PMC:7252096 / 14157-16755
Annnotations
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 |