LitCovid-sentences  

PMC:7371427 / 9641-22061 JSONTXT 12 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T53 0-9 Sentence denotes Figure 2.
T54 11-114 Sentence denotes Triangulation of knowledge synthesis with ACE2 expression profile by scRNAseq across cells and tissues.
T55 115-326 Sentence denotes Scatterplot shows comparison of percentage of cells with non-zero expression (x-axis) against literature-derived associations: local score (y-axis and size of circles) and global score (transparency of circles).
T56 327-446 Sentence denotes Data includes cell types identified from ~1.8 million human cells and 462,000 mouse cells cumulatively from 72 studies.
T57 447-476 Sentence denotes Figure 2—figure supplement 1.
T58 478-551 Sentence denotes ACE2 expression in cell types from murine and human pancreas by scRNAseq.
T59 552-890 Sentence denotes (A) Ace2 expression in pancreatic cell types from the Tabula Muris study (Tabula Muris Consortium et al., 2018), including polypeptide (gamma) and alpha cells. (B) ACE2 expression in pancreatic cell types from human samples (Muraro et al., 2016; Segerstolpe et al., 2016; Grün et al., 2016), with notable absence in gamma and alpha cells.
T60 891-920 Sentence denotes Figure 2—figure supplement 2.
T61 922-1001 Sentence denotes Multimodal analysis of ACE2 expression using bulk RNA-seq, proteomics, and IHC.
T62 1002-1071 Sentence denotes (A) ACE2 expression by bulk RNA-seq across healthy tissues from GTEx.
T63 1072-1520 Sentence denotes Gray box highlights the tissues with highest expression including small intestine and kidney; green arrow indicates lung. (B–C) Expression of ACE2 and other coronavirus receptors by proteomics across over 20 healthy human tissues from the Human Proteome Map (B) and the Human Protein Atlas (C). (D) IHC stained images showing ACE2 expression in the kidney, small intestine, and colon, with minimal or low expression detected in respiratory tissues.
T64 1521-1550 Sentence denotes Figure 2—figure supplement 3.
T65 1552-1682 Sentence denotes ACE2, DPP4, and ANPEP show similar expression profiles in the renal proximal tubule epithelial cells by scRNAseq and bulk RNA-seq.
T66 1683-1905 Sentence denotes (A–C) Cosine similarities between gene expression vectors of all genes and ACE2 (A), DPP4 (B), and ANPEP (C) among all annotated proximal tubule epithelial cells from a human kidney scRNAseq dataset (Stewart et al., 2019).
T67 1906-2144 Sentence denotes ACE2, DPP4, and ANPEP are reciprocally among the most similar genes to each other. (D–F) Analysis of Pearson correlation coefficients between all genes and ACE2 (D), DPP4 (E), and ANPEP (F) from human kidney cortex samples (GTEx; n = 85).
T68 2145-2239 Sentence denotes ACE2, DPP4, and ANPEP are reciprocally among the most strongly correlated genes to each other.
T69 2240-2269 Sentence denotes Figure 2—figure supplement 4.
T70 2271-2324 Sentence denotes Overview of nferX Single Cell platform functionality.
T71 2325-2533 Sentence denotes Use case shows results for a query of Ins1 in the Tabula Muris study. (A) Violin Plot section shows that pancreatic beta cells express Ins1 at the highest level among 148 annotated cell types from 18 tissues.
T72 2534-2748 Sentence denotes Summary statistics for each row indicate the percent of cells within a given cluster expressing Ins1, the mean expression of Ins1 in that cluster, and a metric of expression specificity (Cohen’s D) to each cluster.
T73 2749-3015 Sentence denotes On the left side of the table, ‘Signals’ columns highlight literature-derived associations between Ins1 and the tissue (‘pancreas’) or cell type (e.g. ‘pancreatic beta cells’). (B) Dimensionality reduction-based visualization of all ~100,600 cells from Tabula Muris.
T74 3016-3335 Sentence denotes Left-sided plot colors cells (points) based on Ins1 expression in the individual cell; right-sided plot colors cells based on a selected metadata variable (here, tissue of origin). (C) List of cluster-defining genes for a selected cell population - by default, any cell population which highly expresses the query gene.
T75 3336-3420 Sentence denotes Here, cluster-defining genes for pancreatic beta cells include Ins1, Ins2, and Iapp.
T76 3421-3541 Sentence denotes Blue box highlights functionality to triangulate such cluster-defining gene lists with any literature query of interest.
T77 3542-3571 Sentence denotes Figure 2—figure supplement 5.
T78 3573-3662 Sentence denotes Assessment of DPP4, ANPEP, and TMPRSS2 across healthy tissues using bulk RNA-seq and IHC.
T79 3663-4087 Sentence denotes (A–C) GTEx tissues with highest expression observed for DPP4 (A), ANPEP (B), and TMPRSS2 (C). (D) Assessment of ACE2 expression along with other coronavirus receptors in non-GTEx tissues from the Janssen BodyMap dataset (bulk RNA-seq). (E) IHC staining showing that DPP4 and ANPEP are apically expressed in the small intestine (top), while DPP4, ANPEP, and TMPRSS2 are all expressed apically in renal tubular cells (bottom).
T80 4088-4117 Sentence denotes Figure 2—figure supplement 6.
T81 4119-4208 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in the adult and fetal human kidney.
T82 4209-4572 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, G) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B, H) from adult (A–B) and fetal (G–H) human kidney samples (Stewart et al., 2019). (C–F) Violin plot visualization of gene expression for ACE2 (C), TMPRSS2 (D), ANPEP (E), and DPP4 (F) in adult human kidney scRNAseq dataset.
T83 4573-4674 Sentence denotes Automated literature synthesis highlights strong associations of ACE2, DPP4, and ANPEP to the kidney.
T84 4675-4704 Sentence denotes Figure 2—figure supplement 7.
T85 4706-4789 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in the human and murine heart.
T86 4790-5144 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, C, E) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B, D, F) from multiple studies: (A–B) human heart (Wang et al., 2020b), (C–D) murine heart from Tabula Muris (Tabula Muris Consortium et al., 2018), and (E–F) murine heart from Mouse Cell Atlas (Han et al., 2018).
T87 5145-5174 Sentence denotes Figure 2—figure supplement 8.
T88 5176-5247 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in adipose tissue.
T89 5248-5933 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, C, E) and corresponding expression levels of Ace2, Dpp4, Anpep and Tmprss2 (B, D, F) from multiple studies: (A–B) adipose stromovascular fraction from mice treated with PBS or a beta-3 adrenergic agonist (Rajbhandari and Arneson, 2019), (C–D) murine adipose stromovascular fraction from Tabula Muris (Tabula Muris Consortium et al., 2018), and (E–F) adipose tissue from mice subjected to 24 hr of cold shock and processed for single nucleus RNA-sequencing (Rajbhandari and Arneson, 2019). (G–H) Identification of adipocytes as the most likely ACE2-expressing cell type in adipose tissue based on literature associations.
T90 5934-6168 Sentence denotes The query shown is from the nferX Signals platform and effectively extracts any textual fragments which contain [‘ACE2’ or its gene synonyms] AND [displayed terms related to gene expression/protein detection] AND [‘adipose’ OR 'fat'].
T91 6169-6402 Sentence denotes Among these textual fragments, we extract the tokens which represent cell types and calculate enrichments of each cell type among these fragments, normalized by the number of occurrences of this cell type elsewhere in the literature.
T92 6403-6432 Sentence denotes Figure 2—figure supplement 9.
T93 6434-6518 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in the human and murine testis.
T94 6519-6796 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, C) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B, D) from multiple studies: (A–B) adult human testis (Guo et al., 2018), and (C–D) murine testis from Mouse Cell Atlas (Han et al., 2018).
T95 6797-6827 Sentence denotes Figure 2—figure supplement 10.
T96 6829-6912 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in the human and murine ovary.
T97 6913-7188 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, C) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B, D) from multiple studies: (A–B) adult human ovary (Fan et al., 2019), and (C–D) murine ovary from Mouse Cell Atlas (Han et al., 2018).
T98 7189-7219 Sentence denotes Figure 2—figure supplement 11.
T99 7221-7324 Sentence denotes IHC images of coronavirus receptors in healthy pancreas and liver samples from the Human Protein Atlas.
T100 7325-7859 Sentence denotes (A–B) ACE2 expression on the apical surface of gallbladder epithelial cells (A) and on ductal surfaces in the pancreas (B). (C) ANPEP is expressed on apical membranes in pancreatic acini and ducts. (D) TMPRSS2 is expressed on apical membranes in pancreatic acini and ducts. (E) DPP4 is expressed weakly in the pancreas, both on ductal surfaces and in endocrine islets. (F) DPP4 expression in healthy liver. (G) ANPEP expression in healthy liver; ANPEP appears to be the most strongly expressed coronavirus receptor in the human liver.
T101 7860-7890 Sentence denotes Figure 2—figure supplement 12.
T102 7892-7977 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in the human liver and pancreas.
T103 7978-8308 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, C) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B, D) from multiple studies: (A–B) human liver (Aizarani et al., 2019), and (C–D) three integrated studies of human pancreas (Muraro et al., 2016; Segerstolpe et al., 2016; Grün et al., 2016).
T104 8309-8339 Sentence denotes Figure 2—figure supplement 13.
T105 8341-8434 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in human blood, spleen, and bone marrow.
T106 8435-8782 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, C, E) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B, D, F) from multiple studies: (A–B) human peripheral blood mononuclear cells (Single Cell Portal, 2020b), (C–D) human spleen (Madissoon et al., 2020), and (E–F) human bone marrow (Data Browser HCA, 2020).
T107 8783-8813 Sentence denotes Figure 2—figure supplement 14.
T108 8815-8910 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in murine spleen, bone marrow, and thymus.
T109 8911-9195 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, C, E) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B, D, F) from multiple tissues in the Tabula Muris study (Tabula Muris Consortium et al., 2018): (A–B) spleen, (C–D) bone marrow, (E–F) thymus.
T110 9196-9226 Sentence denotes Figure 2—figure supplement 15.
T111 9228-9322 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in human and murine bladder and prostate.
T112 9323-9730 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, C, E, G) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B, D, F, H) from multiple studies: (A–B) human bladder (Yu et al., 2019), (C–D) murine bladder from Tabula Muris (Tabula Muris Consortium et al., 2018), (E–F) murine bladder from Mouse Cell Atlas (Han et al., 2018), and (G–H) human prostate and prostatic urethra.
T113 9731-9761 Sentence denotes Figure 2—figure supplement 16.
T114 9763-9837 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in the murine uterus.
T115 9838-10045 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B) in uterus-derived cells from the Mouse Cell Atlas (Han et al., 2018).
T116 10046-10076 Sentence denotes Figure 2—figure supplement 17.
T117 10078-10182 Sentence denotes Single-cell RNAseq analysis of coronavirus receptors in human and murine central nervous system tissues.
T118 10183-10553 Sentence denotes UMAP-based dimensionality reduction plot denoting cell types (A, C, E) and corresponding expression levels of ACE2, DPP4, ANPEP and TMPRSS2 (B, D, F) in CNS samples from multiple studies: (A–B) murine brain from Tabula Muris (Tabula Muris Consortium et al., 2018), (C–D) murine brain from Mouse Cell Atlas (Han et al., 2018), and (E–F) human retina (Menon et al., 2019).
T119 10554-10584 Sentence denotes Figure 2—figure supplement 18.
T120 10586-10640 Sentence denotes IHC analysis of DPP4 expression in human brain cortex.
T121 10641-10773 Sentence denotes Images from the Human Protein Atlas showing brain cortex samples from three different individuals stained to assess DPP4 expression.
T122 10774-10843 Sentence denotes Staining is notably absent from all cell types in all samples tested.
T123 10844-10874 Sentence denotes Figure 2—figure supplement 19.
T124 10876-10965 Sentence denotes Association of age with ACE2 expression and co-administered drugs with COVID-19 outcomes.
T125 10966-11544 Sentence denotes (A) Among GTEx transverse colon samples (n = 405), ACE2 expression tends to be higher in samples derived from younger individuals. (B) Among GTEx gastroesophageal junction samples, ACE2 expression tends to be higher in samples derived from older individuals. (C) Analysis of differential adverse events between ACE inhibitors and other classes of antihypertensive medications (example shown for beta-blockers), real-world evidence shows that patients taking ACE inhibitors are more likely to experience angioedema of various tissues including the small intestine and epiglottis.
T126 11545-11575 Sentence denotes Figure 2—figure supplement 20.
T127 11577-11658 Sentence denotes Characterization of oral epithelium cluster-defining genes from Xu et al., 2020b.
T128 11659-11819 Sentence denotes From a non-public scRNAseq study, oral mucosal epithelial cells (including tongue-derived epithelial cells) were defined by expression of SFN, KRT6A, and KRT10.
T129 11820-11970 Sentence denotes Assessment of SFN (A), KRT6A (B), and KRT10 (C) expression in tongue cells sequenced in the Tabula Muris study (Tabula Muris Consortium et al., 2018).
T130 11971-12089 Sentence denotes Each gene is most strongly expressed in murine tongue keratinocytes, with expression in basal epidermal cells as well.
T131 12090-12120 Sentence denotes Figure 2—figure supplement 21.
T132 12122-12219 Sentence denotes Expression of ACE2 in respiratory tract associated samples from GEO in comparison to Lung (GTEx).
T133 12220-12369 Sentence denotes Plots showing the comparison expression distribution of ACE2 between samples from lung (GTEx in purple) and samples from four GEO studies (in green).
T134 12370-12420 Sentence denotes The GEO identifiers for each comparison are shown.