PMC:7252096 / 24168-26785
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T2939 | 17-20 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T67027 | 207-221 | Body_part | denotes | terminal ileum | http://purl.org/sig/ont/fma/fma14966 |
| T83560 | 329-331 | Body_part | denotes | v2 | http://purl.org/sig/ont/fma/fma13443|http://purl.org/sig/ont/fma/fma68615 |
| T46338 | 374-379 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T87362 | 424-435 | Body_part | denotes | enterocytes | http://purl.org/sig/ont/fma/fma62122 |
| T54521 | 565-570 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T50831 | 585-601 | Body_part | denotes | epithelial cells | http://purl.org/sig/ont/fma/fma66768 |
| T62270 | 596-601 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T79033 | 730-735 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T15446 | 948-953 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T86947 | 1043-1048 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T44331 | 1129-1139 | Body_part | denotes | intestinal | http://purl.org/sig/ont/fma/fma7199 |
| T57529 | 1188-1199 | Body_part | denotes | enterocytes | http://purl.org/sig/ont/fma/fma62122 |
| T89766 | 1513-1524 | Body_part | denotes | enterocytes | http://purl.org/sig/ont/fma/fma62122 |
| T312 | 1761-1766 | Body_part | denotes | Ileum | http://purl.org/sig/ont/fma/fma7208 |
| T313 | 1821-1826 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T314 | 1856-1861 | Body_part | denotes | ileum | http://purl.org/sig/ont/fma/fma7208 |
| T315 | 1901-1903 | Body_part | denotes | v2 | http://purl.org/sig/ont/fma/fma13443|http://purl.org/sig/ont/fma/fma68615 |
| T317 | 1921-1926 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T318 | 2092-2108 | Body_part | denotes | epithelial cells | http://purl.org/sig/ont/fma/fma66768 |
| T319 | 2103-2108 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T320 | 2152-2167 | Body_part | denotes | epithelial cell | http://purl.org/sig/ont/fma/fma66768 |
| T87682 | 2163-2167 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T322 | 2212-2217 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T323 | 2221-2225 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T324 | 2265-2270 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T325 | 2288-2293 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T326 | 2431-2442 | Body_part | denotes | enterocytes | http://purl.org/sig/ont/fma/fma62122 |
| T327 | 2584-2589 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T328 | 2610-2615 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T50 | 216-221 | Body_part | denotes | ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
| T51 | 1761-1766 | Body_part | denotes | Ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
| T52 | 1856-1861 | Body_part | denotes | ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T113 | 68-77 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T114 | 509-513 | Disease | denotes | STAR | http://purl.obolibrary.org/obo/MONDO_0010408 |
| T115 | 1093-1108 | Disease | denotes | viral infection | http://purl.obolibrary.org/obo/MONDO_0005108 |
| T116 | 1099-1108 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T117 | 1254-1270 | Disease | denotes | immunodeficiency | http://purl.obolibrary.org/obo/MONDO_0021094 |
| T118 | 1355-1364 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T119 | 1417-1421 | Disease | denotes | STAR | http://purl.obolibrary.org/obo/MONDO_0010408 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T20186 | 37-40 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T57465 | 114-119 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T93198 | 216-221 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | ileum |
| T83396 | 225-226 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T43873 | 227-232 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T28803 | 292-294 | http://purl.obolibrary.org/obo/CLO_0050510 | denotes | 18 |
| T19355 | 346-347 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1700 | 374-379 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T95432 | 505-507 | http://purl.obolibrary.org/obo/CLO_0008933 | denotes | S5 |
| T83039 | 551-552 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T51135 | 565-570 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T52141 | 585-595 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
| T53994 | 596-601 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T85302 | 624-629 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T30460 | 639-641 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
| T9138 | 639-641 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
| T1331 | 642-643 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T72210 | 687-694 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T20348 | 730-735 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T58863 | 878-886 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activity |
| T12453 | 948-953 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T26941 | 966-971 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T82818 | 995-997 | http://purl.obolibrary.org/obo/CLO_0008933 | denotes | S5 |
| T65896 | 1043-1048 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T33034 | 1129-1139 | http://purl.obolibrary.org/obo/UBERON_0000160 | denotes | intestinal |
| T65650 | 1129-1139 | http://www.ebi.ac.uk/efo/EFO_0000834 | denotes | intestinal |
| T52849 | 1248-1253 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T24962 | 1271-1276 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T6117 | 1344-1350 | http://purl.obolibrary.org/obo/NCBITaxon_33208 | denotes | animal |
| T57895 | 1410-1414 | http://purl.obolibrary.org/obo/CLO_0001185 | denotes | 2018 |
| T63260 | 1542-1549 | http://purl.obolibrary.org/obo/NCBITaxon_33208 | denotes | animals |
| T21836 | 1744-1746 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
| T95974 | 1744-1746 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
| T63745 | 1747-1752 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | Human |
| T54544 | 1761-1766 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | Ileum |
| T32257 | 1789-1790 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T13453 | 1821-1826 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T98229 | 1850-1855 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T85540 | 1856-1861 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | ileum |
| T33298 | 1869-1870 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T98131 | 1921-1926 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T94550 | 2092-2102 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
| T88352 | 2103-2108 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T25360 | 2111-2112 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T50898 | 2152-2162 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
| T57631 | 2163-2167 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T33621 | 2212-2217 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T56038 | 2221-2225 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T38142 | 2265-2270 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T7647 | 2288-2293 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T40176 | 2408-2413 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T53351 | 2507-2514 | http://purl.obolibrary.org/obo/NCBITaxon_33208 | denotes | animals |
| T18464 | 2565-2569 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T46734 | 2584-2589 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T89430 | 2610-2615 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T94 | 505-507 | Chemical | denotes | S5 | http://purl.obolibrary.org/obo/CHEBI_29386 |
| T95 | 639-641 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
| T96 | 995-997 | Chemical | denotes | S5 | http://purl.obolibrary.org/obo/CHEBI_29386 |
| T97 | 1744-1746 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
| T98 | 2115-2117 | Chemical | denotes | Co | http://purl.obolibrary.org/obo/CHEBI_27638 |
| T99 | 2386-2396 | Chemical | denotes | interferon | http://purl.obolibrary.org/obo/CHEBI_52999 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T91940 | 844-863 | http://purl.obolibrary.org/obo/GO_0008152 | denotes | metabolic processes |
| T24720 | 1093-1108 | http://purl.obolibrary.org/obo/GO_0016032 | denotes | viral infection |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T150 | 0-138 | Sentence | denotes | Persistent viral RNA in rectal swabs has been detected in pediatric infection, even after negative nasopharyngeal tests (Xu et al., 2020). |
| T151 | 139-523 | Sentence | denotes | In an additional dataset consisting of endoscopic biopsies from the terminal ileum of a human pediatric cohort (n = 13 donors, ranging in age from 10 to 18 years old), collected with 10X 3′ v2, we confirmed a large abundance of ACE2 + cells with selective expression within absorptive enterocytes (29.7% ACE2 +, FDR-adjusted p = 2.46E−100) (Figures 3D and 3E; Table S5; STAR Methods). |
| T152 | 524-649 | Sentence | denotes | Furthermore, we identified a subset (888 cells, ∼6.5% of all epithelial cells) that co-express both genes (Figures S2 A–S2C). |
| T153 | 650-999 | Sentence | denotes | We performed differential expression testing and GO-term enrichment using these cells relative to matched non-expressers to highlight putative biological functions enriched within them, such as metabolic processes and catalytic activity, and to identify shared phenotypes of ACE2 + TMPRSS2 + ileal cells across both human and NHP cohorts (Table S5). |
| T154 | 1000-1149 | Sentence | denotes | We speculate that viral targeting of these cells, taken from patients without overt clinical viral infection, might help explain intestinal symptoms. |
| T155 | 1150-1431 | Sentence | denotes | Finally, we compared ileal absorptive enterocytes from healthy NHPs and NHPs infected with simian-human immunodeficiency virus (SHIV) and then treated for 6 months with anti-retroviral therapy (animal and infection characteristics published in Colonna et al., 2018) (STAR Methods). |
| T156 | 1432-1736 | Sentence | denotes | We found significant upregulation of ACE2, STAT1, and IFI6 within the absorptive enterocytes of SHIV-infected animals (which maintain chronically elevated amounts of IFNs and ISGs) compared with those of uninfected controls (FDR-adjusted p < 2E-7) (Figure S2D) (Deeks et al., 2017, Utay and Douek, 2016). |
| T157 | 1737-1787 | Sentence | denotes | Figure S2 Human and NHP Ileum, Related to Figure 3 |
| T158 | 1788-1792 | Sentence | denotes | (A). |
| T159 | 1793-1928 | Sentence | denotes | Top: tSNE projection of all cells from healthy pediatric human ileum within a previously-unpublished 10x 3′ v2 dataset (115,569 cells). |
| T160 | 1929-1986 | Sentence | denotes | Black: higher expression of ACE2 (left), TMPRSS2 (right). |
| T161 | 1987-1994 | Sentence | denotes | Bottom: |
| T162 | 1995-2079 | Sentence | denotes | Corresponding violin plots of expression values for ACE2 (left) and TMPRSS2 (right). |
| T163 | 2080-2109 | Sentence | denotes | Solid line: epithelial cells. |
| T164 | 2110-2114 | Sentence | denotes | (B). |
| T165 | 2115-2175 | Sentence | denotes | Co-expression of ACE2 and TMPRSS2 by epithelial cell subset. |
| T166 | 2176-2233 | Sentence | denotes | Number indicates % of ACE2+TMPRSS2+ cells by cell subset. |
| T167 | 2234-2347 | Sentence | denotes | (C). tSNE projection of 13,689 cells as in Figure 3D, cells colored by co-expression of ACE2 and TMPRSS2 (black). |
| T168 | 2348-2352 | Sentence | denotes | (D). |
| T169 | 2353-2523 | Sentence | denotes | Expression of ACE2 and canonical interferon-responsive genes among absorptive enterocytes from Healthy (n = 2) and SHIV-infected, anti-retroviral treated animals (n = 3). |
| T170 | 2524-2579 | Sentence | denotes | Bonferroni-adjusted p-values by Wilcoxon test (healthy: |
| T171 | 2580-2605 | Sentence | denotes | 510 cells, SHIV-infected: |
| T172 | 2606-2617 | Sentence | denotes | 636 cells). |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T11 | 1254-1270 | Phenotype | denotes | immunodeficiency | http://purl.obolibrary.org/obo/HP_0002721 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 675 | 1747-1752 | Species | denotes | Human | Tax:9606 |
| 681 | 1957-1961 | Gene | denotes | ACE2 | Gene:59272 |
| 682 | 1970-1977 | Gene | denotes | TMPRSS2 | Gene:7113 |
| 683 | 2047-2051 | Gene | denotes | ACE2 | Gene:59272 |
| 684 | 2063-2070 | Gene | denotes | TMPRSS2 | Gene:7113 |
| 685 | 1850-1855 | Species | denotes | human | Tax:9606 |
| 690 | 2132-2136 | Gene | denotes | ACE2 | Gene:59272 |
| 691 | 2141-2148 | Gene | denotes | TMPRSS2 | Gene:7113 |
| 692 | 2198-2202 | Gene | denotes | ACE2 | Gene:59272 |
| 693 | 2203-2210 | Gene | denotes | TMPRSS2 | Gene:7113 |
| 696 | 2322-2326 | Gene | denotes | ACE2 | Gene:59272 |
| 697 | 2331-2338 | Gene | denotes | TMPRSS2 | Gene:7113 |
| 702 | 2367-2371 | Gene | denotes | ACE2 | Gene:59272 |
| 703 | 2386-2396 | Gene | denotes | interferon | Gene:3439 |
| 704 | 2468-2481 | Disease | denotes | SHIV-infected | MESH:D007239 |
| 705 | 2591-2604 | Disease | denotes | SHIV-infected | MESH:D007239 |
| 725 | 367-371 | Gene | denotes | ACE2 | Gene:59272 |
| 726 | 443-447 | Gene | denotes | ACE2 | Gene:59272 |
| 727 | 925-929 | Gene | denotes | ACE2 | Gene:59272 |
| 728 | 932-939 | Gene | denotes | TMPRSS2 | Gene:7113 |
| 729 | 1469-1473 | Gene | denotes | ACE2 | Gene:59272 |
| 730 | 1475-1480 | Gene | denotes | STAT1 | Gene:6772 |
| 731 | 1486-1490 | Gene | denotes | IFI6 | Gene:2537 |
| 732 | 509-513 | Gene | denotes | STAR | Gene:6770 |
| 733 | 1417-1421 | Gene | denotes | STAR | Gene:6770 |
| 734 | 227-232 | Species | denotes | human | Tax:9606 |
| 735 | 966-971 | Species | denotes | human | Tax:9606 |
| 736 | 1061-1069 | Species | denotes | patients | Tax:9606 |
| 737 | 1241-1276 | Species | denotes | simian-human immunodeficiency virus | Tax:57667 |
| 738 | 1278-1282 | Species | denotes | SHIV | Tax:57667 |
| 739 | 68-77 | Disease | denotes | infection | MESH:D007239 |
| 740 | 1099-1108 | Disease | denotes | infection | MESH:D007239 |
| 741 | 1213-1235 | Disease | denotes | NHPs and NHPs infected | MESH:D007239 |
| 742 | 1355-1364 | Disease | denotes | infection | MESH:D007239 |
| 743 | 1528-1541 | Disease | denotes | SHIV-infected | MESH:D007239 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32413319-32284613-20790466 | 132-136 | 32284613 | denotes | 2020 |
| 32413319-30361514-20790467 | 1410-1414 | 30361514 | denotes | 2018 |
| 32413319-27941242-20790468 | 1708-1712 | 27941242 | denotes | 2017 |
| 32413319-27500281-20790469 | 1730-1734 | 27500281 | denotes | 2016 |