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PMC:7354481 / 11561-15193 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T70 30-36 Body_part denotes Genome http://purl.org/sig/ont/fma/fma84116
T71 62-68 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T72 320-326 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T73 657-662 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T74 909-915 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T75 1009-1011 Body_part denotes V3 http://purl.org/sig/ont/fma/fma13442
T76 1312-1318 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T77 1626-1630 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T78 1754-1758 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T79 2097-2101 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T80 2144-2148 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T81 2470-2476 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T82 3183-3187 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T12 1626-1630 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T47 51-59 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 136-140 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T49 309-317 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 582-590 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 898-906 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 1645-1653 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 1717-1725 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 2499-2503 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408
T55 2720-2723 Disease denotes MDS http://purl.obolibrary.org/obo/MONDO_0009532|http://purl.obolibrary.org/obo/MONDO_0018881
T57 2984-2987 Disease denotes PAM http://purl.obolibrary.org/obo/MONDO_0018959

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T108 418-424 http://purl.obolibrary.org/obo/NCBITaxon_9005 denotes Turkey
T109 434-440 http://purl.obolibrary.org/obo/NCBITaxon_9005 denotes Turkey
T110 580-581 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 614-615 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 649-662 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T113 691-697 http://purl.obolibrary.org/obo/NCBITaxon_9005 denotes Turkey
T114 920-925 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T115 1009-1011 http://purl.obolibrary.org/obo/CLO_0050428 denotes V3
T116 1087-1095 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T117 1626-1630 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T118 1626-1630 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T119 1749-1753 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T120 1749-1753 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T121 1749-1753 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T122 1749-1753 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T123 1749-1753 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T124 1749-1753 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T125 1749-1753 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T126 1749-1753 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T127 1754-1764 http://purl.obolibrary.org/obo/CLO_0000031 denotes cell lines
T128 2097-2107 http://purl.obolibrary.org/obo/CLO_0000031 denotes cell lines
T129 2111-2112 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 2144-2154 http://purl.obolibrary.org/obo/CLO_0000031 denotes cell lines
T131 2254-2255 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 2457-2469 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Homo sapiens
T133 2505-2507 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T134 2903-2908 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T135 2959-2964 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T136 3183-3187 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T137 3512-3514 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T138 3578-3579 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T139 3598-3603 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T20 1518-1525 Chemical denotes Pathway http://purl.obolibrary.org/obo/CHEBI_34922
T21 2984-2987 Chemical denotes PAM http://purl.obolibrary.org/obo/CHEBI_51135|http://purl.obolibrary.org/obo/CHEBI_60882

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T72 0-2 Sentence denotes 2.
T73 3-23 Sentence denotes Material and Methods
T74 25-29 Sentence denotes 2.1.
T75 30-46 Sentence denotes Genome Sequences
T76 47-304 Sentence denotes The SARS-CoV-2 genome sequences from China, Italy, Spain (Valencia), and those for MERS, SARS, OC43 and 229E were obtained from NCBI (GenBank: NC_045512.2, LC528232.1, MT066156.1, MT198652.2, KT225476.2, NC_004718.3, NC_006213.1, NC_002645.1, respectively).
T77 305-566 Sentence denotes The SARS-CoV-2 genome sequences from England (hCoV-19/England/20136087804/2020|EPI_ISL_420910, no treatment) and Turkey (hCoV-19/Turkey/GLAB-CoV008/2020) were obtained from the China National Bioinformatics Center, GISAID database [23] (https://www.gisaid.org).
T78 567-789 Sentence denotes In addition, a SARS-CoV-2 strain isolated from a Turkish patient, and infected to Vero E6 cells passage 4 sequence (hCoV-19/Turkey/ERAGEM-001/2020;) was used for alignment studies with the miRBase mature miRNA search tool.
T79 791-810 Sentence denotes 2.2. miR Prediction
T80 811-989 Sentence denotes The miRTarget and miRBase programmes were used to predict the similarities between the SARS-CoV-2 genome and human miRs; e-value <10 and score >70 were considered as significant.
T81 990-1135 Sentence denotes DianaTools miRPath V3 were then used to create heat maps for pathways affected by selected miRs, focusing on the microT-CDS version 5.0 database.
T82 1136-1196 Sentence denotes The p value threshold was 0.05 and microT threshold was 0.8.
T83 1197-1254 Sentence denotes Heatmap analysis was done with pathway intersection [24].
T84 1256-1260 Sentence denotes 2.3.
T85 1261-1305 Sentence denotes Mutational Analysis of Potential miRNA Sites
T86 1306-1511 Sentence denotes Viral genome sequencing data was obtained from the GISAID database (https://www.gisaid.org), and analysed as multiple sequence alignments using the Clustal Omega at EBI (www.ebi.ac.uk/Tools/msa/clustalo/).
T87 1513-1517 Sentence denotes 2.4.
T88 1518-1534 Sentence denotes Pathway Analysis
T89 1535-1765 Sentence denotes Bioproject data was obtained from PRJNA615032 bioproject trancriptome data, which includes lung biopsies from SARS-CoV-2-infected patients and healthy volunteers as well as mock and SARS-CoV-2-transfected NHEB and A549 cell lines.
T90 1766-1924 Sentence denotes The data have been deposited with links to BioProject accession number PRJNA615032 in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/).
T91 1925-2001 Sentence denotes All the selected data were reanalysed at the Rosalind bioinformatics server.
T92 2002-2186 Sentence denotes Data analysis was performed according to 1.5 fold change between untransfected and transfected cell lines in a data pool calculation for both cell lines at p < 0.05 significance level.
T93 2187-2342 Sentence denotes Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA, USA).
T94 2343-2382 Sentence denotes Reads were trimmed using cutadapt [25].
T95 2383-2430 Sentence denotes Quality scores were assessed using FastQC [26].
T96 2431-2509 Sentence denotes Reads were aligned to the Homo sapiens genome built by GRCh38 using STAR [27].
T97 2510-2644 Sentence denotes Individual sample reads were quantified using HTseq [28] and normalized via relative log expression (RLE) using DESeq2 R library [29].
T98 2645-2785 Sentence denotes Read distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC [30].
T99 2786-2888 Sentence denotes DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
T100 2889-3106 Sentence denotes Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (partitioning around medoids) method using the fpc R library (https://cran.r-project.org/web/packages/fpc/index.html).
T101 3107-3237 Sentence denotes Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies.
T102 3238-3383 Sentence denotes The topGO R library [31], was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction.
T103 3384-3539 Sentence denotes Several database sources were referenced for enrichment analysis, including Interpro [32], NCBI [33], MSigDB [34,35], REACTOME [36], and WikiPathways [37].
T104 3540-3632 Sentence denotes Enrichment was calculated relative to a set of background genes relevant for the experiment.

2_test

Id Subject Object Predicate Lexical cue
32512929-24935956-144200712 537-539 24935956 denotes 23
32512929-28382917-144200713 1250-1252 28382917 denotes 24
32512929-25977294-144200714 2378-2380 25977294 denotes 25
32512929-23104886-144200715 2563-2565 23104886 denotes 28
32512929-25260700-144200716 2640-2642 25260700 denotes 29
32512929-25516281-144200717 2781-2783 25516281 denotes 30
32512929-22743226-144200718 3259-3261 22743226 denotes 31
32512929-30398656-144200719 3481-3483 30398656 denotes 33
32512929-19854944-144200720 3494-3496 19854944 denotes 34
32512929-29145629-144200721 3535-3537 29145629 denotes 37

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
199 51-61 Species denotes SARS-CoV-2 Tax:2697049
200 309-319 Species denotes SARS-CoV-2 Tax:2697049
201 351-358 Species denotes hCoV-19 Tax:2697049
202 418-424 Species denotes Turkey Tax:9103
203 426-433 Species denotes hCoV-19 Tax:2697049
204 434-440 Species denotes Turkey Tax:9103
205 582-592 Species denotes SARS-CoV-2 Tax:2697049
206 624-631 Species denotes patient Tax:9606
207 683-690 Species denotes hCoV-19 Tax:2697049
208 691-697 Species denotes Turkey Tax:9103
209 142-146 Species denotes OC43 Tax:31631
210 151-155 Species denotes 229E Tax:11137
211 446-449 Species denotes CoV Tax:11118
212 130-134 Disease denotes MERS MESH:D018352
213 637-645 Disease denotes infected MESH:D007239
216 898-908 Species denotes SARS-CoV-2 Tax:2697049
217 920-925 Species denotes human Tax:9606
219 1471-1474 Gene denotes EBI Gene:6907
226 2499-2503 Gene denotes STAR Gene:6770
227 1665-1673 Species denotes patients Tax:9606
228 1717-1727 Species denotes SARS-CoV-2 Tax:2697049
229 2457-2469 Species denotes Homo sapiens Tax:9606
230 1645-1664 Disease denotes SARS-CoV-2-infected MESH:C000657245
231 1749-1753 CellLine denotes A549 CVCL:0023