allcells-pseudobulk data  (AllCells LLC)

Journal: Nature genetics

Article Title: A single-cell and spatially resolved atlas of human breast cancers

doi: 10.1038/s41588-021-00911-1

Figure Lengend Snippet: a, Bar and boxplot (inset) of the Pearson correlation for 45 cell-types between the actual cell-fractions captured by scRNA-Seq and the CIBERSORTx predicted fractions from pseudo-bulk expression profiles (*denotes significance p<0.05, two-sided correlation coefficient). Inset box plot depicts the first and third quartiles as the lower and upper bounds, respectively. The whiskers represent 1.5x the interquartile range and the centre depicts the median. b, Barplot comparing the Pearson correlation for cell-types between the actual cell-fractions captured by scRNA-Seq and the CIBERSORTx (red) and DWLS (blue) predicted fractions from pseudo-bulk expression profiles (*denotes significance p<0.05, two-sided correlation coefficient). c, Boxplot comparing the CIBERSORTx predicted scSubtype and Cycling cell-fractions in each METABRIC tumor, stratified by PAM50 subtypes (n = 1,608; 209 Basal, 224 Her2, 700 LumA and 475 LumB). Box plots depicted as described in b. d, Heatmap of ecotypes formed from the common METABRIC tumors (columns) identified from combining ecotypes generated using CIBERSORTx with all 32 significantly correlated cell-types (rows), when using CIBERSORTx on pseudo-bulk samples. e-f, Relative proportion of the PAM50 subtypes (e) and major cell-types (f) in each ecotype, when combining CIBERSORTx consensus clustering results. g-h, Kaplan-Meier (KM) plot of all patients with common tumors in each of the ecotypes (g) and patients with tumors in ecotypes E4 and E7 (h), when combining CIBERSORTx consensus clustering results. p-values calculated using the log-rank test. i-j, Relative proportion of the PAM50 molecular subtypes (i) and major cell-types (j) of the common tumors from combining CIBERSORT and DWLS generated ecotypes. k, KM plot of the patients with tumors in ecotypes E4 and E7, formed from combining CIBERSORT and DWLS generated ecotypes. p-value calculated using the log-rank test. l, Relative proportion of the METABRIC integrative cluster annotations of the tumors in each ecotype, as determined using CIBERSORTx across all cell-types.

Article Snippet: We first identified tumors that shared the same “concordant” subtype from both Allcells-Pseudobulk PAM50 calls and TCGA hierarchical clustering based subtype classifications ( Supplementary Table 3 ).

Techniques: Expressing, Generated

Journal: Nature genetics

Article Title: A single-cell and spatially resolved atlas of human breast cancers

doi: 10.1038/s41588-021-00911-1

Figure Lengend Snippet: a-b, Hierarchical Clustering of Allcells-Pseudobulk (indicated by yellow stars) and Ribozero mRNA-Seq (indicated by blue stars) profiles of the patient samples with TCGA patient mRNA-Seq data. a, View of the basal cluster showing pairing of Allcells-Pseudobulk and Ribozero mRNA-Seq profiles of 2 representative tumors (CID4495 and CID4515) in the present study. b, View of the luminal cluster showing pairing of Allcells-Pseudobulk and Ribozero mRNA-Seq profiles of 4 representative tumors (CID4067, CID4463, CID4290 and CID3948) in the present study. c, Heatmap of scSubtype gene sets across the training and test samples in each individual group. Colored outlined boxes highlighting the top expressed genes per group. d, Barplot representing proportions of scSubtype calls in individual samples. Test dataset samples are highlighted within the golden colored outline. e, Scatterplot of individual cancer cells plotted according to the Proliferation score (x-axis) and Differentiation – DScore (y-axis). Individual cells are colored based on the scSubtype calls. f, Scatterplot of individual TCGA breast tumors plotted according to the Proliferation score (x-axis) and Differentiation – DScore (y-axis). Individual patients are colored based on the PAM50 subtype calls.

Article Snippet: We first identified tumors that shared the same “concordant” subtype from both Allcells-Pseudobulk PAM50 calls and TCGA hierarchical clustering based subtype classifications ( Supplementary Table 3 ).

Techniques:

Journal: Nature genetics

Article Title: A single-cell and spatially resolved atlas of human breast cancers

doi: 10.1038/s41588-021-00911-1

Figure Lengend Snippet: Deconvolution of breast cancer cohorts using single-cell signatures reveals robust ecotypes associated with patient survival and intrinsic subtypes. a, Consensus clustering of all tumors (columns) in METABRIC showing nine robust tumor ecotypes and 4 groups of cell enrichments from 45 cell-types in the breast cancer cell taxonomy. Total 1,985 tumors (E1 = 266, E2= 269, E3 = 205, E4 = 263, E5 = 195, E6 = 215, E7 = 199, E8 = 213, E9 = 160). b, Relative proportion of the PAM50 molecular subtypes of the tumors in each ecotype. c, Relative average proportion of the major cell-types enriched in the tumors in each ecotype. d-f, Kaplan-Meier (KM) plot of the patients with tumors in each of the nine ecotypes (d), patients with tumors in ecotypes E2 and E7 (e), patients with tumors in ecotypes E4 and E7 (f). p-values calculated using the log-rank test. g, Summary of the major epithelial, immune and stromal cell types identified in this study grouped by their major (inner), minor and subset (outer) level classification tiers.

Article Snippet: We first identified tumors that shared the same “concordant” subtype from both Allcells-Pseudobulk PAM50 calls and TCGA hierarchical clustering based subtype classifications ( Supplementary Table 3 ).

Techniques: