PMC:7354481 / 15715-18216
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T87 | 158-164 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T88 | 181-185 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T89 | 292-297 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T90 | 309-316 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T91 | 372-377 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T92 | 442-449 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T93 | 559-564 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T94 | 576-583 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T95 | 750-755 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T96 | 826-833 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T97 | 998-1002 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T98 | 1083-1090 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T99 | 1676-1684 | Body_part | denotes | cytokine | http://purl.org/sig/ont/fma/fma84050 |
| T100 | 1685-1693 | Body_part | denotes | cytokine | http://purl.org/sig/ont/fma/fma84050 |
| T101 | 1925-1931 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T102 | 2050-2057 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T103 | 2091-2098 | Body_part | denotes | synapse | http://purl.org/sig/ont/fma/fma67408 |
| T104 | 2349-2366 | Body_part | denotes | glycosaminoglycan | http://purl.org/sig/ont/fma/fma63011 |
| T105 | 2380-2395 | Body_part | denotes | heparan sulfate | http://purl.org/sig/ont/fma/fma63023 |
| T106 | 2396-2403 | Body_part | denotes | heparin | http://purl.org/sig/ont/fma/fma82839 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T62 | 147-155 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T63 | 298-306 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T64 | 431-439 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T65 | 565-573 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T66 | 722-730 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T67 | 837-845 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T68 | 970-978 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T144 | 74-80 | http://purl.obolibrary.org/obo/NCBITaxon_9005 | denotes | Turkey |
| T145 | 181-190 | http://purl.obolibrary.org/obo/CLO_0000031 | denotes | cell line |
| T146 | 285-297 | http://purl.obolibrary.org/obo/CLO_0051719 | denotes | VeroE6 cells |
| T147 | 365-377 | http://purl.obolibrary.org/obo/CLO_0051719 | denotes | VeroE6 cells |
| T148 | 552-564 | http://purl.obolibrary.org/obo/CLO_0051719 | denotes | VeroE6 cells |
| T149 | 682-683 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T150 | 742-755 | http://purl.obolibrary.org/obo/CLO_0051719 | denotes | Vero E6 cells |
| T151 | 948-949 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T152 | 990-1002 | http://purl.obolibrary.org/obo/CLO_0051719 | denotes | Vero E6 cell |
| T153 | 1042-1047 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T154 | 1433-1437 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | Test |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T23 | 1618-1624 | Chemical | denotes | Glycan | http://purl.obolibrary.org/obo/CHEBI_18154 |
| T24 | 1753-1761 | Chemical | denotes | morphine | http://purl.obolibrary.org/obo/CHEBI_17303|http://purl.obolibrary.org/obo/CHEBI_58097 |
| T26 | 1790-1801 | Chemical | denotes | xenobiotics | http://purl.obolibrary.org/obo/CHEBI_35703 |
| T27 | 1805-1820 | Chemical | denotes | cytochrome P450 | http://purl.obolibrary.org/obo/CHEBI_38559 |
| T28 | 1805-1815 | Chemical | denotes | cytochrome | http://purl.obolibrary.org/obo/CHEBI_4056 |
| T29 | 2100-2108 | Chemical | denotes | morphine | http://purl.obolibrary.org/obo/CHEBI_17303|http://purl.obolibrary.org/obo/CHEBI_58097 |
| T31 | 2137-2148 | Chemical | denotes | xenobiotics | http://purl.obolibrary.org/obo/CHEBI_35703 |
| T32 | 2152-2167 | Chemical | denotes | cytochrome P450 | http://purl.obolibrary.org/obo/CHEBI_38559 |
| T33 | 2152-2162 | Chemical | denotes | cytochrome | http://purl.obolibrary.org/obo/CHEBI_4056 |
| T34 | 2349-2366 | Chemical | denotes | glycosaminoglycan | http://purl.obolibrary.org/obo/CHEBI_18085 |
| T35 | 2380-2395 | Chemical | denotes | heparan sulfate | http://purl.obolibrary.org/obo/CHEBI_28815 |
| T36 | 2380-2387 | Chemical | denotes | heparan | http://purl.obolibrary.org/obo/CHEBI_24500 |
| T37 | 2388-2395 | Chemical | denotes | sulfate | http://purl.obolibrary.org/obo/CHEBI_16189 |
| T38 | 2396-2403 | Chemical | denotes | heparin | http://purl.obolibrary.org/obo/CHEBI_28304 |
| T39 | 2420-2428 | Chemical | denotes | O-glycan | http://purl.obolibrary.org/obo/CHEBI_59521 |
| T40 | 2447-2454 | Chemical | denotes | vitamin | http://purl.obolibrary.org/obo/CHEBI_33229 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T23 | 1618-1637 | http://purl.obolibrary.org/obo/GO_0000271 | denotes | Glycan biosynthesis |
| T24 | 1625-1637 | http://purl.obolibrary.org/obo/GO_0009058 | denotes | biosynthesis |
| T25 | 1776-1786 | http://purl.obolibrary.org/obo/GO_0008152 | denotes | metabolism |
| T26 | 1805-1815 | http://purl.obolibrary.org/obo/GO_0045158 | denotes | cytochrome |
| T27 | 1805-1815 | http://purl.obolibrary.org/obo/GO_0045157 | denotes | cytochrome |
| T28 | 1805-1815 | http://purl.obolibrary.org/obo/GO_0045156 | denotes | cytochrome |
| T29 | 1805-1815 | http://purl.obolibrary.org/obo/GO_0008121 | denotes | cytochrome |
| T30 | 2123-2133 | http://purl.obolibrary.org/obo/GO_0008152 | denotes | metabolism |
| T31 | 2152-2162 | http://purl.obolibrary.org/obo/GO_0045158 | denotes | cytochrome |
| T32 | 2152-2162 | http://purl.obolibrary.org/obo/GO_0045157 | denotes | cytochrome |
| T33 | 2152-2162 | http://purl.obolibrary.org/obo/GO_0045156 | denotes | cytochrome |
| T34 | 2152-2162 | http://purl.obolibrary.org/obo/GO_0008121 | denotes | cytochrome |
| T35 | 2349-2379 | http://purl.obolibrary.org/obo/GO_0006024 | denotes | glycosaminoglycan biosynthesis |
| T36 | 2367-2379 | http://purl.obolibrary.org/obo/GO_0009058 | denotes | biosynthesis |
| T37 | 2422-2441 | http://purl.obolibrary.org/obo/GO_0000271 | denotes | glycan biosynthesis |
| T38 | 2429-2441 | http://purl.obolibrary.org/obo/GO_0009058 | denotes | biosynthesis |
| T39 | 2455-2464 | http://purl.obolibrary.org/obo/GO_0007586 | denotes | digestion |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T1 | 2380-2395 | GlycoEpitope | denotes | heparan sulfate | http://www.glycoepitope.jp/epitopes/EP0086 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T112 | 0-655 | Sentence | denotes | We have found five highly significant miRs from four different countries; Turkey, Italy, Spain, and the UK; one RefSeq sequence from Wuhan and one SARS-CoV-2 genome from the VeroE6 cell line: miR-8066 (e-values; 1.6 for Wuhan, 2.8 for Valencia, 1.6 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-5197-3p (e-values; 1.6 for Wuhan, 2.1 for VeroE6 cells, 2.8 for Valencia and 1.9 for both Italy and England SARS-CoV-2 genomes), and miR-3611 (e-values; 2.8 for Wuhan, 3.3 for Valencia and 2.8 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-3934-3p (e-values; 3.4–5.0), and miR-1307-3p (e-values; 4.3–6.3). |
| T113 | 656-756 | Sentence | denotes | We could, however, detect a similar alignment with miR-1307-3p in SARS-CoV-2-infected Vero E6 cells. |
| T114 | 757-920 | Sentence | denotes | Additionally, we found that the same miR sequences exist within four genomes of SARS-CoV-2, within the lower e-values of 5.0–10.0 were miR-3691-3p and miR-1468-5p. |
| T115 | 921-1008 | Sentence | denotes | Again, miR-3691-3p was not a positive hit in the SARS-CoV-2-infected Vero E6 cell line. |
| T116 | 1009-1091 | Sentence | denotes | All of these miR similarities to human miRs were conserved in all studied genomes. |
| T117 | 1092-1193 | Sentence | denotes | We then used DianaTools to identify the potential pathways to which these miRs contribute (Figure 1). |
| T118 | 1194-1301 | Sentence | denotes | The functional characterizations of these highly conserved miRs were analyzed with KEGG molecular pathways. |
| T119 | 1302-1531 | Sentence | denotes | The selected intersected pathways were analyzed as significant targets as p value 0.05 with threshold value 0.8 and Fisher’s Exact Test (hypergeometric distribution) calculations by miRPath version 3.0 in the microT-CDS database. |
| T120 | 1532-1832 | Sentence | denotes | As shown in Figure 1. miR-8066 and miR-5197-3p are critical on TGF-β and mucin type O-Glycan biosynthesis pathways. miR-8066 is also related to cytokine-cytokine receptor interaction. miR-5197 is significantly related to morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. |
| T121 | 1833-2179 | Sentence | denotes | These two miRs were highly conserved, and their coexistence was significant within the four-genome search. miR-3611 was the other leading miR, which possesses co-occurrence potential with miR-8066 and miR-5197 in all genomes that were effective on GABAergic synapse, morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. |
| T122 | 2180-2501 | Sentence | denotes | Although co-occurrences of miR-1468-5p and miR-1307-3p were similar to miR-3611, it was less effective on all evaluated metabolic pathways. miR-3934-3p was effective on glycosaminoglycan biosynthesis—heparan sulfate/heparin, other types of O-glycan biosynthesis, and vitamin digestion-absorption mechanisms, respectively. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 282 | 192-200 | Gene | denotes | miR-8066 | Gene:102465868 |
| 283 | 456-464 | Gene | denotes | miR-3611 | Gene:100500890 |
| 284 | 908-916 | Gene | denotes | miR-1468 | Gene:100302115 |
| 285 | 1554-1562 | Gene | denotes | miR-8066 | Gene:102465868 |
| 286 | 1595-1600 | Gene | denotes | TGF-β | Gene:7039 |
| 287 | 1605-1610 | Gene | denotes | mucin | Gene:100508689 |
| 288 | 1648-1656 | Gene | denotes | miR-8066 | Gene:102465868 |
| 289 | 1716-1724 | Gene | denotes | miR-5197 | Gene:100846991 |
| 290 | 1940-1948 | Gene | denotes | miR-3611 | Gene:100500890 |
| 291 | 2021-2029 | Gene | denotes | miR-8066 | Gene:102465868 |
| 292 | 2034-2042 | Gene | denotes | miR-5197 | Gene:100846991 |
| 293 | 2207-2215 | Gene | denotes | miR-1468 | Gene:100302115 |
| 294 | 2251-2259 | Gene | denotes | miR-3611 | Gene:100500890 |
| 295 | 74-80 | Species | denotes | Turkey | Tax:9103 |
| 296 | 147-157 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 297 | 298-308 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 298 | 431-441 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 299 | 565-575 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 300 | 837-847 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 301 | 1042-1047 | Species | denotes | human | Tax:9606 |
| 302 | 707-718 | Chemical | denotes | miR-1307-3p | |
| 303 | 928-939 | Chemical | denotes | miR-3691-3p | |
| 304 | 1616-1624 | Chemical | denotes | O-Glycan | |
| 305 | 1753-1761 | Chemical | denotes | morphine | MESH:D009020 |
| 306 | 2100-2108 | Chemical | denotes | morphine | MESH:D009020 |
| 307 | 2320-2331 | Chemical | denotes | miR-3934-3p | |
| 308 | 2349-2366 | Chemical | denotes | glycosaminoglycan | MESH:D006025 |
| 309 | 2380-2395 | Chemical | denotes | heparan sulfate | MESH:D006497 |
| 310 | 2396-2403 | Chemical | denotes | heparin | MESH:D006493 |
| 311 | 2420-2428 | Chemical | denotes | O-glycan | |
| 312 | 722-741 | Disease | denotes | SARS-CoV-2-infected | MESH:C000657245 |
| 313 | 970-989 | Disease | denotes | SARS-CoV-2-infected | MESH:C000657245 |
| 314 | 174-180 | CellLine | denotes | VeroE6 | CVCL:0574 |
| 315 | 285-291 | CellLine | denotes | VeroE6 | CVCL:0574 |
| 316 | 365-371 | CellLine | denotes | VeroE6 | CVCL:0574 |
| 317 | 552-558 | CellLine | denotes | VeroE6 | CVCL:0574 |