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LitCovid-PD-FMA-UBERON

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T62","span":{"begin":147,"end":155},"obj":"Disease"},{"id":"T63","span":{"begin":298,"end":306},"obj":"Disease"},{"id":"T64","span":{"begin":431,"end":439},"obj":"Disease"},{"id":"T65","span":{"begin":565,"end":573},"obj":"Disease"},{"id":"T66","span":{"begin":722,"end":730},"obj":"Disease"},{"id":"T67","span":{"begin":837,"end":845},"obj":"Disease"},{"id":"T68","span":{"begin":970,"end":978},"obj":"Disease"}],"attributes":[{"id":"A62","pred":"mondo_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A63","pred":"mondo_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A64","pred":"mondo_id","subj":"T64","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A65","pred":"mondo_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A66","pred":"mondo_id","subj":"T66","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A67","pred":"mondo_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A68","pred":"mondo_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"We have found five highly significant miRs from four different countries; Turkey, Italy, Spain, and the UK; one RefSeq sequence from Wuhan and one SARS-CoV-2 genome from the VeroE6 cell line: miR-8066 (e-values; 1.6 for Wuhan, 2.8 for Valencia, 1.6 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-5197-3p (e-values; 1.6 for Wuhan, 2.1 for VeroE6 cells, 2.8 for Valencia and 1.9 for both Italy and England SARS-CoV-2 genomes), and miR-3611 (e-values; 2.8 for Wuhan, 3.3 for Valencia and 2.8 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-3934-3p (e-values; 3.4–5.0), and miR-1307-3p (e-values; 4.3–6.3). We could, however, detect a similar alignment with miR-1307-3p in SARS-CoV-2-infected Vero E6 cells. Additionally, we found that the same miR sequences exist within four genomes of SARS-CoV-2, within the lower e-values of 5.0–10.0 were miR-3691-3p and miR-1468-5p. Again, miR-3691-3p was not a positive hit in the SARS-CoV-2-infected Vero E6 cell line. All of these miR similarities to human miRs were conserved in all studied genomes. We then used DianaTools to identify the potential pathways to which these miRs contribute (Figure 1). The functional characterizations of these highly conserved miRs were analyzed with KEGG molecular pathways. The selected intersected pathways were analyzed as significant targets as p value 0.05 with threshold value 0.8 and Fisher’s Exact Test (hypergeometric distribution) calculations by miRPath version 3.0 in the microT-CDS database. As shown in Figure 1. miR-8066 and miR-5197-3p are critical on TGF-β and mucin type O-Glycan biosynthesis pathways. miR-8066 is also related to cytokine-cytokine receptor interaction. miR-5197 is significantly related to morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. These two miRs were highly conserved, and their coexistence was significant within the four-genome search. miR-3611 was the other leading miR, which possesses co-occurrence potential with miR-8066 and miR-5197 in all genomes that were effective on GABAergic synapse, morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. Although co-occurrences of miR-1468-5p and miR-1307-3p were similar to miR-3611, it was less effective on all evaluated metabolic pathways. miR-3934-3p was effective on glycosaminoglycan biosynthesis—heparan sulfate/heparin, other types of O-glycan biosynthesis, and vitamin digestion-absorption mechanisms, respectively."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T144","span":{"begin":74,"end":80},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9005"},{"id":"T145","span":{"begin":181,"end":190},"obj":"http://purl.obolibrary.org/obo/CLO_0000031"},{"id":"T146","span":{"begin":285,"end":297},"obj":"http://purl.obolibrary.org/obo/CLO_0051719"},{"id":"T147","span":{"begin":365,"end":377},"obj":"http://purl.obolibrary.org/obo/CLO_0051719"},{"id":"T148","span":{"begin":552,"end":564},"obj":"http://purl.obolibrary.org/obo/CLO_0051719"},{"id":"T149","span":{"begin":682,"end":683},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T150","span":{"begin":742,"end":755},"obj":"http://purl.obolibrary.org/obo/CLO_0051719"},{"id":"T151","span":{"begin":948,"end":949},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T152","span":{"begin":990,"end":1002},"obj":"http://purl.obolibrary.org/obo/CLO_0051719"},{"id":"T153","span":{"begin":1042,"end":1047},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T154","span":{"begin":1433,"end":1437},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"text":"We have found five highly significant miRs from four different countries; Turkey, Italy, Spain, and the UK; one RefSeq sequence from Wuhan and one SARS-CoV-2 genome from the VeroE6 cell line: miR-8066 (e-values; 1.6 for Wuhan, 2.8 for Valencia, 1.6 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-5197-3p (e-values; 1.6 for Wuhan, 2.1 for VeroE6 cells, 2.8 for Valencia and 1.9 for both Italy and England SARS-CoV-2 genomes), and miR-3611 (e-values; 2.8 for Wuhan, 3.3 for Valencia and 2.8 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-3934-3p (e-values; 3.4–5.0), and miR-1307-3p (e-values; 4.3–6.3). We could, however, detect a similar alignment with miR-1307-3p in SARS-CoV-2-infected Vero E6 cells. Additionally, we found that the same miR sequences exist within four genomes of SARS-CoV-2, within the lower e-values of 5.0–10.0 were miR-3691-3p and miR-1468-5p. Again, miR-3691-3p was not a positive hit in the SARS-CoV-2-infected Vero E6 cell line. All of these miR similarities to human miRs were conserved in all studied genomes. We then used DianaTools to identify the potential pathways to which these miRs contribute (Figure 1). The functional characterizations of these highly conserved miRs were analyzed with KEGG molecular pathways. The selected intersected pathways were analyzed as significant targets as p value 0.05 with threshold value 0.8 and Fisher’s Exact Test (hypergeometric distribution) calculations by miRPath version 3.0 in the microT-CDS database. As shown in Figure 1. miR-8066 and miR-5197-3p are critical on TGF-β and mucin type O-Glycan biosynthesis pathways. miR-8066 is also related to cytokine-cytokine receptor interaction. miR-5197 is significantly related to morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. These two miRs were highly conserved, and their coexistence was significant within the four-genome search. miR-3611 was the other leading miR, which possesses co-occurrence potential with miR-8066 and miR-5197 in all genomes that were effective on GABAergic synapse, morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. Although co-occurrences of miR-1468-5p and miR-1307-3p were similar to miR-3611, it was less effective on all evaluated metabolic pathways. miR-3934-3p was effective on glycosaminoglycan biosynthesis—heparan sulfate/heparin, other types of O-glycan biosynthesis, and vitamin digestion-absorption mechanisms, respectively."}

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T23","span":{"begin":1618,"end":1637},"obj":"http://purl.obolibrary.org/obo/GO_0000271"},{"id":"T24","span":{"begin":1625,"end":1637},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T25","span":{"begin":1776,"end":1786},"obj":"http://purl.obolibrary.org/obo/GO_0008152"},{"id":"T26","span":{"begin":1805,"end":1815},"obj":"http://purl.obolibrary.org/obo/GO_0045158"},{"id":"T27","span":{"begin":1805,"end":1815},"obj":"http://purl.obolibrary.org/obo/GO_0045157"},{"id":"T28","span":{"begin":1805,"end":1815},"obj":"http://purl.obolibrary.org/obo/GO_0045156"},{"id":"T29","span":{"begin":1805,"end":1815},"obj":"http://purl.obolibrary.org/obo/GO_0008121"},{"id":"T30","span":{"begin":2123,"end":2133},"obj":"http://purl.obolibrary.org/obo/GO_0008152"},{"id":"T31","span":{"begin":2152,"end":2162},"obj":"http://purl.obolibrary.org/obo/GO_0045158"},{"id":"T32","span":{"begin":2152,"end":2162},"obj":"http://purl.obolibrary.org/obo/GO_0045157"},{"id":"T33","span":{"begin":2152,"end":2162},"obj":"http://purl.obolibrary.org/obo/GO_0045156"},{"id":"T34","span":{"begin":2152,"end":2162},"obj":"http://purl.obolibrary.org/obo/GO_0008121"},{"id":"T35","span":{"begin":2349,"end":2379},"obj":"http://purl.obolibrary.org/obo/GO_0006024"},{"id":"T36","span":{"begin":2367,"end":2379},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T37","span":{"begin":2422,"end":2441},"obj":"http://purl.obolibrary.org/obo/GO_0000271"},{"id":"T38","span":{"begin":2429,"end":2441},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T39","span":{"begin":2455,"end":2464},"obj":"http://purl.obolibrary.org/obo/GO_0007586"}],"text":"We have found five highly significant miRs from four different countries; Turkey, Italy, Spain, and the UK; one RefSeq sequence from Wuhan and one SARS-CoV-2 genome from the VeroE6 cell line: miR-8066 (e-values; 1.6 for Wuhan, 2.8 for Valencia, 1.6 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-5197-3p (e-values; 1.6 for Wuhan, 2.1 for VeroE6 cells, 2.8 for Valencia and 1.9 for both Italy and England SARS-CoV-2 genomes), and miR-3611 (e-values; 2.8 for Wuhan, 3.3 for Valencia and 2.8 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-3934-3p (e-values; 3.4–5.0), and miR-1307-3p (e-values; 4.3–6.3). We could, however, detect a similar alignment with miR-1307-3p in SARS-CoV-2-infected Vero E6 cells. Additionally, we found that the same miR sequences exist within four genomes of SARS-CoV-2, within the lower e-values of 5.0–10.0 were miR-3691-3p and miR-1468-5p. Again, miR-3691-3p was not a positive hit in the SARS-CoV-2-infected Vero E6 cell line. All of these miR similarities to human miRs were conserved in all studied genomes. We then used DianaTools to identify the potential pathways to which these miRs contribute (Figure 1). The functional characterizations of these highly conserved miRs were analyzed with KEGG molecular pathways. The selected intersected pathways were analyzed as significant targets as p value 0.05 with threshold value 0.8 and Fisher’s Exact Test (hypergeometric distribution) calculations by miRPath version 3.0 in the microT-CDS database. As shown in Figure 1. miR-8066 and miR-5197-3p are critical on TGF-β and mucin type O-Glycan biosynthesis pathways. miR-8066 is also related to cytokine-cytokine receptor interaction. miR-5197 is significantly related to morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. These two miRs were highly conserved, and their coexistence was significant within the four-genome search. miR-3611 was the other leading miR, which possesses co-occurrence potential with miR-8066 and miR-5197 in all genomes that were effective on GABAergic synapse, morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. Although co-occurrences of miR-1468-5p and miR-1307-3p were similar to miR-3611, it was less effective on all evaluated metabolic pathways. miR-3934-3p was effective on glycosaminoglycan biosynthesis—heparan sulfate/heparin, other types of O-glycan biosynthesis, and vitamin digestion-absorption mechanisms, respectively."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":2380,"end":2395},"obj":"GlycoEpitope"}],"attributes":[{"id":"A1","pred":"glyco_epitope_db_id","subj":"T1","obj":"http://www.glycoepitope.jp/epitopes/EP0086"}],"text":"We have found five highly significant miRs from four different countries; Turkey, Italy, Spain, and the UK; one RefSeq sequence from Wuhan and one SARS-CoV-2 genome from the VeroE6 cell line: miR-8066 (e-values; 1.6 for Wuhan, 2.8 for Valencia, 1.6 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-5197-3p (e-values; 1.6 for Wuhan, 2.1 for VeroE6 cells, 2.8 for Valencia and 1.9 for both Italy and England SARS-CoV-2 genomes), and miR-3611 (e-values; 2.8 for Wuhan, 3.3 for Valencia and 2.8 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-3934-3p (e-values; 3.4–5.0), and miR-1307-3p (e-values; 4.3–6.3). We could, however, detect a similar alignment with miR-1307-3p in SARS-CoV-2-infected Vero E6 cells. Additionally, we found that the same miR sequences exist within four genomes of SARS-CoV-2, within the lower e-values of 5.0–10.0 were miR-3691-3p and miR-1468-5p. Again, miR-3691-3p was not a positive hit in the SARS-CoV-2-infected Vero E6 cell line. All of these miR similarities to human miRs were conserved in all studied genomes. We then used DianaTools to identify the potential pathways to which these miRs contribute (Figure 1). The functional characterizations of these highly conserved miRs were analyzed with KEGG molecular pathways. The selected intersected pathways were analyzed as significant targets as p value 0.05 with threshold value 0.8 and Fisher’s Exact Test (hypergeometric distribution) calculations by miRPath version 3.0 in the microT-CDS database. As shown in Figure 1. miR-8066 and miR-5197-3p are critical on TGF-β and mucin type O-Glycan biosynthesis pathways. miR-8066 is also related to cytokine-cytokine receptor interaction. miR-5197 is significantly related to morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. These two miRs were highly conserved, and their coexistence was significant within the four-genome search. miR-3611 was the other leading miR, which possesses co-occurrence potential with miR-8066 and miR-5197 in all genomes that were effective on GABAergic synapse, morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. Although co-occurrences of miR-1468-5p and miR-1307-3p were similar to miR-3611, it was less effective on all evaluated metabolic pathways. miR-3934-3p was effective on glycosaminoglycan biosynthesis—heparan sulfate/heparin, other types of O-glycan biosynthesis, and vitamin digestion-absorption mechanisms, respectively."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T112","span":{"begin":0,"end":655},"obj":"Sentence"},{"id":"T113","span":{"begin":656,"end":756},"obj":"Sentence"},{"id":"T114","span":{"begin":757,"end":920},"obj":"Sentence"},{"id":"T115","span":{"begin":921,"end":1008},"obj":"Sentence"},{"id":"T116","span":{"begin":1009,"end":1091},"obj":"Sentence"},{"id":"T117","span":{"begin":1092,"end":1193},"obj":"Sentence"},{"id":"T118","span":{"begin":1194,"end":1301},"obj":"Sentence"},{"id":"T119","span":{"begin":1302,"end":1531},"obj":"Sentence"},{"id":"T120","span":{"begin":1532,"end":1832},"obj":"Sentence"},{"id":"T121","span":{"begin":1833,"end":2179},"obj":"Sentence"},{"id":"T122","span":{"begin":2180,"end":2501},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"We have found five highly significant miRs from four different countries; Turkey, Italy, Spain, and the UK; one RefSeq sequence from Wuhan and one SARS-CoV-2 genome from the VeroE6 cell line: miR-8066 (e-values; 1.6 for Wuhan, 2.8 for Valencia, 1.6 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-5197-3p (e-values; 1.6 for Wuhan, 2.1 for VeroE6 cells, 2.8 for Valencia and 1.9 for both Italy and England SARS-CoV-2 genomes), and miR-3611 (e-values; 2.8 for Wuhan, 3.3 for Valencia and 2.8 for both Italy and England, 2.8 for VeroE6 cells SARS-CoV-2 genomes); miR-3934-3p (e-values; 3.4–5.0), and miR-1307-3p (e-values; 4.3–6.3). We could, however, detect a similar alignment with miR-1307-3p in SARS-CoV-2-infected Vero E6 cells. Additionally, we found that the same miR sequences exist within four genomes of SARS-CoV-2, within the lower e-values of 5.0–10.0 were miR-3691-3p and miR-1468-5p. Again, miR-3691-3p was not a positive hit in the SARS-CoV-2-infected Vero E6 cell line. All of these miR similarities to human miRs were conserved in all studied genomes. We then used DianaTools to identify the potential pathways to which these miRs contribute (Figure 1). The functional characterizations of these highly conserved miRs were analyzed with KEGG molecular pathways. The selected intersected pathways were analyzed as significant targets as p value 0.05 with threshold value 0.8 and Fisher’s Exact Test (hypergeometric distribution) calculations by miRPath version 3.0 in the microT-CDS database. As shown in Figure 1. miR-8066 and miR-5197-3p are critical on TGF-β and mucin type O-Glycan biosynthesis pathways. miR-8066 is also related to cytokine-cytokine receptor interaction. miR-5197 is significantly related to morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. These two miRs were highly conserved, and their coexistence was significant within the four-genome search. miR-3611 was the other leading miR, which possesses co-occurrence potential with miR-8066 and miR-5197 in all genomes that were effective on GABAergic synapse, morphine addiction and metabolism of xenobiotics by cytochrome P450 mechanisms. Although co-occurrences of miR-1468-5p and miR-1307-3p were similar to miR-3611, it was less effective on all evaluated metabolic pathways. miR-3934-3p was effective on glycosaminoglycan biosynthesis—heparan sulfate/heparin, other types of O-glycan biosynthesis, and vitamin digestion-absorption mechanisms, respectively."}

LitCovid-PubTator

PMC:7354481 / 15715-18216 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7354481 / 15715-18216 JSON TXT