PMC:7519301 / 17918-19435
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T74 | 204-211 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T75 | 402-410 | Body_part | denotes | Appendix | http://purl.org/sig/ont/fma/fma14542 |
| T76 | 855-871 | Body_part | denotes | structural genes | http://purl.org/sig/ont/fma/fma74402 |
| T77 | 1263-1271 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T157 | 158-159 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T158 | 382-386 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T159 | 459-460 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T160 | 635-641 | http://purl.obolibrary.org/obo/CLO_0002821 | denotes | dS > 1 |
| T161 | 635-641 | http://purl.obolibrary.org/obo/CLO_0002822 | denotes | dS > 1 |
| T162 | 762-767 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T163 | 866-871 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T164 | 898-903 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T165 | 920-924 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T166 | 948-951 | http://purl.obolibrary.org/obo/CLO_0008190 | denotes | Per |
| T167 | 1022-1026 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T168 | 1105-1110 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T169 | 1175-1176 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T58 | 204-211 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T59 | 312-314 | Chemical | denotes | SD | http://purl.obolibrary.org/obo/CHEBI_74807 |
| T60 | 399-401 | Chemical | denotes | SI | http://purl.obolibrary.org/obo/CHEBI_90326 |
| T61 | 417-419 | Chemical | denotes | S4 | http://purl.obolibrary.org/obo/CHEBI_29401 |
| T62 | 632-634 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
| T63 | 742-744 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
| T64 | 1263-1271 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 290 | 814-819 | Gene | denotes | ORF10 | Gene:43740576 |
| 291 | 795-796 | Gene | denotes | M | Gene:43740571 |
| 292 | 113-114 | Gene | denotes | N | Gene:43740575 |
| 293 | 101-102 | Gene | denotes | S | Gene:43740568 |
| 294 | 632-634 | Chemical | denotes | dN | MESH:C022306 |
| 295 | 635-637 | Chemical | denotes | dS | MESH:D003903 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T114 | 0-194 | Sentence | denotes | Using phylogenetically informed models (as described above), we identified two sites, residue 614 in S and 13 in N, that were under diversifying selection in a majority of subsampled alignments. |
| T115 | 195-510 | Sentence | denotes | For each protein, subsampled alignments tended to have more sites under purifying selection (median = 7.34 ± 4.06% [±SD]) than under diversifying selection (3.10 ± 1.92%) (Mann−Whitney U test, P = 0.057; SI Appendix, Fig. S4) (purifying selection is indicative of a decrease in genetic diversity in the population). |
| T116 | 511-722 | Sentence | denotes | Likewise, for each codon separately, the proportion of each phylogeny (i.e., the percentage of total branch length) with dN/dS > 1 was small, indicating diversifying selection was episodic and limited (Fig. 3A). |
| T117 | 723-947 | Sentence | denotes | Global measures of dN/dS varied across genes, ranging from 0.35 ± 0.02 (M) to 1.43 ± 0.24 (ORF10), and were significantly lower for structural genes compared to nonstructural genes (Mann−Whitney U test, P = 0.042) (Fig. 3B). |
| T118 | 948-1244 | Sentence | denotes | Per-lineage nonsynonymous substitution rates were comparable (Student’s t test, P = 0.218) in structural (0.0011 ± 0.021) and nonstructural (0.0012 ± 0.028) genes, although some subsampled alignments showed rates that could be a hundred times higher than the median over all alignments (Fig. 3C). |
| T119 | 1245-1517 | Sentence | denotes | Across structural proteins, mutations were disproportionately neutral: >70.3% of branch length evolved under neutral (or negative) selection for all sites, and over half of all branch length evolved under neutral (or negative) selection for >82.8% of sites (Fig. 3D) (29). |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32868447-22807683-132542396 | 1513-1515 | 22807683 | denotes | 29 |