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SC2disease: a manually curated database of single-cell transcriptome for human diseases
Tianyi Zhao1, Shuxuan Lyu2, Guilin Lu1
1School of Computer Science, Northwestern Polytechnical University, Xi'an 710072, China.
Nucleic Acids Research
|October 3, 2020
Summary
SC2disease is a new database detailing gene expression in human diseases at the single-cell level. It aids research by comparing cell types and linking genes to disease traits for better understanding of cellular heterogeneity.
Area of Science:
- Genomics
- Bioinformatics
- Cell Biology
Background:
- Single-cell RNA sequencing (scRNA-seq) enables detailed analysis of cellular heterogeneity in diseases.
- Existing resources lack comprehensive, hierarchical databases of human disease gene expression at the cellular level.
Purpose of the Study:
- To develop SC2disease, a manually curated database of gene expression profiles across cell types and diseases.
- To provide a systematic resource for studying cellular heterogeneity and cell-type-specific genes in human diseases.
Main Methods:
- Literature review of scRNA-seq studies on human diseases prior to March 2020.
- Development of the SC2disease database, summarizing data by disease, tissue, and cell type.
- Reanalysis of gene expression matrices using a unified pipeline for improved comparability.
Main Results:
- SC2disease contains 946,481 entries across 341 cell types, 29 tissues, and 25 diseases.
- Each entry includes comparisons of differentially expressed genes between cell types, tissues, and health statuses.
- Cell-type-specific genes were compared with genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) to infer trait-specific cell types.
Conclusions:
- SC2disease offers a valuable resource for understanding disease mechanisms at the cellular level.
- The database facilitates the identification of cell-type-specific disease associations.
- Integration with GWAS data provides insights into the cellular basis of disease traits.
