PMC:7321036 / 108039-108968 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7321036","sourcedb":"PMC","sourceid":"7321036","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7321036","text":"Phosphorylation 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).","tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T33","span":{"begin":65,"end":76},"obj":"Body_part"},{"id":"T34","span":{"begin":547,"end":555},"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"},{"subj":"T33","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T34","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T56","span":{"begin":49,"end":54},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T57","span":{"begin":55,"end":59},"obj":"http://purl.obolibrary.org/obo/CLO_0009141"},{"id":"T58","span":{"begin":55,"end":59},"obj":"http://purl.obolibrary.org/obo/CLO_0050980"},{"id":"T59","span":{"begin":379,"end":380},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T60","span":{"begin":495,"end":496},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T61","span":{"begin":577,"end":583},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T62","span":{"begin":861,"end":863},"obj":"http://purl.obolibrary.org/obo/CLO_0002105"},{"id":"T63","span":{"begin":861,"end":863},"obj":"http://purl.obolibrary.org/obo/CLO_0051742"}],"attributes":[{"subj":"T56","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T57","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T58","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T59","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T60","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T61","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T62","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T63","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T57668","span":{"begin":65,"end":76},"obj":"Chemical"},{"id":"T58962","span":{"begin":65,"end":70},"obj":"Chemical"},{"id":"T27942","span":{"begin":71,"end":76},"obj":"Chemical"},{"id":"T6743","span":{"begin":547,"end":555},"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"},{"subj":"T57668","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T58962","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T27942","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T6743","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T16","span":{"begin":0,"end":15},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T17","span":{"begin":111,"end":126},"obj":"http://purl.obolibrary.org/obo/GO_0016310"}],"attributes":[{"subj":"T16","pred":"source","obj":"LitCovid-PD-GO-BP"},{"subj":"T17","pred":"source","obj":"LitCovid-PD-GO-BP"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"2341","span":{"begin":49,"end":54},"obj":"Species"}],"attributes":[{"id":"A2341","pred":"tao:has_database_id","subj":"2341","obj":"Tax:9606"},{"subj":"2341","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T927","span":{"begin":0,"end":331},"obj":"Sentence"},{"id":"T928","span":{"begin":332,"end":531},"obj":"Sentence"},{"id":"T929","span":{"begin":532,"end":642},"obj":"Sentence"},{"id":"T930","span":{"begin":643,"end":819},"obj":"Sentence"},{"id":"T931","span":{"begin":820,"end":929},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T927","pred":"source","obj":"LitCovid-sentences"},{"subj":"T928","pred":"source","obj":"LitCovid-sentences"},{"subj":"T929","pred":"source","obj":"LitCovid-sentences"},{"subj":"T930","pred":"source","obj":"LitCovid-sentences"},{"subj":"T931","pred":"source","obj":"LitCovid-sentences"}]},{"project":"2_test","denotations":[{"id":"32645325-18024473-20773116","span":{"begin":470,"end":474},"obj":"18024473"},{"id":"32645325-31691815-20773117","span":{"begin":636,"end":640},"obj":"31691815"},{"id":"32645325-22455463-20773118","span":{"begin":813,"end":817},"obj":"22455463"}],"attributes":[{"subj":"32645325-18024473-20773116","pred":"source","obj":"2_test"},{"subj":"32645325-31691815-20773117","pred":"source","obj":"2_test"},{"subj":"32645325-22455463-20773118","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#9b93ec","default":true},{"id":"LitCovid-PD-CLO","color":"#a4ec93"},{"id":"LitCovid-PD-CHEBI","color":"#ec93be"},{"id":"LitCovid-PD-GO-BP","color":"#93d8ec"},{"id":"LitCovid-PubTator","color":"#ece593"},{"id":"LitCovid-sentences","color":"#cb93ec"},{"id":"2_test","color":"#93ecb1"}]}]}}