ABC portal: a single-cell database and web server for blood cells

Abstract

ABC portal (http://abc.sklehabc.com) is a database and web portal containing 198 single-cell transcriptomic datasets of development, differentiation and disorder of blood/immune cells. All the datasets were re-annotated with a manually curated and unified single-cell reference, especially for the haematopoietic stem and progenitor cells. ABC portal provides web-based interactive analysis modules, especially a comprehensive cell-cell communication analysis and disease-related gene signature analysis. Importantly, ABC portal allows customized sample selection based on a combination of several metadata for downstream analysis and comparison analysis across datasets. ABC portal also allows users to select multiple cell types for analysis in the modules. Together, ABC portal provides an interactive interface of single-cell data exploration and re-analysis with customized analysis modules for the researchers and clinicians, and will facilitate understanding of haematopoiesis and blood/immune disorders.

Figure 1.

Scheme of ABC portal.

Figure 2.

Statistics of datasets in ABC portal. (A) Number of datasets summarized by species. (B) Number of datasets summarized by tissue source. (C) Dataset summary by types of blood disorder. (D) Number of datasets from healthy conditions summarized by lineage. (E) Dataset summary by sequencing platforms.

Figure 3.

Reference for human datasets. (A) UMAP of cell types of the integrated reference dataset. (B) Feature plots for marker genes. (C) Heat map of marker gene expression for each cell type. (D) UMAP of reference split by dataset. (E) Bar plot of cell fractions in HSPC and myeloid cells. Statistical significance determined using chi-square test; *P < 0.05; **P < 0.01; ***P < 0.001. Red asterisk, FBM versus HCA_BM; blue asterisk, FBM versus HCA_CB; green asterisk, HCA_BM versus HCA_CB.

Figure 4.

Data searching and exploration page. (A) Data searching page. (B) Data exploration page for the selected dataset. Red box highlights the switch for using consensus cell annotation. (C) Pop-up window for adding more filter conditions. (D) Data exploration page with results, metainfo and process tabs. Red box highlights the user-selected subsets of data saved for downstream analysis.

Figure 5.

UMAP module. (A) UMAP module with different coloring modes (red box). (B) UMAP of cells colored by cell types. (C) Annotated cell types of malignant cells. (D) Gene expression of DNTT highlighted in UMAP. (E) Violin plot of gene expression by sample in selected cell type.

Figure 6.

Signature expression module and LR network module. (A) Signature expression module with signatures of blood disorder-related genes (red box). (B) Signature expression comparing across cell types. (C) LR network module with three functional tabs (red box). (D) An example of LR network results. (E) LR strength from ligands of a selected cell type to receptors of other cell types.

Figure 7.

Dataset comparison page. (A) Compare page (green box). (B) Dataset selection Pop-up. (C) Cell fraction comparison. (D) Gene expression comparison for a selected gene and cell type across samples from different datasets.