PMC:7321036 / 111429-112373 JSONTXT

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T209","span":{"begin":270,"end":337},"obj":"SO:0000704"}],"text":"Annotations for protein complexes were obtained from CORUM v3.0 database (Giurgiu et al., 2019). Overall significance of changes of phosphosites of a protein complex was inferred from the log2 fold change of individual phosphosites of protein members of the complex using the same Z-test based approach described for estimation of kinase activities. Among the 3512 complexes, 1070 complexes with phosphorylation changes obtained from 4 or more phosphosites were considered. Of these, 67 complexes had significant phosphorylation change (-log10(p value) from Z-test \u003e 2.5) in at least one time point. In order to select non-redundant complexes, we first constructed a complex term tree based on distances (1-Jaccard Similarity Coefficients of shared genes) between the significant complexes. The term tree was cut at a specific level (h = 0.99) to identify clusters of non-redundant complexes. The largest complex was selected from each cluster."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T39","span":{"begin":16,"end":33},"obj":"Body_part"},{"id":"T40","span":{"begin":16,"end":23},"obj":"Body_part"},{"id":"T41","span":{"begin":150,"end":165},"obj":"Body_part"},{"id":"T42","span":{"begin":235,"end":242},"obj":"Body_part"}],"attributes":[{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma67906"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A41","pred":"fma_id","subj":"T41","obj":"http://purl.org/sig/ont/fma/fma67906"},{"id":"A42","pred":"fma_id","subj":"T42","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Annotations for protein complexes were obtained from CORUM v3.0 database (Giurgiu et al., 2019). Overall significance of changes of phosphosites of a protein complex was inferred from the log2 fold change of individual phosphosites of protein members of the complex using the same Z-test based approach described for estimation of kinase activities. Among the 3512 complexes, 1070 complexes with phosphorylation changes obtained from 4 or more phosphosites were considered. Of these, 67 complexes had significant phosphorylation change (-log10(p value) from Z-test \u003e 2.5) in at least one time point. In order to select non-redundant complexes, we first constructed a complex term tree based on distances (1-Jaccard Similarity Coefficients of shared genes) between the significant complexes. The term tree was cut at a specific level (h = 0.99) to identify clusters of non-redundant complexes. The largest complex was selected from each cluster."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T87","span":{"begin":16,"end":33},"obj":"http://purl.obolibrary.org/obo/GO_0043234"},{"id":"T88","span":{"begin":148,"end":149},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T89","span":{"begin":150,"end":165},"obj":"http://purl.obolibrary.org/obo/GO_0043234"},{"id":"T90","span":{"begin":283,"end":287},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T91","span":{"begin":338,"end":348},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T92","span":{"begin":560,"end":564},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T93","span":{"begin":665,"end":666},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T94","span":{"begin":749,"end":754},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T95","span":{"begin":816,"end":817},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Annotations for protein complexes were obtained from CORUM v3.0 database (Giurgiu et al., 2019). Overall significance of changes of phosphosites of a protein complex was inferred from the log2 fold change of individual phosphosites of protein members of the complex using the same Z-test based approach described for estimation of kinase activities. Among the 3512 complexes, 1070 complexes with phosphorylation changes obtained from 4 or more phosphosites were considered. Of these, 67 complexes had significant phosphorylation change (-log10(p value) from Z-test \u003e 2.5) in at least one time point. In order to select non-redundant complexes, we first constructed a complex term tree based on distances (1-Jaccard Similarity Coefficients of shared genes) between the significant complexes. The term tree was cut at a specific level (h = 0.99) to identify clusters of non-redundant complexes. The largest complex was selected from each cluster."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T60056","span":{"begin":16,"end":23},"obj":"Chemical"},{"id":"T88216","span":{"begin":150,"end":157},"obj":"Chemical"},{"id":"T23786","span":{"begin":235,"end":242},"obj":"Chemical"}],"attributes":[{"id":"A84326","pred":"chebi_id","subj":"T60056","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A85582","pred":"chebi_id","subj":"T88216","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A66909","pred":"chebi_id","subj":"T23786","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"Annotations for protein complexes were obtained from CORUM v3.0 database (Giurgiu et al., 2019). Overall significance of changes of phosphosites of a protein complex was inferred from the log2 fold change of individual phosphosites of protein members of the complex using the same Z-test based approach described for estimation of kinase activities. Among the 3512 complexes, 1070 complexes with phosphorylation changes obtained from 4 or more phosphosites were considered. Of these, 67 complexes had significant phosphorylation change (-log10(p value) from Z-test \u003e 2.5) in at least one time point. In order to select non-redundant complexes, we first constructed a complex term tree based on distances (1-Jaccard Similarity Coefficients of shared genes) between the significant complexes. The term tree was cut at a specific level (h = 0.99) to identify clusters of non-redundant complexes. The largest complex was selected from each cluster."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T30","span":{"begin":331,"end":348},"obj":"http://purl.obolibrary.org/obo/GO_0016301"},{"id":"T31","span":{"begin":396,"end":411},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T32","span":{"begin":513,"end":528},"obj":"http://purl.obolibrary.org/obo/GO_0016310"}],"text":"Annotations for protein complexes were obtained from CORUM v3.0 database (Giurgiu et al., 2019). Overall significance of changes of phosphosites of a protein complex was inferred from the log2 fold change of individual phosphosites of protein members of the complex using the same Z-test based approach described for estimation of kinase activities. Among the 3512 complexes, 1070 complexes with phosphorylation changes obtained from 4 or more phosphosites were considered. Of these, 67 complexes had significant phosphorylation change (-log10(p value) from Z-test \u003e 2.5) in at least one time point. In order to select non-redundant complexes, we first constructed a complex term tree based on distances (1-Jaccard Similarity Coefficients of shared genes) between the significant complexes. The term tree was cut at a specific level (h = 0.99) to identify clusters of non-redundant complexes. The largest complex was selected from each cluster."}

{"project":"LitCovid-sentences","denotations":[{"id":"T948","span":{"begin":0,"end":96},"obj":"Sentence"},{"id":"T949","span":{"begin":97,"end":349},"obj":"Sentence"},{"id":"T950","span":{"begin":350,"end":473},"obj":"Sentence"},{"id":"T951","span":{"begin":474,"end":599},"obj":"Sentence"},{"id":"T952","span":{"begin":600,"end":790},"obj":"Sentence"},{"id":"T953","span":{"begin":791,"end":892},"obj":"Sentence"},{"id":"T954","span":{"begin":893,"end":944},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Annotations for protein complexes were obtained from CORUM v3.0 database (Giurgiu et al., 2019). Overall significance of changes of phosphosites of a protein complex was inferred from the log2 fold change of individual phosphosites of protein members of the complex using the same Z-test based approach described for estimation of kinase activities. Among the 3512 complexes, 1070 complexes with phosphorylation changes obtained from 4 or more phosphosites were considered. Of these, 67 complexes had significant phosphorylation change (-log10(p value) from Z-test \u003e 2.5) in at least one time point. In order to select non-redundant complexes, we first constructed a complex term tree based on distances (1-Jaccard Similarity Coefficients of shared genes) between the significant complexes. The term tree was cut at a specific level (h = 0.99) to identify clusters of non-redundant complexes. The largest complex was selected from each cluster."}

{"project":"2_test","denotations":[{"id":"32645325-30357367-20773122","span":{"begin":90,"end":94},"obj":"30357367"}],"text":"Annotations for protein complexes were obtained from CORUM v3.0 database (Giurgiu et al., 2019). Overall significance of changes of phosphosites of a protein complex was inferred from the log2 fold change of individual phosphosites of protein members of the complex using the same Z-test based approach described for estimation of kinase activities. Among the 3512 complexes, 1070 complexes with phosphorylation changes obtained from 4 or more phosphosites were considered. Of these, 67 complexes had significant phosphorylation change (-log10(p value) from Z-test \u003e 2.5) in at least one time point. In order to select non-redundant complexes, we first constructed a complex term tree based on distances (1-Jaccard Similarity Coefficients of shared genes) between the significant complexes. The term tree was cut at a specific level (h = 0.99) to identify clusters of non-redundant complexes. The largest complex was selected from each cluster."}