PMC:7321036 / 108001-108968 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T33","span":{"begin":103,"end":114},"obj":"Body_part"},{"id":"T34","span":{"begin":585,"end":593},"obj":"Body_part"}],"attributes":[{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Clustering of phosphorylation changes\nPhosphorylation sites with one-to-one mapping to human S, T or Y amino acids and showing significant change in phosphorylation (abs(log2FC) \u003e 1 and adjusted p value \u003c 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. 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. Phosphorylated proteins in each cluster were tested for enrichment of Reactome pathways (Jassal et al., 2020). 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). The pathway terms were obtained from the c2 category (Reactome) of Molecular Signature Database (MSigDBv6.1)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T56","span":{"begin":87,"end":92},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T57","span":{"begin":93,"end":97},"obj":"http://purl.obolibrary.org/obo/CLO_0009141"},{"id":"T58","span":{"begin":93,"end":97},"obj":"http://purl.obolibrary.org/obo/CLO_0050980"},{"id":"T59","span":{"begin":417,"end":418},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T60","span":{"begin":533,"end":534},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T61","span":{"begin":615,"end":621},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T62","span":{"begin":899,"end":901},"obj":"http://purl.obolibrary.org/obo/CLO_0002105"},{"id":"T63","span":{"begin":899,"end":901},"obj":"http://purl.obolibrary.org/obo/CLO_0051742"}],"text":"Clustering of phosphorylation changes\nPhosphorylation sites with one-to-one mapping to human S, T or Y amino acids and showing significant change in phosphorylation (abs(log2FC) \u003e 1 and adjusted p value \u003c 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. 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. Phosphorylated proteins in each cluster were tested for enrichment of Reactome pathways (Jassal et al., 2020). 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). The pathway terms were obtained from the c2 category (Reactome) of Molecular Signature Database (MSigDBv6.1)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T57668","span":{"begin":103,"end":114},"obj":"Chemical"},{"id":"T58962","span":{"begin":103,"end":108},"obj":"Chemical"},{"id":"T27942","span":{"begin":109,"end":114},"obj":"Chemical"},{"id":"T6743","span":{"begin":585,"end":593},"obj":"Chemical"}],"attributes":[{"id":"A54036","pred":"chebi_id","subj":"T57668","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A59701","pred":"chebi_id","subj":"T58962","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A27189","pred":"chebi_id","subj":"T27942","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A16903","pred":"chebi_id","subj":"T6743","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"Clustering of phosphorylation changes\nPhosphorylation sites with one-to-one mapping to human S, T or Y amino acids and showing significant change in phosphorylation (abs(log2FC) \u003e 1 and adjusted p value \u003c 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. 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. Phosphorylated proteins in each cluster were tested for enrichment of Reactome pathways (Jassal et al., 2020). 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). The pathway terms were obtained from the c2 category (Reactome) of Molecular Signature Database (MSigDBv6.1)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T15","span":{"begin":14,"end":29},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T16","span":{"begin":38,"end":53},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T17","span":{"begin":149,"end":164},"obj":"http://purl.obolibrary.org/obo/GO_0016310"}],"text":"Clustering of phosphorylation changes\nPhosphorylation sites with one-to-one mapping to human S, T or Y amino acids and showing significant change in phosphorylation (abs(log2FC) \u003e 1 and adjusted p value \u003c 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. 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. Phosphorylated proteins in each cluster were tested for enrichment of Reactome pathways (Jassal et al., 2020). 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). The pathway terms were obtained from the c2 category (Reactome) of Molecular Signature Database (MSigDBv6.1)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"2341","span":{"begin":87,"end":92},"obj":"Species"}],"attributes":[{"id":"A2341","pred":"tao:has_database_id","subj":"2341","obj":"Tax:9606"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Clustering of phosphorylation changes\nPhosphorylation sites with one-to-one mapping to human S, T or Y amino acids and showing significant change in phosphorylation (abs(log2FC) \u003e 1 and adjusted p value \u003c 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. 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. Phosphorylated proteins in each cluster were tested for enrichment of Reactome pathways (Jassal et al., 2020). 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). The pathway terms were obtained from the c2 category (Reactome) of Molecular Signature Database (MSigDBv6.1)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T926","span":{"begin":0,"end":37},"obj":"Sentence"},{"id":"T927","span":{"begin":38,"end":369},"obj":"Sentence"},{"id":"T928","span":{"begin":370,"end":569},"obj":"Sentence"},{"id":"T929","span":{"begin":570,"end":680},"obj":"Sentence"},{"id":"T930","span":{"begin":681,"end":857},"obj":"Sentence"},{"id":"T931","span":{"begin":858,"end":967},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Clustering of phosphorylation changes\nPhosphorylation sites with one-to-one mapping to human S, T or Y amino acids and showing significant change in phosphorylation (abs(log2FC) \u003e 1 and adjusted p value \u003c 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. 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. Phosphorylated proteins in each cluster were tested for enrichment of Reactome pathways (Jassal et al., 2020). 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). The pathway terms were obtained from the c2 category (Reactome) of Molecular Signature Database (MSigDBv6.1)."}

{"project":"2_test","denotations":[{"id":"32645325-18024473-20773116","span":{"begin":508,"end":512},"obj":"18024473"},{"id":"32645325-31691815-20773117","span":{"begin":674,"end":678},"obj":"31691815"},{"id":"32645325-22455463-20773118","span":{"begin":851,"end":855},"obj":"22455463"}],"text":"Clustering of phosphorylation changes\nPhosphorylation sites with one-to-one mapping to human S, T or Y amino acids and showing significant change in phosphorylation (abs(log2FC) \u003e 1 and adjusted p value \u003c 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. 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. Phosphorylated proteins in each cluster were tested for enrichment of Reactome pathways (Jassal et al., 2020). 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). The pathway terms were obtained from the c2 category (Reactome) of Molecular Signature Database (MSigDBv6.1)."}