PMC:7402624 / 28213-29490 JSON TXT

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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T13","span":{"begin":1117,"end":1130},"obj":"Body_part"}],"attributes":[{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0034922"}],"text":"(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"1054","span":{"begin":273,"end":278},"obj":"Gene"},{"id":"1055","span":{"begin":302,"end":307},"obj":"Gene"},{"id":"1056","span":{"begin":336,"end":341},"obj":"Gene"},{"id":"1057","span":{"begin":360,"end":363},"obj":"Gene"},{"id":"1058","span":{"begin":825,"end":830},"obj":"Gene"},{"id":"1059","span":{"begin":1269,"end":1276},"obj":"Species"},{"id":"1060","span":{"begin":483,"end":492},"obj":"Species"},{"id":"1061","span":{"begin":561,"end":570},"obj":"Species"},{"id":"1062","span":{"begin":376,"end":380},"obj":"Chemical"},{"id":"1063","span":{"begin":415,"end":417},"obj":"Chemical"},{"id":"1064","span":{"begin":432,"end":436},"obj":"Chemical"},{"id":"1065","span":{"begin":155,"end":157},"obj":"Disease"}],"attributes":[{"id":"A1054","pred":"tao:has_database_id","subj":"1054","obj":"Gene:643"},{"id":"A1055","pred":"tao:has_database_id","subj":"1055","obj":"Gene:643"},{"id":"A1056","pred":"tao:has_database_id","subj":"1056","obj":"Gene:643"},{"id":"A1057","pred":"tao:has_database_id","subj":"1057","obj":"Gene:920"},{"id":"A1058","pred":"tao:has_database_id","subj":"1058","obj":"Gene:127262"},{"id":"A1059","pred":"tao:has_database_id","subj":"1059","obj":"Tax:100569"},{"id":"A1060","pred":"tao:has_database_id","subj":"1060","obj":"Tax:2697049"},{"id":"A1061","pred":"tao:has_database_id","subj":"1061","obj":"Tax:2697049"},{"id":"A1065","pred":"tao:has_database_id","subj":"1065","obj":"MESH:D006816"}],"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":"(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T220","span":{"begin":43,"end":45},"obj":"Disease"},{"id":"T221","span":{"begin":121,"end":123},"obj":"Disease"},{"id":"T222","span":{"begin":155,"end":157},"obj":"Disease"},{"id":"T223","span":{"begin":415,"end":417},"obj":"Disease"},{"id":"T224","span":{"begin":471,"end":473},"obj":"Disease"},{"id":"T225","span":{"begin":483,"end":487},"obj":"Disease"},{"id":"T226","span":{"begin":561,"end":565},"obj":"Disease"}],"attributes":[{"id":"A220","pred":"mondo_id","subj":"T220","obj":"http://purl.obolibrary.org/obo/MONDO_0019035"},{"id":"A221","pred":"mondo_id","subj":"T221","obj":"http://purl.obolibrary.org/obo/MONDO_0019035"},{"id":"A222","pred":"mondo_id","subj":"T222","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A223","pred":"mondo_id","subj":"T223","obj":"http://purl.obolibrary.org/obo/MONDO_0019035"},{"id":"A224","pred":"mondo_id","subj":"T224","obj":"http://purl.obolibrary.org/obo/MONDO_0019035"},{"id":"A225","pred":"mondo_id","subj":"T225","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A226","pred":"mondo_id","subj":"T226","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T489","span":{"begin":1,"end":2},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T490","span":{"begin":46,"end":52},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T491","span":{"begin":63,"end":64},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T492","span":{"begin":155,"end":162},"obj":"http://purl.obolibrary.org/obo/CLO_0050940"},{"id":"T493","span":{"begin":224,"end":231},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T494","span":{"begin":316,"end":322},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T495","span":{"begin":354,"end":371},"obj":"http://purl.obolibrary.org/obo/CL_0000895"},{"id":"T496","span":{"begin":422,"end":431},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T497","span":{"begin":537,"end":546},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T498","span":{"begin":629,"end":636},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T499","span":{"begin":667,"end":673},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T500","span":{"begin":899,"end":905},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T501","span":{"begin":1031,"end":1038},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T502","span":{"begin":1115,"end":1121},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T503","span":{"begin":1228,"end":1235},"obj":"http://purl.obolibrary.org/obo/CL_0000236"}],"text":"(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T187","span":{"begin":43,"end":45},"obj":"Chemical"},{"id":"T189","span":{"begin":121,"end":123},"obj":"Chemical"},{"id":"T191","span":{"begin":155,"end":157},"obj":"Chemical"},{"id":"T192","span":{"begin":415,"end":417},"obj":"Chemical"},{"id":"T194","span":{"begin":471,"end":473},"obj":"Chemical"},{"id":"T196","span":{"begin":768,"end":775},"obj":"Chemical"},{"id":"T197","span":{"begin":993,"end":998},"obj":"Chemical"}],"attributes":[{"id":"A187","pred":"chebi_id","subj":"T187","obj":"http://purl.obolibrary.org/obo/CHEBI_53319"},{"id":"A188","pred":"chebi_id","subj":"T187","obj":"http://purl.obolibrary.org/obo/CHEBI_60686"},{"id":"A189","pred":"chebi_id","subj":"T189","obj":"http://purl.obolibrary.org/obo/CHEBI_53319"},{"id":"A190","pred":"chebi_id","subj":"T189","obj":"http://purl.obolibrary.org/obo/CHEBI_60686"},{"id":"A191","pred":"chebi_id","subj":"T191","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A192","pred":"chebi_id","subj":"T192","obj":"http://purl.obolibrary.org/obo/CHEBI_53319"},{"id":"A193","pred":"chebi_id","subj":"T192","obj":"http://purl.obolibrary.org/obo/CHEBI_60686"},{"id":"A194","pred":"chebi_id","subj":"T194","obj":"http://purl.obolibrary.org/obo/CHEBI_53319"},{"id":"A195","pred":"chebi_id","subj":"T194","obj":"http://purl.obolibrary.org/obo/CHEBI_60686"},{"id":"A196","pred":"chebi_id","subj":"T196","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A197","pred":"chebi_id","subj":"T197","obj":"http://purl.obolibrary.org/obo/CHEBI_24433"}],"text":"(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T172","span":{"begin":0,"end":1277},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster."}