PMC:7073332 / 45559-46565 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"1145","span":{"begin":591,"end":598},"obj":"Species"},{"id":"1146","span":{"begin":860,"end":864},"obj":"Species"},{"id":"1153","span":{"begin":452,"end":460},"obj":"Disease"},{"id":"1154","span":{"begin":560,"end":577},"obj":"Disease"},{"id":"1155","span":{"begin":711,"end":723},"obj":"Disease"},{"id":"1156","span":{"begin":634,"end":640},"obj":"CellLine"},{"id":"1157","span":{"begin":724,"end":730},"obj":"CellLine"}],"attributes":[{"id":"A1145","pred":"tao:has_database_id","subj":"1145","obj":"Tax:9606"},{"id":"A1146","pred":"tao:has_database_id","subj":"1146","obj":"Tax:694448"},{"id":"A1153","pred":"tao:has_database_id","subj":"1153","obj":"MESH:D007239"},{"id":"A1154","pred":"tao:has_database_id","subj":"1154","obj":"MESH:C000657245"},{"id":"A1155","pred":"tao:has_database_id","subj":"1155","obj":"MESH:D018352"},{"id":"A1156","pred":"tao:has_database_id","subj":"1156","obj":"CVCL:0609"},{"id":"A1157","pred":"tao:has_database_id","subj":"1157","obj":"CVCL:0609"}],"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":"Our key methodology is that a drug combination is therapeutically effective only if it follows a specific relationship to the disease module, as captured by Complementary Exposure patterns in targets’ modules of both drugs without overlapping toxic mechanisms28.\n\nGene set enrichment analysis\nWe performed the gene set enrichment analysis as an additional prioritization method. We first collected three differential gene expression data sets of hosts infected by HCoVs from the NCBI Gene Expression Omnibus (GEO). Among them, two transcriptome data sets were SARS-CoV-infected samples from patient’s peripheral blood94 (GSE1739) and Calu-3 cells95 (GSE33267), respectively. One transcriptome data set was MERS-CoV-infected Calu-3 cells96 (GSE122876). Adjusted P value less than 0.01 was defined as differentially expressed genes. These data sets were used as HCoV–host signatures to evaluate the treatment effects of drugs. Differential gene expression in cells treated with various drugs were retrieved f"}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T211","span":{"begin":264,"end":268},"obj":"Body_part"},{"id":"T212","span":{"begin":310,"end":314},"obj":"Body_part"},{"id":"T213","span":{"begin":417,"end":421},"obj":"Body_part"},{"id":"T214","span":{"begin":484,"end":488},"obj":"Body_part"},{"id":"T215","span":{"begin":938,"end":942},"obj":"Body_part"},{"id":"T216","span":{"begin":957,"end":962},"obj":"Body_part"}],"attributes":[{"id":"A211","pred":"fma_id","subj":"T211","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A212","pred":"fma_id","subj":"T212","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A213","pred":"fma_id","subj":"T213","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A214","pred":"fma_id","subj":"T214","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A215","pred":"fma_id","subj":"T215","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A216","pred":"fma_id","subj":"T216","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Our key methodology is that a drug combination is therapeutically effective only if it follows a specific relationship to the disease module, as captured by Complementary Exposure patterns in targets’ modules of both drugs without overlapping toxic mechanisms28.\n\nGene set enrichment analysis\nWe performed the gene set enrichment analysis as an additional prioritization method. We first collected three differential gene expression data sets of hosts infected by HCoVs from the NCBI Gene Expression Omnibus (GEO). Among them, two transcriptome data sets were SARS-CoV-infected samples from patient’s peripheral blood94 (GSE1739) and Calu-3 cells95 (GSE33267), respectively. One transcriptome data set was MERS-CoV-infected Calu-3 cells96 (GSE122876). Adjusted P value less than 0.01 was defined as differentially expressed genes. These data sets were used as HCoV–host signatures to evaluate the treatment effects of drugs. Differential gene expression in cells treated with various drugs were retrieved f"}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T161","span":{"begin":560,"end":568},"obj":"Disease"}],"attributes":[{"id":"A161","pred":"mondo_id","subj":"T161","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Our key methodology is that a drug combination is therapeutically effective only if it follows a specific relationship to the disease module, as captured by Complementary Exposure patterns in targets’ modules of both drugs without overlapping toxic mechanisms28.\n\nGene set enrichment analysis\nWe performed the gene set enrichment analysis as an additional prioritization method. We first collected three differential gene expression data sets of hosts infected by HCoVs from the NCBI Gene Expression Omnibus (GEO). Among them, two transcriptome data sets were SARS-CoV-infected samples from patient’s peripheral blood94 (GSE1739) and Calu-3 cells95 (GSE33267), respectively. One transcriptome data set was MERS-CoV-infected Calu-3 cells96 (GSE122876). Adjusted P value less than 0.01 was defined as differentially expressed genes. These data sets were used as HCoV–host signatures to evaluate the treatment effects of drugs. Differential gene expression in cells treated with various drugs were retrieved f"}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T311","span":{"begin":28,"end":29},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T312","span":{"begin":95,"end":96},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T313","span":{"begin":264,"end":268},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T314","span":{"begin":310,"end":314},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T315","span":{"begin":417,"end":421},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T316","span":{"begin":484,"end":488},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T317","span":{"begin":634,"end":640},"obj":"http://purl.obolibrary.org/obo/CLO_0002192"},{"id":"T318","span":{"begin":724,"end":730},"obj":"http://purl.obolibrary.org/obo/CLO_0002192"},{"id":"T319","span":{"begin":824,"end":829},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T320","span":{"begin":938,"end":942},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T321","span":{"begin":957,"end":962},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"Our key methodology is that a drug combination is therapeutically effective only if it follows a specific relationship to the disease module, as captured by Complementary Exposure patterns in targets’ modules of both drugs without overlapping toxic mechanisms28.\n\nGene set enrichment analysis\nWe performed the gene set enrichment analysis as an additional prioritization method. We first collected three differential gene expression data sets of hosts infected by HCoVs from the NCBI Gene Expression Omnibus (GEO). Among them, two transcriptome data sets were SARS-CoV-infected samples from patient’s peripheral blood94 (GSE1739) and Calu-3 cells95 (GSE33267), respectively. One transcriptome data set was MERS-CoV-infected Calu-3 cells96 (GSE122876). Adjusted P value less than 0.01 was defined as differentially expressed genes. These data sets were used as HCoV–host signatures to evaluate the treatment effects of drugs. Differential gene expression in cells treated with various drugs were retrieved f"}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T482","span":{"begin":30,"end":34},"obj":"Chemical"},{"id":"T483","span":{"begin":217,"end":222},"obj":"Chemical"},{"id":"T484","span":{"begin":918,"end":923},"obj":"Chemical"},{"id":"T485","span":{"begin":984,"end":989},"obj":"Chemical"}],"attributes":[{"id":"A482","pred":"chebi_id","subj":"T482","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"},{"id":"A483","pred":"chebi_id","subj":"T483","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"},{"id":"A484","pred":"chebi_id","subj":"T484","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"},{"id":"A485","pred":"chebi_id","subj":"T485","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"}],"text":"Our key methodology is that a drug combination is therapeutically effective only if it follows a specific relationship to the disease module, as captured by Complementary Exposure patterns in targets’ modules of both drugs without overlapping toxic mechanisms28.\n\nGene set enrichment analysis\nWe performed the gene set enrichment analysis as an additional prioritization method. We first collected three differential gene expression data sets of hosts infected by HCoVs from the NCBI Gene Expression Omnibus (GEO). Among them, two transcriptome data sets were SARS-CoV-infected samples from patient’s peripheral blood94 (GSE1739) and Calu-3 cells95 (GSE33267), respectively. One transcriptome data set was MERS-CoV-infected Calu-3 cells96 (GSE122876). Adjusted P value less than 0.01 was defined as differentially expressed genes. These data sets were used as HCoV–host signatures to evaluate the treatment effects of drugs. Differential gene expression in cells treated with various drugs were retrieved f"}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T63","span":{"begin":417,"end":432},"obj":"http://purl.obolibrary.org/obo/GO_0010467"},{"id":"T64","span":{"begin":484,"end":499},"obj":"http://purl.obolibrary.org/obo/GO_0010467"},{"id":"T65","span":{"begin":938,"end":953},"obj":"http://purl.obolibrary.org/obo/GO_0010467"}],"text":"Our key methodology is that a drug combination is therapeutically effective only if it follows a specific relationship to the disease module, as captured by Complementary Exposure patterns in targets’ modules of both drugs without overlapping toxic mechanisms28.\n\nGene set enrichment analysis\nWe performed the gene set enrichment analysis as an additional prioritization method. We first collected three differential gene expression data sets of hosts infected by HCoVs from the NCBI Gene Expression Omnibus (GEO). Among them, two transcriptome data sets were SARS-CoV-infected samples from patient’s peripheral blood94 (GSE1739) and Calu-3 cells95 (GSE33267), respectively. One transcriptome data set was MERS-CoV-infected Calu-3 cells96 (GSE122876). Adjusted P value less than 0.01 was defined as differentially expressed genes. These data sets were used as HCoV–host signatures to evaluate the treatment effects of drugs. Differential gene expression in cells treated with various drugs were retrieved f"}

{"project":"LitCovid-sentences","denotations":[{"id":"T270","span":{"begin":0,"end":262},"obj":"Sentence"},{"id":"T271","span":{"begin":264,"end":292},"obj":"Sentence"},{"id":"T272","span":{"begin":293,"end":378},"obj":"Sentence"},{"id":"T273","span":{"begin":379,"end":514},"obj":"Sentence"},{"id":"T274","span":{"begin":515,"end":674},"obj":"Sentence"},{"id":"T275","span":{"begin":675,"end":751},"obj":"Sentence"},{"id":"T276","span":{"begin":752,"end":830},"obj":"Sentence"},{"id":"T277","span":{"begin":831,"end":924},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Our key methodology is that a drug combination is therapeutically effective only if it follows a specific relationship to the disease module, as captured by Complementary Exposure patterns in targets’ modules of both drugs without overlapping toxic mechanisms28.\n\nGene set enrichment analysis\nWe performed the gene set enrichment analysis as an additional prioritization method. We first collected three differential gene expression data sets of hosts infected by HCoVs from the NCBI Gene Expression Omnibus (GEO). Among them, two transcriptome data sets were SARS-CoV-infected samples from patient’s peripheral blood94 (GSE1739) and Calu-3 cells95 (GSE33267), respectively. One transcriptome data set was MERS-CoV-infected Calu-3 cells96 (GSE122876). Adjusted P value less than 0.01 was defined as differentially expressed genes. These data sets were used as HCoV–host signatures to evaluate the treatment effects of drugs. Differential gene expression in cells treated with various drugs were retrieved f"}

{"project":"2_test","denotations":[{"id":"32194980-30867426-19614266","span":{"begin":259,"end":261},"obj":"30867426"},{"id":"32194980-15655079-19614267","span":{"begin":617,"end":619},"obj":"15655079"},{"id":"32194980-23631916-19614268","span":{"begin":646,"end":648},"obj":"23631916"},{"id":"32194980-30631056-19614269","span":{"begin":736,"end":738},"obj":"30631056"}],"text":"Our key methodology is that a drug combination is therapeutically effective only if it follows a specific relationship to the disease module, as captured by Complementary Exposure patterns in targets’ modules of both drugs without overlapping toxic mechanisms28.\n\nGene set enrichment analysis\nWe performed the gene set enrichment analysis as an additional prioritization method. We first collected three differential gene expression data sets of hosts infected by HCoVs from the NCBI Gene Expression Omnibus (GEO). Among them, two transcriptome data sets were SARS-CoV-infected samples from patient’s peripheral blood94 (GSE1739) and Calu-3 cells95 (GSE33267), respectively. One transcriptome data set was MERS-CoV-infected Calu-3 cells96 (GSE122876). Adjusted P value less than 0.01 was defined as differentially expressed genes. These data sets were used as HCoV–host signatures to evaluate the treatment effects of drugs. Differential gene expression in cells treated with various drugs were retrieved f"}