PMC:7321036 / 106836-107999 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T205 40-59 SP_6;NCBITaxon:9606 denotes h significant up an
T206 104-139 SO:0000704 denotes Gene Ontology (GO Biological Proces

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T29 104-108 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T30 479-483 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T31 754-758 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T32 1007-1011 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T44 31-36 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T45 79-85 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T46 104-108 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T47 165-183 http://purl.obolibrary.org/obo/GO_0005575 denotes Cellular Component
T48 200-205 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T49 479-483 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T50 522-524 http://purl.obolibrary.org/obo/CLO_0002131 denotes c5
T51 754-758 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T52 786-787 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 865-870 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T54 941-942 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 1007-1011 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T917 0-22 Sentence denotes GO enrichment analysis
T918 23-191 Sentence denotes Sets of genes with significant up and down effects were tested for enrichment of Gene Ontology (GO Biological Process, Molecular Function and Cellular Component) terms.
T919 192-319 Sentence denotes Sets of genes were either combined across time points (Figure 1I) or collected separately per time point (Figures S1F and S1G).
T920 320-474 Sentence denotes The over-representation analysis (ORA) was performed using the enricher function of clusterProfiler package (version 3.12.0) in R with default parameters.
T921 475-606 Sentence denotes The gene ontology terms were obtained from the c5 category of Molecular Signature Database (MSigDBv7.1) (Subramanian et al., 2005).
T922 607-720 Sentence denotes Significant GO terms (adjusted p value < 0.01) were identified and further refined to select non-redundant terms.
T923 721-912 Sentence denotes In order to select non-redundant gene sets, we first constructed a GO term tree based on distances (1-Jaccard Similarity Coefficients of shared genes in MSigDB) between the significant terms.
T924 913-1017 Sentence denotes The GO term tree was cut at a specific level (h = 0.99) to identify clusters of non-redundant gene sets.
T925 1018-1163 Sentence denotes For results with multiple significant terms belonging to the same cluster, we selected the most significant term (i.e., lowest adjusted p value).

2_test

Id Subject Object Predicate Lexical cue
32645325-16199517-20773115 600-604 16199517 denotes 2005