PMC:7321036 / 19435-20957 JSON TXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T101","span":{"begin":23,"end":31},"obj":"Disease"},{"id":"T102","span":{"begin":303,"end":312},"obj":"Disease"},{"id":"T103","span":{"begin":549,"end":558},"obj":"Disease"},{"id":"T104","span":{"begin":697,"end":705},"obj":"Disease"},{"id":"T105","span":{"begin":745,"end":753},"obj":"Disease"},{"id":"T106","span":{"begin":1384,"end":1393},"obj":"Disease"}],"attributes":[{"id":"A101","pred":"mondo_id","subj":"T101","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A102","pred":"mondo_id","subj":"T102","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A103","pred":"mondo_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A104","pred":"mondo_id","subj":"T104","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A105","pred":"mondo_id","subj":"T105","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A106","pred":"mondo_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"The recently published SARS-CoV-2 virus-human protein-protein interaction map identified 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins (Gordon et al., 2020). Here we found some of these host proteins (40 of 332) to be significantly differentially phosphorylated upon infection (Figure 3 ). Virus-host protein-protein interactions could drive changes in phosphorylation by affecting host protein subcellular localization or by sterically blocking kinase access. Furthermore, phosphorylation of these proteins upon infection may signify an additional mode of functional control over these potential dependency and restriction factors.\nFigure 3 Phosphorylation on SARS-CoV-2 Virus-Human Interacting Proteins\nThe SARS-CoV-2 virus-host protein-protein interaction map (Gordon et al., 2020) found 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins. Here we found 40 of 332 proteins significantly differentially phosphorylated across at least two time points (adjusted p \u003c 0.05 and absolute value of log2 fold change [abs(log2FC)] \u003e 1). Viral proteins are shown as red diamonds. Interacting human proteins are shown as gray circles. PHs emanate from human proteins, colored by their log2 fold change compared with uninfected control samples (red, increase; blue, decrease) at each time point (0, 2, 4, 8, 12, and 24 h after infection) in a clockwise fashion. An interactive version of phosphorylation data can be found at https://kroganlab.ucsf.edu/network-maps."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T37818","span":{"begin":34,"end":39},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T76637","span":{"begin":40,"end":53},"obj":"http://purl.obolibrary.org/obo/PR_000029067"},{"id":"T69944","span":{"begin":93,"end":107},"obj":"http://purl.obolibrary.org/obo/PR_000029067"},{"id":"T77643","span":{"begin":125,"end":127},"obj":"http://purl.obolibrary.org/obo/CLO_0050509"},{"id":"T26743","span":{"begin":326,"end":331},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T76801","span":{"begin":708,"end":713},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T10288","span":{"begin":714,"end":719},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T39350","span":{"begin":756,"end":761},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T96781","span":{"begin":831,"end":845},"obj":"http://purl.obolibrary.org/obo/PR_000029067"},{"id":"T23709","span":{"begin":863,"end":865},"obj":"http://purl.obolibrary.org/obo/CLO_0050509"},{"id":"T92566","span":{"begin":1151,"end":1165},"obj":"http://purl.obolibrary.org/obo/PR_000029067"},{"id":"T70112","span":{"begin":1210,"end":1224},"obj":"http://purl.obolibrary.org/obo/PR_000029067"},{"id":"T31688","span":{"begin":1359,"end":1363},"obj":"http://purl.obolibrary.org/obo/CLO_0001382"},{"id":"T99883","span":{"begin":1398,"end":1399},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The recently published SARS-CoV-2 virus-human protein-protein interaction map identified 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins (Gordon et al., 2020). Here we found some of these host proteins (40 of 332) to be significantly differentially phosphorylated upon infection (Figure 3 ). Virus-host protein-protein interactions could drive changes in phosphorylation by affecting host protein subcellular localization or by sterically blocking kinase access. Furthermore, phosphorylation of these proteins upon infection may signify an additional mode of functional control over these potential dependency and restriction factors.\nFigure 3 Phosphorylation on SARS-CoV-2 Virus-Human Interacting Proteins\nThe SARS-CoV-2 virus-host protein-protein interaction map (Gordon et al., 2020) found 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins. Here we found 40 of 332 proteins significantly differentially phosphorylated across at least two time points (adjusted p \u003c 0.05 and absolute value of log2 fold change [abs(log2FC)] \u003e 1). Viral proteins are shown as red diamonds. Interacting human proteins are shown as gray circles. PHs emanate from human proteins, colored by their log2 fold change compared with uninfected control samples (red, increase; blue, decrease) at each time point (0, 2, 4, 8, 12, and 24 h after infection) in a clockwise fashion. An interactive version of phosphorylation data can be found at https://kroganlab.ucsf.edu/network-maps."}

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T106","span":{"begin":389,"end":404},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T107","span":{"begin":443,"end":455},"obj":"http://purl.obolibrary.org/obo/GO_0051179"},{"id":"T108","span":{"begin":510,"end":525},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T109","span":{"begin":678,"end":693},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T110","span":{"begin":1445,"end":1460},"obj":"http://purl.obolibrary.org/obo/GO_0016310"}],"text":"The recently published SARS-CoV-2 virus-human protein-protein interaction map identified 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins (Gordon et al., 2020). Here we found some of these host proteins (40 of 332) to be significantly differentially phosphorylated upon infection (Figure 3 ). Virus-host protein-protein interactions could drive changes in phosphorylation by affecting host protein subcellular localization or by sterically blocking kinase access. Furthermore, phosphorylation of these proteins upon infection may signify an additional mode of functional control over these potential dependency and restriction factors.\nFigure 3 Phosphorylation on SARS-CoV-2 Virus-Human Interacting Proteins\nThe SARS-CoV-2 virus-host protein-protein interaction map (Gordon et al., 2020) found 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins. Here we found 40 of 332 proteins significantly differentially phosphorylated across at least two time points (adjusted p \u003c 0.05 and absolute value of log2 fold change [abs(log2FC)] \u003e 1). Viral proteins are shown as red diamonds. Interacting human proteins are shown as gray circles. PHs emanate from human proteins, colored by their log2 fold change compared with uninfected control samples (red, increase; blue, decrease) at each time point (0, 2, 4, 8, 12, and 24 h after infection) in a clockwise fashion. An interactive version of phosphorylation data can be found at https://kroganlab.ucsf.edu/network-maps."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"312","span":{"begin":697,"end":707},"obj":"Species"},{"id":"313","span":{"begin":714,"end":719},"obj":"Species"},{"id":"319","span":{"begin":745,"end":755},"obj":"Species"},{"id":"320","span":{"begin":831,"end":836},"obj":"Species"},{"id":"321","span":{"begin":1151,"end":1156},"obj":"Species"},{"id":"322","span":{"begin":1210,"end":1215},"obj":"Species"},{"id":"323","span":{"begin":1384,"end":1393},"obj":"Disease"},{"id":"329","span":{"begin":23,"end":33},"obj":"Species"},{"id":"330","span":{"begin":40,"end":45},"obj":"Species"},{"id":"331","span":{"begin":93,"end":98},"obj":"Species"},{"id":"332","span":{"begin":303,"end":312},"obj":"Disease"},{"id":"333","span":{"begin":549,"end":558},"obj":"Disease"}],"attributes":[{"id":"A312","pred":"tao:has_database_id","subj":"312","obj":"Tax:2697049"},{"id":"A313","pred":"tao:has_database_id","subj":"313","obj":"Tax:9606"},{"id":"A319","pred":"tao:has_database_id","subj":"319","obj":"Tax:2697049"},{"id":"A320","pred":"tao:has_database_id","subj":"320","obj":"Tax:9606"},{"id":"A321","pred":"tao:has_database_id","subj":"321","obj":"Tax:9606"},{"id":"A322","pred":"tao:has_database_id","subj":"322","obj":"Tax:9606"},{"id":"A323","pred":"tao:has_database_id","subj":"323","obj":"MESH:D007239"},{"id":"A329","pred":"tao:has_database_id","subj":"329","obj":"Tax:2697049"},{"id":"A330","pred":"tao:has_database_id","subj":"330","obj":"Tax:9606"},{"id":"A331","pred":"tao:has_database_id","subj":"331","obj":"Tax:9606"},{"id":"A332","pred":"tao:has_database_id","subj":"332","obj":"MESH:D007239"},{"id":"A333","pred":"tao:has_database_id","subj":"333","obj":"MESH:D007239"}],"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":"The recently published SARS-CoV-2 virus-human protein-protein interaction map identified 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins (Gordon et al., 2020). Here we found some of these host proteins (40 of 332) to be significantly differentially phosphorylated upon infection (Figure 3 ). Virus-host protein-protein interactions could drive changes in phosphorylation by affecting host protein subcellular localization or by sterically blocking kinase access. Furthermore, phosphorylation of these proteins upon infection may signify an additional mode of functional control over these potential dependency and restriction factors.\nFigure 3 Phosphorylation on SARS-CoV-2 Virus-Human Interacting Proteins\nThe SARS-CoV-2 virus-host protein-protein interaction map (Gordon et al., 2020) found 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins. Here we found 40 of 332 proteins significantly differentially phosphorylated across at least two time points (adjusted p \u003c 0.05 and absolute value of log2 fold change [abs(log2FC)] \u003e 1). Viral proteins are shown as red diamonds. Interacting human proteins are shown as gray circles. PHs emanate from human proteins, colored by their log2 fold change compared with uninfected control samples (red, increase; blue, decrease) at each time point (0, 2, 4, 8, 12, and 24 h after infection) in a clockwise fashion. An interactive version of phosphorylation data can be found at https://kroganlab.ucsf.edu/network-maps."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T130","span":{"begin":0,"end":193},"obj":"Sentence"},{"id":"T131","span":{"begin":194,"end":325},"obj":"Sentence"},{"id":"T132","span":{"begin":326,"end":496},"obj":"Sentence"},{"id":"T133","span":{"begin":497,"end":668},"obj":"Sentence"},{"id":"T134","span":{"begin":669,"end":740},"obj":"Sentence"},{"id":"T135","span":{"begin":741,"end":909},"obj":"Sentence"},{"id":"T136","span":{"begin":910,"end":1096},"obj":"Sentence"},{"id":"T137","span":{"begin":1097,"end":1138},"obj":"Sentence"},{"id":"T138","span":{"begin":1139,"end":1192},"obj":"Sentence"},{"id":"T139","span":{"begin":1193,"end":1418},"obj":"Sentence"},{"id":"T140","span":{"begin":1419,"end":1522},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The recently published SARS-CoV-2 virus-human protein-protein interaction map identified 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins (Gordon et al., 2020). Here we found some of these host proteins (40 of 332) to be significantly differentially phosphorylated upon infection (Figure 3 ). Virus-host protein-protein interactions could drive changes in phosphorylation by affecting host protein subcellular localization or by sterically blocking kinase access. Furthermore, phosphorylation of these proteins upon infection may signify an additional mode of functional control over these potential dependency and restriction factors.\nFigure 3 Phosphorylation on SARS-CoV-2 Virus-Human Interacting Proteins\nThe SARS-CoV-2 virus-host protein-protein interaction map (Gordon et al., 2020) found 332 human proteins interacting with 27 (26 wild-type and 1 mutant) viral proteins. Here we found 40 of 332 proteins significantly differentially phosphorylated across at least two time points (adjusted p \u003c 0.05 and absolute value of log2 fold change [abs(log2FC)] \u003e 1). Viral proteins are shown as red diamonds. Interacting human proteins are shown as gray circles. PHs emanate from human proteins, colored by their log2 fold change compared with uninfected control samples (red, increase; blue, decrease) at each time point (0, 2, 4, 8, 12, and 24 h after infection) in a clockwise fashion. An interactive version of phosphorylation data can be found at https://kroganlab.ucsf.edu/network-maps."}