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scCancerExplorer: a comprehensive database for interactively exploring single-cell multi-omics data of human
Changzhi Huang1,2, Zekai Liu1, Yunlei Guo1
1State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China.
Nucleic Acids Research
|November 18, 2024
Summary
scCancerExplorer is a new database for exploring single-cell multi-omics cancer data. It integrates genomic, epigenomic, and transcriptomic data for 50 cancer types, aiding cancer research.
Area of Science:
- Cancer Biology
- Genomics
- Epigenetics
- Transcriptomics
- Bioinformatics
Background:
- Genomic, epigenomic, and transcriptomic alterations are key features of cancer.
- Epigenetic regulation is crucial in cancer development and progression.
- Single-cell epigenome data offers new avenues for cancer research, but integrated databases are lacking.
Purpose of the Study:
- To develop a comprehensive, user-friendly database for interactive exploration of single-cell multi-omics data in human pan-cancer.
- To address the gap in existing databases for single-cell epigenome data analysis.
- To facilitate the investigation of gene expression, chromatin accessibility, DNA methylation, and genomic variations across 50 cancer types.
Main Methods:
- Development of scCancerExplorer, a database integrating single-cell genome, epigenome (chromatin accessibility, DNA methylation), and transcriptome data.
- Implementation of five interactive modules: Integrated multi-omics analysis, Single-cell transcriptome, Single-cell epigenome, Single-cell genome, and TCGA analysis.
- Inclusion of functionalities for analyzing gene expression, transcription factor activity, DNA methylation, copy number variations, and TCGA survival data.
Main Results:
- scCancerExplorer provides interactive exploration of single-cell multi-omics data for 50 human cancer types.
- The database enables users to investigate gene expression, chromatin accessibility, DNA methylation, copy number variations, and transcription factor activity.
- Users can perform TCGA survival analysis directly within the platform.
Conclusions:
- scCancerExplorer is a novel database that bridges the gap between complex single-cell multi-omics data and researchers.
- Its rich, interactive functions distinguish it from previous resources, facilitating deeper insights into pan-cancer single-cell data.
- The database is expected to accelerate progress in cancer research by enabling easier access and analysis of multi-omics data.
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