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PMC:7519301 / 17850-20079
Annnotations
LitCovid-PD-FMA-UBERON
Id | Subject | Object | Predicate | Lexical cue | fma_id |
---|---|---|---|---|---|
T73 | 29-35 | Body_part | denotes | Genome | http://purl.org/sig/ont/fma/fma84116 |
T74 | 272-279 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
T75 | 470-478 | Body_part | denotes | Appendix | http://purl.org/sig/ont/fma/fma14542 |
T76 | 923-939 | Body_part | denotes | structural genes | http://purl.org/sig/ont/fma/fma74402 |
T77 | 1331-1339 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
T78 | 1627-1633 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
T79 | 1773-1777 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T80 | 2019-2023 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T81 | 2172-2187 | Body_part | denotes | structural gene | http://purl.org/sig/ont/fma/fma74402 |
LitCovid-PD-MONDO
Id | Subject | Object | Predicate | Lexical cue | mondo_id |
---|---|---|---|---|---|
T93 | 18-26 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T94 | 18-22 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T95 | 1616-1624 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T96 | 1616-1620 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T157 | 226-227 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T158 | 450-454 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
T159 | 527-528 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T160 | 703-709 | http://purl.obolibrary.org/obo/CLO_0002821 | denotes | dS > 1 |
T161 | 703-709 | http://purl.obolibrary.org/obo/CLO_0002822 | denotes | dS > 1 |
T162 | 830-835 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
T163 | 934-939 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
T164 | 966-971 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
T165 | 988-992 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
T166 | 1016-1019 | http://purl.obolibrary.org/obo/CLO_0008190 | denotes | Per |
T167 | 1090-1094 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
T168 | 1173-1178 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
T169 | 1243-1244 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T170 | 1636-1637 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
T171 | 1724-1730 | http://purl.obolibrary.org/obo/CLO_0002821 | denotes | dS > 1 |
T172 | 1724-1730 | http://purl.obolibrary.org/obo/CLO_0002822 | denotes | dS > 1 |
T173 | 1748-1749 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
T174 | 1773-1777 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T175 | 1967-1972 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
T176 | 2019-2023 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T177 | 2183-2187 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
LitCovid-PD-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T58 | 272-279 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
T59 | 380-382 | Chemical | denotes | SD | http://purl.obolibrary.org/obo/CHEBI_74807 |
T60 | 467-469 | Chemical | denotes | SI | http://purl.obolibrary.org/obo/CHEBI_90326 |
T61 | 485-487 | Chemical | denotes | S4 | http://purl.obolibrary.org/obo/CHEBI_29401 |
T62 | 700-702 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
T63 | 810-812 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
T64 | 1331-1339 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
T65 | 1721-1723 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
T66 | 1763-1765 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
T67 | 1779-1781 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
T68 | 1833-1835 | Chemical | denotes | SD | http://purl.obolibrary.org/obo/CHEBI_74807 |
LitCovid-PubTator
Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
---|---|---|---|---|---|
283 | 18-28 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
290 | 882-887 | Gene | denotes | ORF10 | Gene:43740576 |
291 | 863-864 | Gene | denotes | M | Gene:43740571 |
292 | 181-182 | Gene | denotes | N | Gene:43740575 |
293 | 169-170 | Gene | denotes | S | Gene:43740568 |
294 | 700-702 | Chemical | denotes | dN | MESH:C022306 |
295 | 703-705 | Chemical | denotes | dS | MESH:D003903 |
297 | 1616-1626 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
LitCovid-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T113 | 0-67 | Sentence | denotes | Most Sites in the SARS-CoV-2 Genome Were under Purifying Selection. |
T114 | 68-262 | 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 | 263-578 | 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 | 579-790 | 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 | 791-1015 | 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 | 1016-1312 | 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 | 1313-1585 | 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). |
T120 | 1586-1593 | Sentence | denotes | Fig. 3. |
T121 | 1595-1812 | Sentence | denotes | Evolution across the SARS-CoV-2 genome. (A) Bar plot of the average percentage of branch length under diversifying selection (dN/dS > 1) for each site. (B) Bar plot of dN/dS per gene (dN = dS is shown as dashed line). |
T122 | 1813-1973 | Sentence | denotes | Error bars indicate SD across subsampled alignments. (C) Box plot of nonsynonymous substitutions per lineage per site across structural and nonstructural genes. |
T123 | 1974-2188 | Sentence | denotes | Values across subsampled alignments for each gene are plotted. (D) Average percentage (over subsampled alignments) of branch lengths evolving under neutral (or negative) selection per site for each structural gene. |
T124 | 2189-2229 | Sentence | denotes | Median values are shown by dashed lines. |
2_test
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
32868447-22807683-132542396 | 1581-1583 | 22807683 | denotes | 29 |