PMC:7640975 / 15888-17366 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T108","span":{"begin":88,"end":93},"obj":"Body_part"},{"id":"T109","span":{"begin":112,"end":116},"obj":"Body_part"},{"id":"T110","span":{"begin":543,"end":550},"obj":"Body_part"},{"id":"T111","span":{"begin":737,"end":744},"obj":"Body_part"},{"id":"T112","span":{"begin":1248,"end":1255},"obj":"Body_part"},{"id":"T113","span":{"begin":1256,"end":1263},"obj":"Body_part"}],"attributes":[{"id":"A108","pred":"fma_id","subj":"T108","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A109","pred":"fma_id","subj":"T109","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A110","pred":"fma_id","subj":"T110","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A111","pred":"fma_id","subj":"T111","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A112","pred":"fma_id","subj":"T112","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A113","pred":"fma_id","subj":"T113","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"2.8 Bioinformatics Analysis\nThe data for the identified DEPs of PDCoV-infected IPEC-J2 cells were submitted to Gene Ontology (GO) Terms (http://geneontology.org/) for GO analysis, by which the DEPs were assigned into three branches of ontology—biological process (BP), cellular component (CC), and molecular function (MF). GO enrichment analysis for the DEPs was done using the Goatools software (https://github.com/tanghaibao/GOatools) with Fisher’s exact test, and those with a p-value \u003c 0.05 were thought to be significantly enriched. The protein database of clusters of Orthologous Groups (COG; http://www.ncbi.nlm.nih.gov/COG/) was also used to assign possible functions to the identified DEPs. The Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/) pathway analyses were performed to reveal the potential functions of the DEPs, which were annotated using the BlastP program of the Diamond software against the KEGG database with a cutoff E-value ≤ 1 × 10–5 and identity ≥0.98. The pathway enrichment statistics were performed using the KOBAS software (http://kobas.cbi.pku.edu.cn/home.do/) with the Fisher’s exact test, and those with p-values \u003c 0.05 were regarded as statistically significant.30,31 Furthermore, the protein–protein interaction networks were created using the online STRING database (http://string-db.org/) and visualized by Cytoscape (https://cytoscape.org/), which was widely used for analyzing the relationships between DEPs.32"}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T23","span":{"begin":319,"end":321},"obj":"Disease"}],"attributes":[{"id":"A23","pred":"mondo_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/MONDO_0009691"},{"id":"A24","pred":"mondo_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/MONDO_0020481"}],"text":"2.8 Bioinformatics Analysis\nThe data for the identified DEPs of PDCoV-infected IPEC-J2 cells were submitted to Gene Ontology (GO) Terms (http://geneontology.org/) for GO analysis, by which the DEPs were assigned into three branches of ontology—biological process (BP), cellular component (CC), and molecular function (MF). GO enrichment analysis for the DEPs was done using the Goatools software (https://github.com/tanghaibao/GOatools) with Fisher’s exact test, and those with a p-value \u003c 0.05 were thought to be significantly enriched. The protein database of clusters of Orthologous Groups (COG; http://www.ncbi.nlm.nih.gov/COG/) was also used to assign possible functions to the identified DEPs. The Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/) pathway analyses were performed to reveal the potential functions of the DEPs, which were annotated using the BlastP program of the Diamond software against the KEGG database with a cutoff E-value ≤ 1 × 10–5 and identity ≥0.98. The pathway enrichment statistics were performed using the KOBAS software (http://kobas.cbi.pku.edu.cn/home.do/) with the Fisher’s exact test, and those with p-values \u003c 0.05 were regarded as statistically significant.30,31 Furthermore, the protein–protein interaction networks were created using the online STRING database (http://string-db.org/) and visualized by Cytoscape (https://cytoscape.org/), which was widely used for analyzing the relationships between DEPs.32"}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T222","span":{"begin":88,"end":93},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T223","span":{"begin":112,"end":116},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T224","span":{"begin":270,"end":288},"obj":"http://purl.obolibrary.org/obo/GO_0005575"},{"id":"T225","span":{"begin":290,"end":292},"obj":"http://purl.obolibrary.org/obo/GO_0005575"},{"id":"T226","span":{"begin":458,"end":462},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T227","span":{"begin":479,"end":482},"obj":"http://purl.obolibrary.org/obo/CLO_0001547"},{"id":"T228","span":{"begin":727,"end":732},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T229","span":{"begin":960,"end":961},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T230","span":{"begin":979,"end":987},"obj":"http://purl.obolibrary.org/obo/CLO_0001040"},{"id":"T231","span":{"begin":1145,"end":1149},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"text":"2.8 Bioinformatics Analysis\nThe data for the identified DEPs of PDCoV-infected IPEC-J2 cells were submitted to Gene Ontology (GO) Terms (http://geneontology.org/) for GO analysis, by which the DEPs were assigned into three branches of ontology—biological process (BP), cellular component (CC), and molecular function (MF). GO enrichment analysis for the DEPs was done using the Goatools software (https://github.com/tanghaibao/GOatools) with Fisher’s exact test, and those with a p-value \u003c 0.05 were thought to be significantly enriched. The protein database of clusters of Orthologous Groups (COG; http://www.ncbi.nlm.nih.gov/COG/) was also used to assign possible functions to the identified DEPs. The Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/) pathway analyses were performed to reveal the potential functions of the DEPs, which were annotated using the BlastP program of the Diamond software against the KEGG database with a cutoff E-value ≤ 1 × 10–5 and identity ≥0.98. The pathway enrichment statistics were performed using the KOBAS software (http://kobas.cbi.pku.edu.cn/home.do/) with the Fisher’s exact test, and those with p-values \u003c 0.05 were regarded as statistically significant.30,31 Furthermore, the protein–protein interaction networks were created using the online STRING database (http://string-db.org/) and visualized by Cytoscape (https://cytoscape.org/), which was widely used for analyzing the relationships between DEPs.32"}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T127","span":{"begin":265,"end":267},"obj":"Chemical"},{"id":"T128","span":{"begin":290,"end":292},"obj":"Chemical"},{"id":"T129","span":{"begin":319,"end":321},"obj":"Chemical"},{"id":"T130","span":{"begin":543,"end":550},"obj":"Chemical"},{"id":"T131","span":{"begin":1248,"end":1255},"obj":"Chemical"},{"id":"T132","span":{"begin":1256,"end":1263},"obj":"Chemical"}],"attributes":[{"id":"A127","pred":"chebi_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/CHEBI_29865"},{"id":"A128","pred":"chebi_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/CHEBI_28940"},{"id":"A129","pred":"chebi_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/CHEBI_74708"},{"id":"A130","pred":"chebi_id","subj":"T130","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A131","pred":"chebi_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A132","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"2.8 Bioinformatics Analysis\nThe data for the identified DEPs of PDCoV-infected IPEC-J2 cells were submitted to Gene Ontology (GO) Terms (http://geneontology.org/) for GO analysis, by which the DEPs were assigned into three branches of ontology—biological process (BP), cellular component (CC), and molecular function (MF). GO enrichment analysis for the DEPs was done using the Goatools software (https://github.com/tanghaibao/GOatools) with Fisher’s exact test, and those with a p-value \u003c 0.05 were thought to be significantly enriched. The protein database of clusters of Orthologous Groups (COG; http://www.ncbi.nlm.nih.gov/COG/) was also used to assign possible functions to the identified DEPs. The Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/) pathway analyses were performed to reveal the potential functions of the DEPs, which were annotated using the BlastP program of the Diamond software against the KEGG database with a cutoff E-value ≤ 1 × 10–5 and identity ≥0.98. The pathway enrichment statistics were performed using the KOBAS software (http://kobas.cbi.pku.edu.cn/home.do/) with the Fisher’s exact test, and those with p-values \u003c 0.05 were regarded as statistically significant.30,31 Furthermore, the protein–protein interaction networks were created using the online STRING database (http://string-db.org/) and visualized by Cytoscape (https://cytoscape.org/), which was widely used for analyzing the relationships between DEPs.32"}

{"project":"LitCovid-sentences","denotations":[{"id":"T85","span":{"begin":0,"end":28},"obj":"Sentence"},{"id":"T86","span":{"begin":29,"end":323},"obj":"Sentence"},{"id":"T87","span":{"begin":324,"end":538},"obj":"Sentence"},{"id":"T88","span":{"begin":539,"end":700},"obj":"Sentence"},{"id":"T89","span":{"begin":701,"end":1007},"obj":"Sentence"},{"id":"T90","span":{"begin":1008,"end":1478},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.8 Bioinformatics Analysis\nThe data for the identified DEPs of PDCoV-infected IPEC-J2 cells were submitted to Gene Ontology (GO) Terms (http://geneontology.org/) for GO analysis, by which the DEPs were assigned into three branches of ontology—biological process (BP), cellular component (CC), and molecular function (MF). GO enrichment analysis for the DEPs was done using the Goatools software (https://github.com/tanghaibao/GOatools) with Fisher’s exact test, and those with a p-value \u003c 0.05 were thought to be significantly enriched. The protein database of clusters of Orthologous Groups (COG; http://www.ncbi.nlm.nih.gov/COG/) was also used to assign possible functions to the identified DEPs. The Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/) pathway analyses were performed to reveal the potential functions of the DEPs, which were annotated using the BlastP program of the Diamond software against the KEGG database with a cutoff E-value ≤ 1 × 10–5 and identity ≥0.98. The pathway enrichment statistics were performed using the KOBAS software (http://kobas.cbi.pku.edu.cn/home.do/) with the Fisher’s exact test, and those with p-values \u003c 0.05 were regarded as statistically significant.30,31 Furthermore, the protein–protein interaction networks were created using the online STRING database (http://string-db.org/) and visualized by Cytoscape (https://cytoscape.org/), which was widely used for analyzing the relationships between DEPs.32"}

{"project":"LitCovid-PubTator","denotations":[{"id":"272","span":{"begin":65,"end":79},"obj":"Disease"},{"id":"273","span":{"begin":80,"end":87},"obj":"CellLine"}],"attributes":[{"id":"A272","pred":"tao:has_database_id","subj":"272","obj":"MESH:D007239"},{"id":"A273","pred":"tao:has_database_id","subj":"273","obj":"CVCL:2246"}],"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":"2.8 Bioinformatics Analysis\nThe data for the identified DEPs of PDCoV-infected IPEC-J2 cells were submitted to Gene Ontology (GO) Terms (http://geneontology.org/) for GO analysis, by which the DEPs were assigned into three branches of ontology—biological process (BP), cellular component (CC), and molecular function (MF). GO enrichment analysis for the DEPs was done using the Goatools software (https://github.com/tanghaibao/GOatools) with Fisher’s exact test, and those with a p-value \u003c 0.05 were thought to be significantly enriched. The protein database of clusters of Orthologous Groups (COG; http://www.ncbi.nlm.nih.gov/COG/) was also used to assign possible functions to the identified DEPs. The Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/) pathway analyses were performed to reveal the potential functions of the DEPs, which were annotated using the BlastP program of the Diamond software against the KEGG database with a cutoff E-value ≤ 1 × 10–5 and identity ≥0.98. The pathway enrichment statistics were performed using the KOBAS software (http://kobas.cbi.pku.edu.cn/home.do/) with the Fisher’s exact test, and those with p-values \u003c 0.05 were regarded as statistically significant.30,31 Furthermore, the protein–protein interaction networks were created using the online STRING database (http://string-db.org/) and visualized by Cytoscape (https://cytoscape.org/), which was widely used for analyzing the relationships between DEPs.32"}