PMC:7252096 / 57909-62133
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T734 | 261-266 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T735 | 272-278 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T736 | 294-301 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T737 | 342-346 | Body_part | denotes | mRNA | http://purl.org/sig/ont/fma/fma67122 |
| T738 | 535-541 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T739 | 616-620 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T740 | 709-714 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T741 | 1025-1029 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T742 | 1094-1099 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T743 | 1186-1190 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T744 | 1565-1569 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T745 | 1867-1872 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T746 | 1957-1961 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T747 | 1966-1971 | Body_part | denotes | ileum | http://purl.org/sig/ont/fma/fma7208 |
| T748 | 1972-1976 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T749 | 2050-2054 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T750 | 2055-2060 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T751 | 2109-2114 | Body_part | denotes | ileum | http://purl.org/sig/ont/fma/fma7208 |
| T752 | 2115-2120 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T753 | 2197-2201 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T754 | 2206-2211 | Body_part | denotes | ileum | http://purl.org/sig/ont/fma/fma7208 |
| T755 | 2212-2216 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T756 | 2279-2283 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T757 | 2284-2289 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T758 | 2312-2316 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T759 | 2317-2322 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T760 | 2345-2350 | Body_part | denotes | ileum | http://purl.org/sig/ont/fma/fma7208 |
| T761 | 2351-2356 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T762 | 2379-2384 | Body_part | denotes | ileum | http://purl.org/sig/ont/fma/fma7208 |
| T763 | 2385-2390 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T764 | 2467-2471 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T765 | 2518-2522 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T766 | 2636-2642 | Body_part | denotes | cell’s | http://purl.org/sig/ont/fma/fma68646 |
| T767 | 2741-2745 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T768 | 2876-2880 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T769 | 2925-2929 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T770 | 3000-3006 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T771 | 3072-3077 | Body_part | denotes | ileum | http://purl.org/sig/ont/fma/fma7208 |
| T772 | 3078-3083 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T773 | 3108-3112 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T774 | 3113-3118 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T775 | 3168-3173 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T776 | 3179-3183 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T777 | 3200-3205 | Body_part | denotes | ileum | http://purl.org/sig/ont/fma/fma7208 |
| T778 | 3257-3262 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T779 | 3328-3333 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T780 | 3361-3366 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T781 | 3560-3565 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T782 | 3581-3585 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T783 | 3643-3663 | Body_part | denotes | cells in the cluster | http://purl.org/sig/ont/fma/fma62807 |
| T784 | 3643-3648 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T785 | 3784-3789 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T786 | 3804-3815 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
| T787 | 3957-3962 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T788 | 4011-4015 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T789 | 4066-4071 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T790 | 4189-4193 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T107 | 272-278 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T108 | 535-541 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T109 | 1957-1961 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T110 | 1966-1971 | Body_part | denotes | ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
| T111 | 2050-2054 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T112 | 2109-2114 | Body_part | denotes | ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
| T113 | 2197-2201 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T114 | 2206-2211 | Body_part | denotes | ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
| T115 | 2279-2283 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T116 | 2312-2316 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T117 | 2345-2350 | Body_part | denotes | ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
| T118 | 2379-2384 | Body_part | denotes | ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
| T119 | 3000-3006 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T120 | 3072-3077 | Body_part | denotes | ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
| T121 | 3108-3112 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T122 | 3179-3183 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T123 | 3200-3205 | Body_part | denotes | ileum | http://purl.obolibrary.org/obo/UBERON_0002116 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T229 | 630-634 | Disease | denotes | STAR | http://purl.obolibrary.org/obo/MONDO_0010408 |
| T230 | 1222-1226 | Disease | denotes | STAR | http://purl.obolibrary.org/obo/MONDO_0010408 |
| T231 | 1330-1334 | Disease | denotes | STAR | http://purl.obolibrary.org/obo/MONDO_0010408 |
| T232 | 3839-3843 | Disease | denotes | STAR | http://purl.obolibrary.org/obo/MONDO_0010408 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1033 | 261-266 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1034 | 270-271 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1035 | 616-620 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1036 | 662-664 | http://purl.obolibrary.org/obo/CLO_0008935 | denotes | S9 |
| T1037 | 668-669 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1038 | 709-714 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1039 | 977-978 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1040 | 1023-1029 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a cell |
| T1041 | 1094-1099 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1042 | 1107-1108 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1043 | 1186-1190 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1044 | 1344-1345 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T1045 | 1424-1425 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1046 | 1487-1488 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1047 | 1565-1569 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1048 | 1599-1600 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1049 | 1651-1653 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T1050 | 1667-1668 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1051 | 1803-1804 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T1052 | 1867-1872 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1053 | 1943-1948 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T1054 | 1949-1956 | http://purl.obolibrary.org/obo/NCBITaxon_9443 | denotes | primate |
| T1055 | 1957-1961 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T1056 | 1957-1961 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T1057 | 1966-1971 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | ileum |
| T1058 | 1972-1976 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1059 | 2050-2054 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T1060 | 2050-2054 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T1061 | 2055-2060 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1062 | 2109-2114 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | ileum |
| T1063 | 2115-2120 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1064 | 2183-2188 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T1065 | 2189-2196 | http://purl.obolibrary.org/obo/NCBITaxon_9443 | denotes | primate |
| T1066 | 2197-2201 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T1067 | 2197-2201 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T1068 | 2206-2211 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | ileum |
| T1069 | 2212-2216 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1070 | 2279-2283 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T1071 | 2279-2283 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T1072 | 2284-2289 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1073 | 2312-2316 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T1074 | 2312-2316 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T1075 | 2317-2322 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1076 | 2345-2350 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | ileum |
| T1077 | 2351-2356 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1078 | 2379-2384 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | ileum |
| T1079 | 2385-2390 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1080 | 2465-2466 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1081 | 2467-2471 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T1082 | 2518-2522 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1083 | 2527-2528 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1084 | 2566-2572 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene’s |
| T1085 | 2636-2642 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell’s |
| T1086 | 2708-2709 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1087 | 2741-2745 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T1088 | 2876-2880 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1089 | 2925-2929 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T1090 | 3015-3016 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1091 | 3072-3077 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | ileum |
| T1092 | 3078-3083 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1093 | 3089-3090 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1094 | 3108-3112 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T1095 | 3108-3112 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T1096 | 3113-3118 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1097 | 3168-3173 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1098 | 3179-3183 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T1099 | 3179-3183 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T1100 | 3200-3205 | http://purl.obolibrary.org/obo/UBERON_0002116 | denotes | ileum |
| T1101 | 3257-3262 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1102 | 3287-3288 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1103 | 3328-3349 | http://purl.obolibrary.org/obo/UBERON_0034922 | denotes | cells in that cluster |
| T1104 | 3361-3366 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1105 | 3537-3538 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1106 | 3560-3565 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T15560 | 3579-3580 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1108 | 3581-3585 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T1109 | 3605-3606 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1110 | 3619-3620 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1111 | 3643-3663 | http://purl.obolibrary.org/obo/UBERON_0034922 | denotes | cells in the cluster |
| T1112 | 3701-3702 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1113 | 3784-3789 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1114 | 3941-3942 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1115 | 3957-3962 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1116 | 3968-3969 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1117 | 4009-4010 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1118 | 4011-4015 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T1119 | 4066-4071 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1120 | 4189-4193 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1121 | 4197-4198 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T24844 | 294-301 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T8439 | 1411-1419 | Chemical | denotes | molecule | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T79599 | 1496-1504 | Chemical | denotes | molecule | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T85971 | 1528-1537 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T22664 | 3801-3803 | Chemical | denotes | II | http://purl.obolibrary.org/obo/CHEBI_74067 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T36 | 995-1005 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcript |
| T37 | 1145-1155 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcript |
| T38 | 1450-1471 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | reverse transcription |
| T39 | 1458-1471 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcription |
| T40 | 1609-1622 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcription |
| T41 | 2450-2460 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcript |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T387 | 0-279 | Sentence | denotes | Additionally, we provide an overall note of caution when interpreting scRNA-seq data for low abundance transcripts like ACE2 and TMPRSS2 because detection inefficiencies might result in an underestimation of the actual frequencies of ACE2 + or ACE2 + TMPRSS2 + cells in a tissue. |
| T388 | 280-448 | Sentence | denotes | Moreover, the protein amounts of each might differ from their mRNA abundances (Genshaft et al., 2016, Jovanovic et al., 2015, Rabani et al., 2011, Shalek et al., 2013). |
| T389 | 449-644 | Sentence | denotes | We also present datasets separately, given that each study differed in its methods of tissue processing and collection, which can influence the frequency of recovered cell subsets (STAR Methods). |
| T390 | 645-739 | Sentence | denotes | We provide Table S9 as a summary of ACE2 + and ACE2 + TMPRSS2 + cells across various datasets. |
| T391 | 740-918 | Sentence | denotes | Moreover, we present Figure S6 , which describes statistical modeling and power calculations underlying detection and dropout of ACE2, to help guide interpretation of these data. |
| T392 | 919-1236 | Sentence | denotes | This includes an examination of the probability to detect a lowly expressed transcript like ACE2 within a cell, as well as upper bound estimates on the percentage of positive cells within a cluster, considering the effects of transcript counts, sequencing depth, and cell numbers in these calculations (STAR Methods). |
| T393 | 1237-1342 | Sentence | denotes | Figure S6 Power Calculations and Statistical Modeling of ACE2 Capture and Dropout Related to STAR Methods |
| T394 | 1343-1347 | Sentence | denotes | (A). |
| T395 | 1348-1570 | Sentence | denotes | Probability of capturing and transcribing at least 1 ACE2 cDNA molecule, as a function of the capture/reverse transcription efficiency for a single molecule and the number of ACE2 molecules expressed in an individual cell. |
| T396 | 1571-1801 | Sentence | denotes | Note that Drop-Seq provides a capture/transcription efficiency of approximately 11-13%, setting a floor on this parameter, and the experimental platforms used in this study are either equivalent or superior (Macosko et al., 2015). |
| T397 | 1802-1806 | Sentence | denotes | (B). |
| T398 | 1807-2011 | Sentence | denotes | Distribution of ACE2 fractional abundance within individual cells’ cDNA libraries (i.e., ACE2 UMIs / total number of reads), across non-human primate lung and ileum cell populations (see Figures 1 and 3). |
| T399 | 2012-2130 | Sentence | denotes | Mean fractional abundance among ACE2+ lung cells = 5.0E-5; mean fractional abundance among ACE2+ ileum cells = 2.7E-4. |
| T400 | 2131-2135 | Sentence | denotes | (C). |
| T401 | 2136-2251 | Sentence | denotes | Distribution of the number of reads within non-human primate lung and ileum cell populations (see Figures 1 and 3). |
| T402 | 2252-2406 | Sentence | denotes | Mean ± SEM reads among all lung cells = 28,512 ± 344; ACE2+ lung cells = 28,553 ± 2,988; all ileum cells = 14,864 ± 288; ACE2+ ileum cells = 10,591 ± 441. |
| T403 | 2407-2411 | Sentence | denotes | (D). |
| T404 | 2412-2656 | Sentence | denotes | Probability of observing at least one transcript for a gene of interest (e.g., ACE2) within an individual cell, as a function of sequencing depth and the gene’s fractional abundance (i.e., ACE2 reads / all reads) within the cell’s cDNA library. |
| T405 | 2657-2942 | Sentence | denotes | Fractional abundance provides the probability that a single read corresponds to the gene of interest, and presented heatmap indicates the probability that at least one read in the total number of reads allocated to the cell (i.e., from 103 to 106) originates from the gene of interest. |
| T406 | 2943-3119 | Sentence | denotes | Mean read depths and ACE2 fractional abundances for each tissue produce a 93.7% probability of detecting at least 1 ACE2 read in ileum cells, and a 76.0% chance for lung cells. |
| T407 | 3120-3235 | Sentence | denotes | Outlined rectangles highlight the regimes where cells from lung (turquoise) and ileum (pink) samples typically lie. |
| T408 | 3236-3240 | Sentence | denotes | (E). |
| T409 | 3241-3350 | Sentence | denotes | Number of ACE2+ cells within each cluster, as a function of average read depth for all cells in that cluster. |
| T410 | 3351-3506 | Sentence | denotes | Number of cells detected as ACE2+ is not correlated with read depth, even across relatively wide ranges of average read depths (Pearson’s r = −0.31, n.s.). |
| T411 | 3507-3511 | Sentence | denotes | (F). |
| T412 | 3512-3664 | Sentence | denotes | Probability of observing a particular number of cells positive for a gene of interest within a cluster, as a function of number of cells in the cluster. |
| T413 | 3665-3853 | Sentence | denotes | Probabilities were calculated under a negative binomial distribution with parameter p = 0.063 (the proportion of ACE2+ cells among type II pneumocytes presented in Figure 1; STAR Methods). |
| T414 | 3854-3929 | Sentence | denotes | The horizontal gray line indicates the arbitrary cut-off value of p = 0.05. |
| T415 | 3930-3934 | Sentence | denotes | (G). |
| T416 | 3935-4224 | Sentence | denotes | Given a population of cells with a known proportion that are positive for a gene of interest, probability of observing no positive cells (i.e., false negative identification of the cluster; solid lines) and probability of observing at least one positive cell as a function of cluster size. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 1746 | 1294-1298 | Gene | denotes | ACE2 | Gene:59272 |
| 1747 | 1330-1334 | Gene | denotes | STAR | Gene:6770 |
| 1750 | 1401-1405 | Gene | denotes | ACE2 | Gene:59272 |
| 1751 | 1523-1527 | Gene | denotes | ACE2 | Gene:59272 |
| 1757 | 1823-1827 | Gene | denotes | ACE2 | Gene:59272 |
| 1758 | 1896-1900 | Gene | denotes | ACE2 | Gene:59272 |
| 1759 | 2044-2048 | Gene | denotes | ACE2 | Gene:59272 |
| 1760 | 2103-2107 | Gene | denotes | ACE2 | Gene:59272 |
| 1761 | 1943-1948 | Species | denotes | human | Tax:9606 |
| 1765 | 2306-2310 | Gene | denotes | ACE2 | Gene:59272 |
| 1766 | 2373-2377 | Gene | denotes | ACE2 | Gene:59272 |
| 1767 | 2183-2188 | Species | denotes | human | Tax:9606 |
| 1772 | 2491-2495 | Gene | denotes | ACE2 | Gene:59272 |
| 1773 | 2601-2605 | Gene | denotes | ACE2 | Gene:59272 |
| 1774 | 2964-2968 | Gene | denotes | ACE2 | Gene:59272 |
| 1775 | 3059-3063 | Gene | denotes | ACE2 | Gene:59272 |
| 1778 | 3251-3255 | Gene | denotes | ACE2 | Gene:59272 |
| 1779 | 3379-3383 | Gene | denotes | ACE2 | Gene:59272 |
| 1782 | 3778-3782 | Gene | denotes | ACE2 | Gene:59272 |
| 1783 | 3839-3843 | Gene | denotes | STAR | Gene:6770 |
| 1796 | 120-124 | Gene | denotes | ACE2 | Gene:59272 |
| 1797 | 129-136 | Gene | denotes | TMPRSS2 | Gene:7113 |
| 1798 | 234-238 | Gene | denotes | ACE2 | Gene:59272 |
| 1799 | 244-248 | Gene | denotes | ACE2 | Gene:59272 |
| 1800 | 251-258 | Gene | denotes | TMPRSS2 | Gene:7113 |
| 1801 | 681-685 | Gene | denotes | ACE2 | Gene:59272 |
| 1802 | 692-696 | Gene | denotes | ACE2 | Gene:59272 |
| 1803 | 699-706 | Gene | denotes | TMPRSS2 | Gene:7113 |
| 1804 | 869-873 | Gene | denotes | ACE2 | Gene:59272 |
| 1805 | 1011-1015 | Gene | denotes | ACE2 | Gene:59272 |
| 1806 | 1222-1226 | Gene | denotes | STAR | Gene:6770 |
| 1807 | 630-634 | Gene | denotes | STAR | Gene:6770 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32413319-27640647-20790504 | 376-380 | 27640647 | denotes | 2016 |
| 32413319-25745177-20790505 | 400-404 | 25745177 | denotes | 2015 |
| 32413319-21516085-20790506 | 421-425 | 21516085 | denotes | 2011 |
| 32413319-23685454-20790507 | 442-446 | 23685454 | denotes | 2013 |
| 32413319-26000488-20790508 | 1795-1799 | 26000488 | denotes | 2015 |