PMC:7252096 / 18497-21224
Annnotations
LitCovid-PD-FMA-UBERON
Id | Subject | Object | Predicate | Lexical cue | fma_id |
---|---|---|---|---|---|
T30868 | 104-108 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
T64579 | 215-231 | Body_part | denotes | epithelial cells | http://purl.org/sig/ont/fma/fma66768 |
T18385 | 226-231 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T26459 | 331-336 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T74490 | 363-374 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
T57427 | 392-403 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
T45527 | 509-513 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
T71902 | 593-604 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
T62436 | 716-727 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
T41832 | 742-747 | Body_part | denotes | Cells | http://purl.org/sig/ont/fma/fma68646 |
T321 | 758-762 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
T76609 | 781-791 | Body_part | denotes | pneumocyte | http://purl.org/sig/ont/fma/fma62499 |
T23388 | 806-810 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
T38118 | 854-859 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T76254 | 967-972 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T70818 | 983-988 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T15181 | 1053-1058 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T16876 | 1265-1269 | Body_part | denotes | Lung | http://purl.org/sig/ont/fma/fma7195 |
T10381 | 1336-1352 | Body_part | denotes | epithelial cells | http://purl.org/sig/ont/fma/fma66768 |
T43874 | 1347-1352 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T26007 | 1360-1365 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T98068 | 1388-1392 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
T99509 | 1399-1405 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
T29624 | 1442-1447 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T89353 | 1463-1468 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T39897 | 1494-1499 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T13798 | 1513-1518 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T19523 | 1531-1542 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
T40933 | 1560-1571 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
T71611 | 1633-1638 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T53856 | 1674-1679 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T6586 | 1683-1689 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
T46157 | 1726-1730 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
T54100 | 1736-1740 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
T47693 | 1756-1761 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T49420 | 1771-1776 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T18542 | 1832-1837 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T45700 | 1849-1854 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T70996 | 2023-2038 | Body_part | denotes | epithelial cell | http://purl.org/sig/ont/fma/fma66768 |
T87517 | 2034-2038 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
T76289 | 2098-2103 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T28685 | 2189-2194 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T55403 | 2235-2239 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T83597 | 2277-2282 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T11799 | 2340-2345 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T14134 | 2370-2381 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
T63492 | 2436-2447 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
T25039 | 2473-2478 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T14862 | 2573-2589 | Body_part | denotes | epithelial cells | http://purl.org/sig/ont/fma/fma66768 |
T38033 | 2584-2589 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
T7095 | 2697-2702 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
Id | Subject | Object | Predicate | Lexical cue | uberon_id |
---|---|---|---|---|---|
T34 | 104-108 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
T35 | 509-513 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
T36 | 1265-1269 | Body_part | denotes | Lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
T37 | 1399-1405 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
T38 | 1683-1689 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
T39 | 1726-1730 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
LitCovid-PD-MONDO
Id | Subject | Object | Predicate | Lexical cue | mondo_id |
---|---|---|---|---|---|
T106 | 283-287 | Disease | denotes | STAR | http://purl.obolibrary.org/obo/MONDO_0010408 |
T107 | 1191-1203 | Disease | denotes | inflammation | http://purl.obolibrary.org/obo/MONDO_0021166 |
T108 | 1243-1255 | Disease | denotes | Tuberculosis | http://purl.obolibrary.org/obo/MONDO_0018076 |
LitCovid-PD-CLO
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T32896 | 12-13 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T62302 | 104-108 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
T49811 | 104-108 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
T83510 | 141-160 | http://purl.obolibrary.org/obo/NCBITaxon_9541 | denotes | Macaca fascicularis |
T95036 | 215-225 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
T34107 | 226-231 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T2157 | 268-270 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
T63441 | 331-336 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T39559 | 376-378 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
T74853 | 509-513 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
T2994 | 509-513 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
T21425 | 561-565 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | Test |
T43594 | 742-747 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | Cells |
T81133 | 758-762 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
T47932 | 806-816 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell types |
T61012 | 854-859 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T89605 | 947-952 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
T35819 | 967-972 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T41200 | 983-988 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T11298 | 1053-1058 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T39187 | 1068-1075 | http://purl.obolibrary.org/obo/UBERON_0001005 | denotes | airways |
T12030 | 1079-1085 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | humans |
T67132 | 1155-1156 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T26933 | 1236-1238 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
T73657 | 1265-1269 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | Lung |
T20633 | 1265-1269 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | Lung |
T61293 | 1313-1314 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
T38285 | 1336-1346 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
T57087 | 1347-1352 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T71105 | 1360-1365 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T63382 | 1388-1397 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell type |
T17198 | 1442-1447 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T82766 | 1463-1468 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T19623 | 1478-1480 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
T37996 | 1494-1499 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T69593 | 1513-1518 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T27809 | 1548-1550 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
T85798 | 1619-1620 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
T80701 | 1633-1638 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T46135 | 1674-1679 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T9290 | 1726-1730 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
T95835 | 1726-1730 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
T64574 | 1736-1745 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell type |
T34712 | 1756-1761 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T48746 | 1771-1776 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T82967 | 1832-1837 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T84738 | 1849-1854 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T48976 | 1953-1957 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | Test |
T44586 | 2008-2013 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
T18907 | 2023-2033 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
T89339 | 2034-2043 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell type |
T66912 | 2098-2103 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T58845 | 2189-2194 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T54918 | 2235-2239 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T45497 | 2277-2282 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T61092 | 2292-2296 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
T69561 | 2340-2345 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T90995 | 2473-2478 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T58071 | 2520-2525 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
T53729 | 2573-2583 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
T23060 | 2584-2589 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T54660 | 2611-2615 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
T48816 | 2697-2702 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
T68923 | 2718-2725 | http://purl.obolibrary.org/obo/NCBITaxon_33208 | denotes | animals |
LitCovid-PD-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T70 | 186-188 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
T71 | 279-281 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
T72 | 360-362 | Chemical | denotes | II | http://purl.obolibrary.org/obo/CHEBI_74067 |
T73 | 590-592 | Chemical | denotes | II | http://purl.obolibrary.org/obo/CHEBI_74067 |
T74 | 647-660 | Chemical | denotes | antimicrobial | http://purl.obolibrary.org/obo/CHEBI_33281 |
T75 | 713-715 | Chemical | denotes | II | http://purl.obolibrary.org/obo/CHEBI_74067 |
T76 | 1176-1179 | Chemical | denotes | IFN | http://purl.obolibrary.org/obo/CHEBI_52999 |
T77 | 1557-1559 | Chemical | denotes | II | http://purl.obolibrary.org/obo/CHEBI_74067 |
T78 | 1603-1605 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
T79 | 1613-1615 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
T80 | 1965-1967 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
T81 | 2203-2208 | Chemical | denotes | group | http://purl.obolibrary.org/obo/CHEBI_24433 |
T82 | 2498-2500 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
T83 | 2679-2681 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
LitCovid-PD-GO-BP
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T85557 | 1191-1203 | http://purl.obolibrary.org/obo/GO_0006954 | denotes | inflammation |
LitCovid-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T105 | 0-297 | Sentence | denotes | Next, using a previously unpublished scRNA-seq dataset consisting of granuloma and adjacent, uninvolved lung samples from Mtb-infected NHPs (Macaca fascicularis) collected with Seq-Well S3, we identified subsets of epithelial cells expressing ACE2 and TMPRSS2 (Figure S1 ; Table S3; STAR Methods). |
T106 | 298-567 | Sentence | denotes | The majority of ACE2 + TMPRSS2 + cells were, once again, type II pneumocytes (22%) and type I pneumocytes (9.7%) and were largely enriched within granulomatous regions compared with those in adjacent uninvolved lung (Figures S1B and S1C) (p = 0.006, Fisher Exact Test). |
T107 | 568-741 | Sentence | denotes | ACE2 + TMPRSS2 + type II pneumocytes expressed significantly higher amounts of antimicrobial effectors such as LCN2 compared with remaining type II pneumocytes (Figure S1D). |
T108 | 742-1011 | Sentence | denotes | Cells with club cell/secretory, type I pneumocyte, and ciliated cell types also contained some ACE2 + TMPRSS2 + cells, but we did not have sufficient power to detect significantly differentially expressed genes between these cells and other cells within those clusters. |
T109 | 1012-1228 | Sentence | denotes | Altogether, we identify ACE2 + TMPRSS2 + cells in lower airways of humans and NHPs with consistent cellular phenotypes and evidence supporting a potential role for IFN-associated inflammation in upregulation of ACE2. |
T110 | 1229-1311 | Sentence | denotes | Figure S1 NHP Tuberculosis Infected Lung and Granuloma, Related to Figures 1 and 2 |
T111 | 1312-1316 | Sentence | denotes | (A). |
T112 | 1317-1448 | Sentence | denotes | UMAP projection of epithelial cells (1,099 cells) colored by annotated cell type, tissue source, and gating as ACE2+TMPRSS2+ cells. |
T113 | 1449-1572 | Sentence | denotes | ACE2+TMPRSS2+ cells comprise 11% of ciliated cells, 16% of club cells, 10% type I pneumocytes, and 22% type II pneumocytes. |
T114 | 1573-1617 | Sentence | denotes | Data generated using Seq-Well S3 (Table S3). |
T115 | 1618-1622 | Sentence | denotes | (B). |
T116 | 1623-1746 | Sentence | denotes | Number of cells (left) and % (right) ACE2+TMPRSS2+ cells by tissue source (granuloma versus uninvolved lung) and cell type. |
T117 | 1747-1902 | Sentence | denotes | Ciliated cells and club cells were omitted from this analysis as we detected too few cells (< 7 total cells) belonging to these clusters in the granulomas. |
T118 | 1903-1969 | Sentence | denotes | Statistical significance assessed by Fisher Exact Test (Table S3). |
T119 | 1970-1974 | Sentence | denotes | (C). |
T120 | 1975-2065 | Sentence | denotes | Dot plot of top cluster defining genes for each epithelial cell type and ACE2 and TMPRSS2. |
T121 | 2066-2240 | Sentence | denotes | Dot size represents fraction of cells expressing, and color intensity represents average log(normalized UMI + 1) among all cells in each group scaled between 0 and 1 by gene. |
T122 | 2241-2394 | Sentence | denotes | ACE2 expression is enriched in club cells (Bimodal test, Bonferroni-corrected p < 0.001), ciliated cells (p < 0.005), and type I pneumocytes (p < 0.001). |
T123 | 2395-2502 | Sentence | denotes | TMPRSS2 expression is enriched in type I pneumocytes (p < 0.001) and ciliated cells (p < 0.001) (Table S3). |
T124 | 2503-2507 | Sentence | denotes | (D). |
T125 | 2508-2727 | Sentence | denotes | Dot plot of genes differentially expressed between ACE2+TMPRSS2+ epithelial cells versus rest (Bimodal test, Bonferroni-corrected p < 0.01, log fold change > 0.5). (Table S3, c = number of cells, n = number of animals). |
LitCovid-PD-HP
Id | Subject | Object | Predicate | Lexical cue | hp_id |
---|---|---|---|---|---|
T7 | 69-78 | Phenotype | denotes | granuloma | http://purl.obolibrary.org/obo/HP_0032252 |
T8 | 1274-1283 | Phenotype | denotes | Granuloma | http://purl.obolibrary.org/obo/HP_0032252 |
T9 | 1698-1707 | Phenotype | denotes | granuloma | http://purl.obolibrary.org/obo/HP_0032252 |
T10 | 1891-1901 | Phenotype | denotes | granulomas | http://purl.obolibrary.org/obo/HP_0032252 |
LitCovid-PubTator
Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
---|---|---|---|---|---|
548 | 1239-1269 | Disease | denotes | NHP Tuberculosis Infected Lung | MESH:D012141 |
549 | 1274-1283 | Disease | denotes | Granuloma | MESH:D006099 |
554 | 1428-1432 | Gene | denotes | ACE2 | Gene:59272 |
555 | 1433-1440 | Gene | denotes | TMPRSS2 | Gene:7113 |
556 | 1449-1453 | Gene | denotes | ACE2 | Gene:59272 |
557 | 1454-1461 | Gene | denotes | TMPRSS2 | Gene:7113 |
562 | 1660-1664 | Gene | denotes | ACE2 | Gene:59272 |
563 | 1665-1672 | Gene | denotes | TMPRSS2 | Gene:7113 |
564 | 1698-1707 | Disease | denotes | granuloma | MESH:D006099 |
565 | 1891-1901 | Disease | denotes | granulomas | MESH:D006099 |
570 | 2048-2052 | Gene | denotes | ACE2 | Gene:59272 |
571 | 2057-2064 | Gene | denotes | TMPRSS2 | Gene:7113 |
572 | 2241-2245 | Gene | denotes | ACE2 | Gene:59272 |
573 | 2395-2402 | Gene | denotes | TMPRSS2 | Gene:7113 |
576 | 2559-2563 | Gene | denotes | ACE2 | Gene:59272 |
577 | 2564-2571 | Gene | denotes | TMPRSS2 | Gene:7113 |
597 | 243-247 | Gene | denotes | ACE2 | Gene:102130864 |
598 | 252-259 | Gene | denotes | TMPRSS2 | Gene:102137447 |
599 | 314-318 | Gene | denotes | ACE2 | Gene:102130864 |
600 | 321-328 | Gene | denotes | TMPRSS2 | Gene:102137447 |
601 | 568-572 | Gene | denotes | ACE2 | Gene:102130864 |
602 | 575-582 | Gene | denotes | TMPRSS2 | Gene:102137447 |
603 | 679-683 | Gene | denotes | LCN2 | Gene:3934 |
604 | 837-841 | Gene | denotes | ACE2 | Gene:102130864 |
605 | 844-851 | Gene | denotes | TMPRSS2 | Gene:102137447 |
606 | 1036-1040 | Gene | denotes | ACE2 | Gene:59272 |
607 | 1043-1050 | Gene | denotes | TMPRSS2 | Gene:7113 |
608 | 1176-1179 | Gene | denotes | IFN | Gene:3439 |
609 | 1223-1227 | Gene | denotes | ACE2 | Gene:59272 |
610 | 283-287 | Gene | denotes | STAR | Gene:102132972 |
611 | 141-160 | Species | denotes | Macaca fascicularis | Tax:9541 |
612 | 1079-1085 | Species | denotes | humans | Tax:9606 |
613 | 69-78 | Disease | denotes | granuloma | MESH:D006099 |
614 | 122-139 | Disease | denotes | Mtb-infected NHPs | MESH:D007239 |
615 | 1191-1203 | Disease | denotes | inflammation | MESH:D007249 |