PMC:7321036 / 110114-111390 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T35","span":{"begin":82,"end":86},"obj":"Body_part"},{"id":"T36","span":{"begin":383,"end":387},"obj":"Body_part"}],"attributes":[{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"In addition to the time-course experiment, we also estimated kinase activities of cell line perturbation in a range of biological conditions using the K-test based approach, from a large resource of previously published phosphoproteomics datasets comprising of 435 biological conditions which include several drug treatments (chlorzoxazone, paclitaxel), inhibitors (EGFRi, AKTi) and cell cycle states (Ochoa et al., 2016). After selecting for kinase activities derived from 3 or more substrates, a total of 214 kinases had activity estimates for at least one biological condition including all 97 kinases which were estimated in the time-course experiment. Of the 435 conditions, 309 conditions with at least one kinase with significantly changing activity (-log10(p value) from Z-test \u003e 2.5) were selected. Individual time points of the infection experiment were correlated with each selected biological condition based on Pearson correlation of their kinase activity profiles. Conditions with significant correlation (5% FDR) with one or more time points were identified. Several conditions corresponded to the same biological treatment (i.e., drug perturbation) in different concentrations. In such cases, the conditions are represented together with strongest correlation."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T389","span":{"begin":838,"end":847},"obj":"Disease"}],"attributes":[{"id":"A389","pred":"mondo_id","subj":"T389","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"In addition to the time-course experiment, we also estimated kinase activities of cell line perturbation in a range of biological conditions using the K-test based approach, from a large resource of previously published phosphoproteomics datasets comprising of 435 biological conditions which include several drug treatments (chlorzoxazone, paclitaxel), inhibitors (EGFRi, AKTi) and cell cycle states (Ochoa et al., 2016). After selecting for kinase activities derived from 3 or more substrates, a total of 214 kinases had activity estimates for at least one biological condition including all 97 kinases which were estimated in the time-course experiment. Of the 435 conditions, 309 conditions with at least one kinase with significantly changing activity (-log10(p value) from Z-test \u003e 2.5) were selected. Individual time points of the infection experiment were correlated with each selected biological condition based on Pearson correlation of their kinase activity profiles. Conditions with significant correlation (5% FDR) with one or more time points were identified. Several conditions corresponded to the same biological treatment (i.e., drug perturbation) in different concentrations. In such cases, the conditions are represented together with strongest correlation."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T74","span":{"begin":68,"end":78},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T75","span":{"begin":82,"end":91},"obj":"http://purl.obolibrary.org/obo/CLO_0000031"},{"id":"T76","span":{"begin":108,"end":109},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T77","span":{"begin":153,"end":157},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T78","span":{"begin":179,"end":180},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T79","span":{"begin":383,"end":387},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T80","span":{"begin":450,"end":460},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T81","span":{"begin":496,"end":497},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T82","span":{"begin":523,"end":531},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T83","span":{"begin":748,"end":756},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T84","span":{"begin":781,"end":785},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T85","span":{"begin":960,"end":968},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"}],"text":"In addition to the time-course experiment, we also estimated kinase activities of cell line perturbation in a range of biological conditions using the K-test based approach, from a large resource of previously published phosphoproteomics datasets comprising of 435 biological conditions which include several drug treatments (chlorzoxazone, paclitaxel), inhibitors (EGFRi, AKTi) and cell cycle states (Ochoa et al., 2016). After selecting for kinase activities derived from 3 or more substrates, a total of 214 kinases had activity estimates for at least one biological condition including all 97 kinases which were estimated in the time-course experiment. Of the 435 conditions, 309 conditions with at least one kinase with significantly changing activity (-log10(p value) from Z-test \u003e 2.5) were selected. Individual time points of the infection experiment were correlated with each selected biological condition based on Pearson correlation of their kinase activity profiles. Conditions with significant correlation (5% FDR) with one or more time points were identified. Several conditions corresponded to the same biological treatment (i.e., drug perturbation) in different concentrations. In such cases, the conditions are represented together with strongest correlation."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T31298","span":{"begin":309,"end":313},"obj":"Chemical"},{"id":"T55659","span":{"begin":326,"end":339},"obj":"Chemical"},{"id":"T66943","span":{"begin":341,"end":351},"obj":"Chemical"},{"id":"T86581","span":{"begin":354,"end":364},"obj":"Chemical"},{"id":"T22512","span":{"begin":1146,"end":1150},"obj":"Chemical"}],"attributes":[{"id":"A25429","pred":"chebi_id","subj":"T31298","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"},{"id":"A34614","pred":"chebi_id","subj":"T55659","obj":"http://purl.obolibrary.org/obo/CHEBI_3655"},{"id":"A15743","pred":"chebi_id","subj":"T66943","obj":"http://purl.obolibrary.org/obo/CHEBI_45863"},{"id":"A99759","pred":"chebi_id","subj":"T86581","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A42503","pred":"chebi_id","subj":"T22512","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"}],"text":"In addition to the time-course experiment, we also estimated kinase activities of cell line perturbation in a range of biological conditions using the K-test based approach, from a large resource of previously published phosphoproteomics datasets comprising of 435 biological conditions which include several drug treatments (chlorzoxazone, paclitaxel), inhibitors (EGFRi, AKTi) and cell cycle states (Ochoa et al., 2016). After selecting for kinase activities derived from 3 or more substrates, a total of 214 kinases had activity estimates for at least one biological condition including all 97 kinases which were estimated in the time-course experiment. Of the 435 conditions, 309 conditions with at least one kinase with significantly changing activity (-log10(p value) from Z-test \u003e 2.5) were selected. Individual time points of the infection experiment were correlated with each selected biological condition based on Pearson correlation of their kinase activity profiles. Conditions with significant correlation (5% FDR) with one or more time points were identified. Several conditions corresponded to the same biological treatment (i.e., drug perturbation) in different concentrations. In such cases, the conditions are represented together with strongest correlation."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T25","span":{"begin":61,"end":78},"obj":"http://purl.obolibrary.org/obo/GO_0016301"},{"id":"T26","span":{"begin":383,"end":393},"obj":"http://purl.obolibrary.org/obo/GO_0007049"},{"id":"T27","span":{"begin":443,"end":460},"obj":"http://purl.obolibrary.org/obo/GO_0016301"},{"id":"T28","span":{"begin":953,"end":968},"obj":"http://purl.obolibrary.org/obo/GO_0016301"}],"text":"In addition to the time-course experiment, we also estimated kinase activities of cell line perturbation in a range of biological conditions using the K-test based approach, from a large resource of previously published phosphoproteomics datasets comprising of 435 biological conditions which include several drug treatments (chlorzoxazone, paclitaxel), inhibitors (EGFRi, AKTi) and cell cycle states (Ochoa et al., 2016). After selecting for kinase activities derived from 3 or more substrates, a total of 214 kinases had activity estimates for at least one biological condition including all 97 kinases which were estimated in the time-course experiment. Of the 435 conditions, 309 conditions with at least one kinase with significantly changing activity (-log10(p value) from Z-test \u003e 2.5) were selected. Individual time points of the infection experiment were correlated with each selected biological condition based on Pearson correlation of their kinase activity profiles. Conditions with significant correlation (5% FDR) with one or more time points were identified. Several conditions corresponded to the same biological treatment (i.e., drug perturbation) in different concentrations. In such cases, the conditions are represented together with strongest correlation."}

{"project":"LitCovid-PubTator","denotations":[{"id":"2351","span":{"begin":326,"end":339},"obj":"Chemical"},{"id":"2352","span":{"begin":341,"end":351},"obj":"Chemical"},{"id":"2353","span":{"begin":838,"end":847},"obj":"Disease"}],"attributes":[{"id":"A2351","pred":"tao:has_database_id","subj":"2351","obj":"MESH:D002753"},{"id":"A2352","pred":"tao:has_database_id","subj":"2352","obj":"MESH:D017239"},{"id":"A2353","pred":"tao:has_database_id","subj":"2353","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":"In addition to the time-course experiment, we also estimated kinase activities of cell line perturbation in a range of biological conditions using the K-test based approach, from a large resource of previously published phosphoproteomics datasets comprising of 435 biological conditions which include several drug treatments (chlorzoxazone, paclitaxel), inhibitors (EGFRi, AKTi) and cell cycle states (Ochoa et al., 2016). After selecting for kinase activities derived from 3 or more substrates, a total of 214 kinases had activity estimates for at least one biological condition including all 97 kinases which were estimated in the time-course experiment. Of the 435 conditions, 309 conditions with at least one kinase with significantly changing activity (-log10(p value) from Z-test \u003e 2.5) were selected. Individual time points of the infection experiment were correlated with each selected biological condition based on Pearson correlation of their kinase activity profiles. Conditions with significant correlation (5% FDR) with one or more time points were identified. Several conditions corresponded to the same biological treatment (i.e., drug perturbation) in different concentrations. In such cases, the conditions are represented together with strongest correlation."}

{"project":"LitCovid-sentences","denotations":[{"id":"T940","span":{"begin":0,"end":422},"obj":"Sentence"},{"id":"T941","span":{"begin":423,"end":656},"obj":"Sentence"},{"id":"T942","span":{"begin":657,"end":807},"obj":"Sentence"},{"id":"T943","span":{"begin":808,"end":978},"obj":"Sentence"},{"id":"T944","span":{"begin":979,"end":1073},"obj":"Sentence"},{"id":"T945","span":{"begin":1074,"end":1193},"obj":"Sentence"},{"id":"T946","span":{"begin":1194,"end":1276},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In addition to the time-course experiment, we also estimated kinase activities of cell line perturbation in a range of biological conditions using the K-test based approach, from a large resource of previously published phosphoproteomics datasets comprising of 435 biological conditions which include several drug treatments (chlorzoxazone, paclitaxel), inhibitors (EGFRi, AKTi) and cell cycle states (Ochoa et al., 2016). After selecting for kinase activities derived from 3 or more substrates, a total of 214 kinases had activity estimates for at least one biological condition including all 97 kinases which were estimated in the time-course experiment. Of the 435 conditions, 309 conditions with at least one kinase with significantly changing activity (-log10(p value) from Z-test \u003e 2.5) were selected. Individual time points of the infection experiment were correlated with each selected biological condition based on Pearson correlation of their kinase activity profiles. Conditions with significant correlation (5% FDR) with one or more time points were identified. Several conditions corresponded to the same biological treatment (i.e., drug perturbation) in different concentrations. In such cases, the conditions are represented together with strongest correlation."}

{"project":"2_test","denotations":[{"id":"32645325-27909043-20773121","span":{"begin":416,"end":420},"obj":"27909043"}],"text":"In addition to the time-course experiment, we also estimated kinase activities of cell line perturbation in a range of biological conditions using the K-test based approach, from a large resource of previously published phosphoproteomics datasets comprising of 435 biological conditions which include several drug treatments (chlorzoxazone, paclitaxel), inhibitors (EGFRi, AKTi) and cell cycle states (Ochoa et al., 2016). After selecting for kinase activities derived from 3 or more substrates, a total of 214 kinases had activity estimates for at least one biological condition including all 97 kinases which were estimated in the time-course experiment. Of the 435 conditions, 309 conditions with at least one kinase with significantly changing activity (-log10(p value) from Z-test \u003e 2.5) were selected. Individual time points of the infection experiment were correlated with each selected biological condition based on Pearson correlation of their kinase activity profiles. Conditions with significant correlation (5% FDR) with one or more time points were identified. Several conditions corresponded to the same biological treatment (i.e., drug perturbation) in different concentrations. In such cases, the conditions are represented together with strongest correlation."}