PMC:7252096 / 42977-44783
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T554 | 108-113 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T555 | 117-124 | Body_part | denotes | tissues | http://purl.org/sig/ont/fma/fma9637 |
| T556 | 193-198 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T557 | 396-403 | Body_part | denotes | tissues | http://purl.org/sig/ont/fma/fma9637 |
| T558 | 407-411 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T559 | 577-581 | Body_part | denotes | skin | http://purl.org/sig/ont/fma/fma7163 |
| T560 | 604-609 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T561 | 707-712 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T562 | 799-803 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T563 | 825-830 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T564 | 835-846 | Body_part | denotes | macrophages | http://purl.org/sig/ont/fma/fma63261 |
| T565 | 1013-1018 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T566 | 1079-1112 | Body_part | denotes | peripheral blood mononuclear cell | http://purl.org/sig/ont/fma/fma86713 |
| T567 | 1108-1112 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T568 | 1194-1210 | Body_part | denotes | Epithelial Cells | http://purl.org/sig/ont/fma/fma66768 |
| T569 | 1205-1210 | Body_part | denotes | Cells | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T83 | 577-581 | Body_part | denotes | skin | http://purl.obolibrary.org/obo/UBERON_0000014 |
| T84 | 1090-1095 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T763 | 12-13 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T764 | 108-113 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T765 | 177-182 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T766 | 187-192 | http://purl.obolibrary.org/obo/CLO_0007836 | denotes | mouse |
| T767 | 193-198 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T768 | 228-229 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T769 | 407-417 | http://purl.obolibrary.org/obo/CLO_0000031 | denotes | cell lines |
| T770 | 517-518 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T771 | 577-581 | http://purl.obolibrary.org/obo/UBERON_0000014 | denotes | skin |
| T772 | 577-581 | http://purl.obolibrary.org/obo/UBERON_0001003 | denotes | skin |
| T773 | 577-581 | http://purl.obolibrary.org/obo/UBERON_0002097 | denotes | skin |
| T774 | 577-581 | http://purl.obolibrary.org/obo/UBERON_0002199 | denotes | skin |
| T775 | 577-581 | http://www.ebi.ac.uk/efo/EFO_0000962 | denotes | skin |
| T776 | 604-609 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T777 | 707-712 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T778 | 799-809 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell types |
| T779 | 819-822 | http://purl.obolibrary.org/obo/PR_000001004 | denotes | CD4 |
| T780 | 823-830 | http://purl.obolibrary.org/obo/CL_0000084 | denotes | T cells |
| T781 | 890-891 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T782 | 1007-1010 | http://purl.obolibrary.org/obo/PR_000001004 | denotes | CD4 |
| T783 | 1013-1025 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cells + type |
| T784 | 1079-1112 | http://purl.obolibrary.org/obo/CL_0000842 | denotes | peripheral blood mononuclear cell |
| T785 | 1079-1112 | http://purl.obolibrary.org/obo/CL_2000001 | denotes | peripheral blood mononuclear cell |
| T786 | 1139-1143 | http://purl.obolibrary.org/obo/CLO_0001185 | denotes | 2018 |
| T787 | 1194-1204 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | Epithelial |
| T788 | 1205-1210 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | Cells |
| T789 | 1263-1264 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T790 | 1304-1309 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T791 | 1313-1318 | http://purl.obolibrary.org/obo/CLO_0007836 | denotes | mouse |
| T792 | 1348-1366 | http://purl.obolibrary.org/obo/PR_000024990 | denotes | Type II interferon |
| T793 | 1535-1536 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T794 | 1661-1666 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T26523 | 1682-1687 | http://purl.obolibrary.org/obo/CLO_0007836 | denotes | mouse |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T230 | 138-141 | Chemical | denotes | IFN | http://purl.obolibrary.org/obo/CHEBI_52999 |
| T231 | 308-311 | Chemical | denotes | IFN | http://purl.obolibrary.org/obo/CHEBI_52999 |
| T232 | 489-491 | Chemical | denotes | II | http://purl.obolibrary.org/obo/CHEBI_74067 |
| T233 | 492-495 | Chemical | denotes | IFN | http://purl.obolibrary.org/obo/CHEBI_52999 |
| T234 | 514-516 | Chemical | denotes | S4 | http://purl.obolibrary.org/obo/CHEBI_29401 |
| T235 | 645-647 | Chemical | denotes | II | http://purl.obolibrary.org/obo/CHEBI_74067 |
| T236 | 648-651 | Chemical | denotes | IFN | http://purl.obolibrary.org/obo/CHEBI_52999 |
| T237 | 936-939 | Chemical | denotes | IFN | http://purl.obolibrary.org/obo/CHEBI_52999 |
| T238 | 1028-1031 | Chemical | denotes | IFN | http://purl.obolibrary.org/obo/CHEBI_52999 |
| T239 | 1170-1172 | Chemical | denotes | S4 | http://purl.obolibrary.org/obo/CHEBI_29401 |
| T240 | 1353-1355 | Chemical | denotes | II | http://purl.obolibrary.org/obo/CHEBI_74067 |
| T241 | 1356-1366 | Chemical | denotes | interferon | http://purl.obolibrary.org/obo/CHEBI_52999 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T27 | 1551-1572 | http://purl.obolibrary.org/obo/GO_0000981 | denotes | transcription factors |
| T28 | 1551-1564 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcription |
| T29 | 1627-1640 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcription |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T274 | 0-342 | Sentence | denotes | Next, using a publicly available resource (interferome.org) that hosts genomic and transcriptomic data from cells or tissues treated with IFN, we queried ACE2 expression within human and mouse cells, searching for datasets with a log2-fold-change of >1 or < −1 compared with untreated samples, including all IFN types (Rusinova et al., 2013). |
| T275 | 343-520 | Sentence | denotes | We recovered 21 datasets spanning 8 distinct primary tissues or cell lines with non-trivial changes in ACE2 expression after both type I and type II IFN treatment (Figure S4 A). |
| T276 | 521-791 | Sentence | denotes | We observed substantial upregulation of ACE2 in primary skin and primary bronchial cells treated with either type I or type II IFN (> 5-fold upregulation compared with that in untreated cells), in strong support of our in vitro data (Figures 5C, 5D, 5G–5L, and S3D–S3F). |
| T277 | 792-1162 | Sentence | denotes | Immune cell types, such as CD4 T cells and macrophages, were noticeably absent from datasets with a significant change in ACE2 expression after IFN stimulation or were even found to downregulate ACE2 (e.g., primary CD4 T cells + type I IFN) (Figure S4A, and in our analysis of scRNA-seq peripheral blood mononuclear cell data from Butler et al., (2018); data not shown). |
| T278 | 1163-1261 | Sentence | denotes | Figure S4 Published Studies of Epithelial Cells Following Interferon Treatment Related to Figure 5 |
| T279 | 1262-1266 | Sentence | denotes | (A). |
| T280 | 1267-1407 | Sentence | denotes | Fold change of ACE2 expression among human or mouse datasets following Type I or Type II interferon treatment compared to untreated control. |
| T281 | 1408-1485 | Sentence | denotes | Generated from publicly available microarray data curated at interferome.org. |
| T282 | 1486-1533 | Sentence | denotes | Includes all studies with abs(fold-change) > 1. |
| T283 | 1534-1538 | Sentence | denotes | (B). |
| T284 | 1539-1697 | Sentence | denotes | Location of transcription factors binding regions spanning −1500 bp to +500 bp from the transcription start site of ACE2 (human, top) or Ace2 (mouse, bottom). |
| T285 | 1698-1806 | Sentence | denotes | Generated from TRANSFAC data using the interferome.org database (Matys et al., 2003, Rusinova et al., 2013). |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 1236 | 1282-1286 | Gene | denotes | ACE2 | Gene:59272 |
| 1237 | 1356-1366 | Gene | denotes | interferon | Gene:3439 |
| 1238 | 1304-1309 | Species | denotes | human | Tax:9606 |
| 1239 | 1313-1318 | Species | denotes | mouse | Tax:10090 |
| 1244 | 1655-1659 | Gene | denotes | ACE2 | Gene:59272 |
| 1245 | 1676-1680 | Gene | denotes | Ace2 | Gene:59272 |
| 1246 | 1661-1666 | Species | denotes | human | Tax:9606 |
| 1247 | 1682-1687 | Species | denotes | mouse | Tax:10090 |
| 1262 | 154-158 | Gene | denotes | ACE2 | Gene:59272 |
| 1263 | 308-311 | Gene | denotes | IFN | Gene:3439 |
| 1264 | 446-450 | Gene | denotes | ACE2 | Gene:70008 |
| 1265 | 561-565 | Gene | denotes | ACE2 | Gene:59272 |
| 1266 | 819-822 | Gene | denotes | CD4 | Gene:920 |
| 1267 | 914-918 | Gene | denotes | ACE2 | Gene:70008 |
| 1268 | 987-991 | Gene | denotes | ACE2 | Gene:70008 |
| 1269 | 1007-1010 | Gene | denotes | CD4 | Gene:920 |
| 1270 | 936-939 | Gene | denotes | IFN | Gene:3439 |
| 1271 | 492-495 | Gene | denotes | IFN | Gene:3439 |
| 1272 | 138-141 | Gene | denotes | IFN | Gene:3439 |
| 1273 | 177-182 | Species | denotes | human | Tax:9606 |
| 1274 | 187-192 | Species | denotes | mouse | Tax:10090 |
| 1275 | 648-651 | Gene | denotes | IFN | Gene:3439 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32413319-23203888-20790483 | 336-340 | 23203888 | denotes | 2013 |
| 32413319-29608179-20790484 | 1139-1143 | 29608179 | denotes | 2018 |
| 32413319-12520026-20790485 | 1777-1781 | 12520026 | denotes | 2003 |
| 32413319-23203888-20790486 | 1800-1804 | 23203888 | denotes | 2013 |