PMC:7321036 / 108039-108968 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T33 65-76 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T34 547-555 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T56 49-54 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T57 55-59 http://purl.obolibrary.org/obo/CLO_0009141 denotes S, T
T58 55-59 http://purl.obolibrary.org/obo/CLO_0050980 denotes S, T
T59 379-380 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 495-496 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 577-583 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T62 861-863 http://purl.obolibrary.org/obo/CLO_0002105 denotes c2
T63 861-863 http://purl.obolibrary.org/obo/CLO_0051742 denotes c2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T57668 65-76 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T58962 65-70 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T27942 71-76 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T6743 547-555 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T16 0-15 http://purl.obolibrary.org/obo/GO_0016310 denotes Phosphorylation
T17 111-126 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2341 49-54 Species denotes human Tax:9606

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T927 0-331 Sentence denotes Phosphorylation sites with one-to-one mapping to human S, T or Y amino acids and showing significant change in phosphorylation (abs(log2FC) > 1 and adjusted p value < 0.05) in one or more conditions were selected and clustered using hierarchical clustering (complete-linkage) with pearson correlation (1-r) as the distance measure.
T928 332-531 Sentence denotes The cluster tree was cut into 5 clusters using a dynamic tree cutting method, cutreeHybrid function in dynamicTreeCut (Langfelder et al., 2008) package in R, with a minimum cluster size of 130 sites.
T929 532-642 Sentence denotes Phosphorylated proteins in each cluster were tested for enrichment of Reactome pathways (Jassal et al., 2020).
T930 643-819 Sentence denotes The over-representation analysis (ORA) was based on the hypergeometric distribution and performed using the enricher function of clusterProfiler package in R (Yu et al., 2012).
T931 820-929 Sentence denotes The pathway terms were obtained from the c2 category (Reactome) of Molecular Signature Database (MSigDBv6.1).

2_test

Id Subject Object Predicate Lexical cue
32645325-18024473-20773116 470-474 18024473 denotes 2008
32645325-31691815-20773117 636-640 31691815 denotes 2020
32645325-22455463-20773118 813-817 22455463 denotes 2012