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PMC:7640975 / 58420-60881 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T487 200-204 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T488 422-427 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T489 527-531 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T490 682-690 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T491 715-719 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T492 786-798 Body_part denotes nuclear pore http://purl.org/sig/ont/fma/fma63148
T493 903-919 Body_part denotes nuclear envelope http://purl.org/sig/ont/fma/fma63888
T494 1082-1086 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T495 1105-1108 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T496 1279-1282 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T497 1397-1400 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T498 1825-1828 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T499 1839-1842 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T500 1921-1924 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T501 2118-2123 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T502 2189-2193 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T503 2343-2348 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T41 794-798 Body_part denotes pore http://purl.obolibrary.org/obo/UBERON_0008915

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T109 1525-1531 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T110 1533-1556 Disease denotes cardiovascular diseases http://purl.obolibrary.org/obo/MONDO_0004995
T111 1683-1692 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T112 1702-1708 Disease denotes dengue http://purl.obolibrary.org/obo/MONDO_0005502
T113 1744-1760 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T114 1858-1867 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T115 2360-2369 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T647 191-204 http://purl.obolibrary.org/obo/CLO_0053408 denotes AKT2 and cell
T648 211-220 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T649 368-377 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T650 422-427 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T651 450-459 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T652 514-519 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T653 527-531 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T654 538-547 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T655 715-719 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T656 726-735 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T657 1001-1011 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T658 1017-1020 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T659 1082-1086 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T660 1197-1198 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T661 1244-1254 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T662 1598-1601 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T663 1666-1673 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T664 1693-1694 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T665 1695-1700 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T666 1709-1714 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T667 1716-1721 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T668 1738-1743 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T669 1761-1766 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T670 1868-1869 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T671 1870-1875 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T672 2053-2058 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T673 2082-2087 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T674 2118-2123 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T675 2253-2258 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T676 2343-2348 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T17429 682-690 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T60 870-884 Chemical denotes macromolecules http://purl.obolibrary.org/obo/CHEBI_33839
T4787 1105-1108 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T60517 1294-1296 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T62319 1397-1400 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T20667 1936-1938 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T59893 2138-2147 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T16 1525-1531 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T17 1533-1556 Phenotype denotes cardiovascular diseases http://purl.obolibrary.org/obo/HP_0001626
T18 1744-1760 Phenotype denotes immunodeficiency http://purl.obolibrary.org/obo/HP_0002721

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T352 186-190 http://purl.obolibrary.org/obo/GO_0004740 denotes PDK1
T353 200-210 http://purl.obolibrary.org/obo/GO_0007049 denotes cell cycle
T354 211-229 http://purl.obolibrary.org/obo/GO_0007165 denotes signaling pathways
T355 211-220 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T356 368-386 http://purl.obolibrary.org/obo/GO_0007165 denotes signaling pathways
T357 368-377 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T358 450-468 http://purl.obolibrary.org/obo/GO_0007165 denotes signaling pathways
T359 450-459 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T360 527-537 http://purl.obolibrary.org/obo/GO_0007049 denotes cell cycle
T361 538-555 http://purl.obolibrary.org/obo/GO_0007165 denotes signaling pathway
T362 538-547 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T363 715-725 http://purl.obolibrary.org/obo/GO_0007049 denotes cell cycle
T364 726-743 http://purl.obolibrary.org/obo/GO_0007165 denotes signaling pathway
T365 726-735 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T366 1082-1100 http://purl.obolibrary.org/obo/GO_0008283 denotes cell proliferation
T367 1105-1115 http://purl.obolibrary.org/obo/GO_0006281 denotes DNA repair
T368 1136-1142 http://purl.obolibrary.org/obo/GO_0016538 denotes cyclin
T369 1165-1178 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T370 1228-1243 http://purl.obolibrary.org/obo/GO_0006351 denotes transcriptional
T371 1397-1407 http://purl.obolibrary.org/obo/GO_0006281 denotes DNA repair
T372 1412-1421 http://purl.obolibrary.org/obo/GO_0097194 denotes apoptosis
T373 1412-1421 http://purl.obolibrary.org/obo/GO_0006915 denotes apoptosis
T374 1561-1578 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T375 1561-1578 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T376 1958-1977 http://purl.obolibrary.org/obo/GO_0019083 denotes viral transcription
T377 1964-1977 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T378 2024-2037 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T379 2189-2207 http://purl.obolibrary.org/obo/GO_0009299 denotes mRNA transcription
T380 2194-2207 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T340 0-230 Sentence denotes Finally, we sought to uncover the hidden interaction networks among the DEPs using STRING analysis, and discovered three major functional networks consisting of the RIG-I-like receptor, PDK1-AKT2 and cell cycle signaling pathways.
T341 231-428 Sentence denotes These findings are in accordance with the results of KEGG pathway analysis, thus further consolidating the credibility of these putative signaling pathways involved in PDCoV-infected IPEC-J2 cells.
T342 429-556 Sentence denotes Given the former two signaling pathways have already been discussed earlier, we next focus on the cell cycle signaling pathway.
T343 557-744 Sentence denotes As can be seen from the network diagram (Figure 6), three small networks with NUP37, SMARCA2, and CDK9 as the respective hub proteins together constitute the cell cycle signaling pathway.
T344 745-2099 Sentence denotes NUP37 is an important constituent of the nuclear pore Nup107–160 subcomplex, which controls the bidirectional trafficking of macromolecules that traverse the nuclear envelope.72 SMARCA2 is an important member of the SWI/SNF family with helicase and ATPase activities, and has been shown to regulate numerous biological processes such as cell proliferation and DNA repair.73 CDK9 paired with cyclin T1 forms the positive transcription elongation factor b (p-TEFb) complex and induces transcriptional activation by hyperphosphorylating RNA polymerase II, and thereby regulating numerous vital cellular functions including proliferation, differentiation, DNA repair and apoptosis.74,75 However, growing studies suggest that CDK9 is also related to many pathologic processes, such as cancer, cardiovascular diseases and viral replication.74 Currently, CDK9 has been demonstrated to be involved in the replication of multiple viruses, such as influenza A virus, dengue virus, human adenovirus, and human immunodeficiency virus.75 For example, CDK9 was found to interact with the viral RNA-dependent RNA polymerases of influenza A virus and facilitate its association with cellular RNA polymerase II, thereby promoting viral transcription.76 CDK9 was also shown to be critical for the transcription of viral early genes and the replication of human adenovirus.
T345 2100-2461 Sentence denotes Treatment of host cells with the CDK9 inhibitor, FIT-039, which functions by suppressing mRNA transcription, can efficiently inhibits the replication of human adenovirus.77 In the present study, CDK9 was significantly downregulated in IPEC-J2 cells upon PDCoV infection; however, the biological functions hidden behind this change warrant further investigation.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1163 186-190 Gene denotes PDK1 Gene:5163
1164 191-195 Gene denotes AKT2 Gene:208
1165 635-640 Gene denotes NUP37 Gene:79023
1166 642-649 Gene denotes SMARCA2 Gene:6595
1167 655-659 Gene denotes CDK9 Gene:100307051
1168 745-750 Gene denotes NUP37 Gene:79023
1169 799-805 Gene denotes Nup107 Gene:57122
1170 923-930 Gene denotes SMARCA2 Gene:6595
1171 1119-1123 Gene denotes CDK9 Gene:100307051
1172 1136-1145 Gene denotes cyclin T1 Gene:904
1173 1466-1470 Gene denotes CDK9 Gene:100307051
1174 1593-1597 Gene denotes CDK9 Gene:1025
1175 1783-1787 Gene denotes CDK9 Gene:1025
1176 1981-1985 Gene denotes CDK9 Gene:1025
1177 2133-2137 Gene denotes CDK9 Gene:1025
1178 2295-2299 Gene denotes CDK9 Gene:100307051
1179 981-989 Gene denotes helicase Gene:164045
1180 1683-1700 Species denotes influenza A virus Tax:11320
1181 1702-1714 Species denotes dengue virus Tax:12637
1182 1716-1732 Species denotes human adenovirus Tax:1907210
1183 1738-1766 Species denotes human immunodeficiency virus Tax:12721
1184 1858-1875 Species denotes influenza A virus Tax:11320
1185 2082-2098 Species denotes human adenovirus Tax:1907210
1186 2253-2269 Species denotes human adenovirus Tax:1907210
1187 2149-2156 Chemical denotes FIT-039 MESH:C000595272
1188 399-413 Disease denotes PDCoV-infected MESH:D007239
1189 1525-1531 Disease denotes cancer MESH:D009369
1190 1533-1556 Disease denotes cardiovascular diseases MESH:D002318
1191 2360-2369 Disease denotes infection MESH:D007239
1192 414-421 CellLine denotes IPEC-J2 CVCL:2246
1193 2335-2342 CellLine denotes IPEC-J2 CVCL:2246