 http://purl.obolibrary.org/obo/GO_0009405 denotes pathogenesis
T57 2239-2254 http://purl.obolibrary.org/obo/GO_0016310 denotes Phosphorylation
T58 2328-2359 http://purl.obolibrary.org/obo/GO_0003700 denotes Transcription Factor Activities
T59 2328-2348 http://purl.obolibrary.org/obo/GO_0000981 denotes Transcription Factor
T60 2328-2341 http://purl.obolibrary.org/obo/GO_0006351 denotes Transcription
T61 2406-2437 http://purl.obolibrary.org/obo/GO_0003700 denotes transcription factor activities
T62 2406-2426 http://purl.obolibrary.org/obo/GO_0000981 denotes transcription factor
T63 2406-2419 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T64 3014-3031 http://purl.obolibrary.org/obo/GO_0016301 denotes kinase activities
T65 3059-3074 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T66 3120-3135 http://purl.obolibrary.org/obo/GO_0006605 denotes protein targets

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T972 0-64 Sentence denotes Table S1 Phosphorylation and Abundance Data, Related to Figure 1
T973 65-132 Sentence denotes Contains proteomic data of Vero E6 cells upon SARS-CoV-2 infection.
T974 133-438 Sentence denotes Find the full list of unfiltered phosphorylation sites occurring upon SARS-CoV-2 infection (PhosphoDataFull tab), full list of protein abundance measurements (AbundanceDataFull tab), and filtered list of all detected phosphorylation sites collapsed into single-site measurements (PhosphoDataFiltered tab).
T975 439-582 Sentence denotes Lastly, find the full list of unfiltered phosphorylation sites upon N protein overexpression in Vero E6 cells (PhosphoNOverexpressionFull tab).
T976 583-634 Sentence denotes Column descriptions are indicated in the final tab.
T977 635-692 Sentence denotes Table S2 Viral Phosphorylation Sites, Related to Figure 2
T978 693-793 Sentence denotes List of phosphosites found on viral proteins from this study as well as from Davidson et al. (2020).
T979 794-847 Sentence denotes Table S3 Enrichments, Related to Figures 1, 4, and S1
T980 848-1134 Sentence denotes Gene ontology enrichments for significantly changed phosphorylation sites (Enrichment.Phosphorylation tab), significantly changed protein abundance (Enrichment.Abundance tab), and phosphorylation dynamics clusters (from Figure 4A) upon SARS-CoV-2 infection (Enrichment.Ph_Clusters tab).
T981 1135-1186 Sentence denotes Column descriptions are indicated in the final tab.
T982 1187-1244 Sentence denotes Table S4 Predicted Kinase Activities, Related to Figure 4
T983 1245-1352 Sentence denotes Full results of predicted kinase activities for each time point post infection with SARS-CoV-2 (Kinase Act.
T984 1353-1415 Sentence denotes Viral Infection tab) and N protein overexpression (Kinase Act.
T985 1416-1438 Sentence denotes N Overexpression tab).
T986 1439-1656 Sentence denotes Kinase activities are inferred as a -log10(p value) of Z-test from the comparison of fold changes in phosphosite measurements of the known substrates against the overall distribution of fold changes across the sample.
T987 1657-1743 Sentence denotes Kinase activities possessing any absolute value change greater than 1.5 are indicated.
T988 1744-1795 Sentence denotes Column descriptions are indicated in the final tab.
T989 1796-1878 Sentence denotes Table S5 Prioritized Phosphorylation Site Review, Related to Figure 7 and Table S8
T990 1879-2081 Sentence denotes Significantly regulated phosphorylation sites upon SARS-CoV-2 infection prioritized as either annotated within the PhosphoSitePlus database or possessing a high functional score (> = 0.75) (Ochoa et al.
T991 2082-2088 Sentence denotes 2020).
T992 2089-2238 Sentence denotes Includes literature context for prioritized phosphorylation sites, including their known functions and proposed relevance to SARS-CoV-2 pathogenesis.
T993 2239-2308 Sentence denotes Phosphorylation sites are partitioned into eight biological contexts.
T994 2309-2380 Sentence denotes Table S6 Predicted Transcription Factor Activities, Related to Figure 6
T995 2381-2536 Sentence denotes Full results of computed transcription factor activities from RNA-seq analysis of SARS-CoV-2 infected human lung cell lines (GSE147507) (Blanco-Melo et al.
T996 2537-2579 Sentence denotes 2020) using DoRothEA (Garcia-Alonso et al.
T997 2580-2586 Sentence denotes 2019).
T998 2587-2641 Sentence denotes Gene symbols, NES scores, and cell lines are depicted.
T999 2642-2695 Sentence denotes Table S7 Cytokine Profiling Data, Related to Figure 6
T1000 2696-2806 Sentence denotes Results from Luminex profiling of SARS-CoV-2 infected ACE2-A549 cells pre-treated with p38 inhibitor SB203580.
T1001 2807-2883 Sentence denotes Supernatants from infected cells were evaluated for 34 cytokines/chemokines.
T1002 2884-2900 Sentence denotes Units are pg/mL.
T1003 2901-2979 Sentence denotes Table S8 Drugs and Compounds, Related to Figures 7 and S5 and Tables S4 and S5
T1004 2980-3092 Sentence denotes Drugs and compounds mapped to top kinase activities (Table S4) and prioritized phosphorylation sites (Table S5).
T1005 3093-3357 Sentence denotes DrugInfo tab depicts known protein targets, approval status, SMILES, supplier, catalog numbers, chembl IDs, annotation of test site and cell line in which tests were performed, IC50 (viral inhibition) and CC50 (cell viability) values for pharmacological profiling.
T1006 3358-3472 Sentence denotes FullDrugResponseData tab depicts mean and standard deviation for drug screening experiments depicted in Figure S5.