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PMC:7252096 / 14157-16755 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T51526 40-44 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T99760 45-50 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T95342 185-189 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T92810 190-196 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T78289 289-293 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T69943 323-328 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T4180 521-532 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T896 546-551 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T59565 598-603 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T50359 639-650 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T31548 698-706 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T33475 751-756 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T71780 895-900 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T13117 1045-1049 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195
T97209 1050-1066 Body_part denotes Epithelial Cells http://purl.org/sig/ont/fma/fma66768
T58447 1061-1066 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T22748 1081-1084 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T72849 1227-1231 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T51464 1232-1238 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T32804 1354-1358 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T159 1442-1447 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T16248 1474-1477 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T57087 1521-1526 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T21872 1571-1575 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T163 1730-1733 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T38697 1750-1753 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T165 1806-1810 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T42440 1896-1901 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T17615 1909-1913 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T67803 1938-1942 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T7984 2049-2054 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T17779 2129-2133 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T52492 2181-2186 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T94798 2266-2277 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T69556 2306-2317 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T7255 2524-2527 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T27 40-44 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T28 185-189 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T29 190-196 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T30 1045-1049 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048
T31 1227-1231 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T32 1232-1238 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T91 346-350 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408
T92 1115-1127 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T93 1471-1473 Disease denotes TB http://purl.obolibrary.org/obo/MONDO_0018076
T94 1486-1488 Disease denotes TB http://purl.obolibrary.org/obo/MONDO_0018076
T95 1586-1590 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408
T96 2532-2534 Disease denotes TB http://purl.obolibrary.org/obo/MONDO_0018076

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T86334 40-44 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T50390 40-44 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T48113 45-50 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T37100 77-83 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T5449 97-98 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31894 185-189 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T2015 185-189 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T45149 289-299 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T83337 323-328 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T80628 338-341 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2 A
T55319 379-384 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T795 439-441 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T51533 439-441 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T66909 546-560 http://purl.obolibrary.org/obo/CLO_0000031 denotes cells, in line
T42173 598-603 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T35738 619-621 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T95623 751-756 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T24497 895-900 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T86794 1045-1066 http://purl.obolibrary.org/obo/CL_0000082 denotes Lung Epithelial Cells
T51443 1137-1142 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T63387 1179-1180 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T35956 1221-1226 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T32379 1227-1231 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T73304 1227-1231 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T7811 1354-1364 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T89005 1414-1415 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37671 1442-1447 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T53946 1521-1526 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells
T21733 1571-1580 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T96107 1602-1603 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T75647 1628-1629 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T62279 1791-1796 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T23408 1806-1815 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T67693 1896-1901 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T25827 1909-1918 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T4783 1930-1931 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67532 1938-1942 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T46104 2049-2054 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T20388 2077-2086 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes are
T2783 2105-2107 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T54985 2105-2107 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T59240 2129-2139 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T38339 2181-2186 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T65003 2243-2248 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T49895 2340-2345 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T27452 2351-2352 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55966 2431-2441 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes; the
T60530 2474-2476 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T6253 2474-2476 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T52423 2508-2513 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T18839 2573-2577 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T75828 2595-2597 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T26490 2595-2597 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T53 221-223 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T54 439-441 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T55 518-520 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T56 636-638 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T57 687-697 Chemical denotes surfactant http://purl.obolibrary.org/obo/CHEBI_35195
T58 698-706 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T59 1150-1152 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T60 1311-1313 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T61 2105-2107 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T62 2474-2476 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T63 2595-2597 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T80 0-246 Sentence denotes To assess whether the findings from NHP lung cells were similarly present in humans, we analyzed a previously unpublished scRNA-seq dataset derived from surgical resections of fibrotic lung tissue collected with Seq-Well S3 (Hughes et al., 2019).
T81 247-443 Sentence denotes Unsupervised analysis identified multiple cell types and subtypes of immune cells (Figures 2 A–2C; STAR Methods), as defined by the genes displayed in Figure 2C (full lists available in Table S2).
T82 444-627 Sentence denotes Here, we found that ACE2 and TMPRSS2 were primarily expressed within type II pneumocytes and ciliated cells, in line with our analysis of the NHP-derived cells (Figures 1 and 2A, 2B).
T83 628-882 Sentence denotes In type II pneumocytes (identified by unique expression of surfactant proteins SFTPC, SFTPB, and SFTPA1), we found 1.4% of cells expressing ACE2 (FDR-adjusted p = 1.35E−21), 34.2% expressing TMPRSS2 (FDR-adjusted p < 1E−300), and 0.8% co-expressing both.
T84 883-1028 Sentence denotes In ciliated cells, we found 7% were ACE2 + (FDR-adjusted p = 5E−64), 24.6% were TMPRSS2 + (FDR-adjusted p = 3.8E−30), and 5.3% co-expressed both.
T85 1029-1177 Sentence denotes Figure 2 Select Lung Epithelial Cells from Control, HIV-1-Infected, and Mycobacterium-tuberculosis-Infected Human Donors Co-Express ACE2 and TMPRSS2
T86 1178-1391 Sentence denotes (A) Schematic of protocol for isolation of human lung tissue from surgical excess, creation of scRNA-seq libraries by using Seq-Well S3, and computational analysis to identify cell types by using unbiased methods.
T87 1392-1520 Sentence denotes Shown on the right is a UMAP projection of 18,915 cells across 8 donors (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients).
T88 1521-1600 Sentence denotes Cells represented by points, colored according to cell type (see STAR Methods).
T89 1601-1694 Sentence denotes (B) UMAP projection as in (A), points colored by detection of ACE2 (top) or TMPRSS2 (bottom).
T90 1695-1763 Sentence denotes Color coding is as follows: black, RNA positive; blue, RNA negative.
T91 1764-2055 Sentence denotes (C) Dot plot of 2 defining genes for each cell type (FDR-adjusted p < 0.001), and ACE2 and TMPRSS2; dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells.
T92 2056-2108 Sentence denotes All cluster-defining genes are provided in Table S2.
T93 2109-2187 Sentence denotes Red arrow indicates cell types with largest proportion of ACE2+TMPRSS2+ cells.
T94 2188-2318 Sentence denotes (D) Volcano plot identifying significantly upregulated genes in ACE2+TMPRSS2+ pneumocytes compared with all remaining pneumocytes.
T95 2319-2403 Sentence denotes Red points represent genes with a FDR-adjusted p < 0.05, and log2(fold change) >1.5.
T96 2404-2477 Sentence denotes Text highlighting specific genes; the full list is available in Table S2.
T97 2478-2579 Sentence denotes (E) Expression of ACE2 across human donors by HIV and TB status (p = 0.009 by likelihood-ratio test).
T98 2580-2598 Sentence denotes See also Table S2.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
430 1161-1165 Gene denotes ACE2 Gene:59272
431 1137-1142 Species denotes Human Tax:9606
432 1081-1095 Disease denotes HIV-1-Infected MESH:D015658
433 1101-1136 Disease denotes Mycobacterium-tuberculosis-Infected MESH:D014376
439 1586-1590 Gene denotes STAR Gene:6770
440 1221-1226 Species denotes human Tax:9606
441 1510-1518 Species denotes patients Tax:9606
442 1474-1477 Species denotes HIV Tax:12721
443 1501-1509 Disease denotes infected MESH:D007239
446 1663-1667 Gene denotes ACE2 Gene:59272
447 1677-1684 Gene denotes TMPRSS2 Gene:7113
452 1846-1850 Gene denotes ACE2 Gene:59272
453 1855-1862 Gene denotes TMPRSS2 Gene:7113
454 2167-2171 Gene denotes ACE2 Gene:59272
455 2172-2179 Gene denotes TMPRSS2 Gene:7113
458 2252-2256 Gene denotes ACE2 Gene:59272
459 2257-2264 Gene denotes TMPRSS2 Gene:7113
464 2496-2500 Gene denotes ACE2 Gene:59272
465 2508-2513 Species denotes human Tax:9606
466 2524-2527 Species denotes HIV Tax:12721
467 2532-2534 Chemical denotes TB MESH:D013725
479 464-468 Gene denotes ACE2 Gene:59272
480 473-480 Gene denotes TMPRSS2 Gene:7113
481 707-712 Gene denotes SFTPC Gene:6440
482 714-719 Gene denotes SFTPB Gene:6439
483 725-731 Gene denotes SFTPA1 Gene:653509
484 768-772 Gene denotes ACE2 Gene:59272
485 819-826 Gene denotes TMPRSS2 Gene:7113
486 919-923 Gene denotes ACE2 Gene:59272
487 963-970 Gene denotes TMPRSS2 Gene:7113
488 346-350 Gene denotes STAR Gene:6770
489 77-83 Species denotes humans Tax:9606