Dec 27, 2024
Notable advances have been made in single-cell RNA sequencing (scRNA-seq) technologies and bioinformatics tools for analyzing scRNA-seq data. These are critical for translating scRNA-seq data into biological and medical information for researchers. Standardized integrated analysis of massive cancer scRNA-seq data is crucial for better supporting cancer-related research and clinical applications. Since its initial release in 2022, CancerSCEM has been widely used in quantifying single-cell gene expression, accurate cell-type annotation, and immune activity research of cancers.
To better adapt to the continuously growing public scRNA-seq data, the research group from the China National Center for Bioinformation (CNCB) has developed CancerSCEM 2.0, an updated resource of cancer single-cell expression map. This work was published in Nucleic Acids Research titled “CancerSCEM 2.0: an updated data resource of single-cell expression map across various human cancers”.
CancerSCEM version 2.0 was launched online in June 2024. Specifically, the metadata and multidimensional analytical results of 1,466 scRNA-seq datasets have been gathered and organized. These datasets cover 127 research projects, 74 human cancer types, and eight construction protocols, and normal samples and samples from healthy peripheral blood produced by the same projects have been systematically included to enable comparative analysis. CancerSCEM 2.0 has further enhanced data analysis and visualizations by adding genome copy number variation assessment, transcription factor enrichment, pseudotime trajectory construction, and scoring seven biological features (e.g., toxicity, inflammation, and stress) at the transcriptome level. Moreover, single-cell metabolic analysis has been carried out, including mapping the distribution of raw metabolic flux, tracking dynamic changes across cell types in 168 metabolic modules and 34 KEGG pathways, and measuring the pairwise metabolic correlations.
CancerSCEM 2.0 is a specimen-centric resource offering user-friendly and well-maintained web interfaces for data browsing, inquiry, visualization, analysis, and download. CancerSCEM 2.0 has introduced a more advanced interactive online analysis platform currently in operation. The platform includes two new modules - CELL and METABOLISM - in addition to the existing GENE and SAMPLE modules, which provide seven newly added analytical functions. All functions can achieve real-time analysis and visualization at the second level. Users can use this platform to conduct multidimensional customized analysis and define cell type-specific or cancer type-specific features, serving as candidate biomarkers for future clinical practice.