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CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines
Zhi-Hui Luo1, Meng-Wei Shi2,3,4,5, Yuan Zhang2,3,4,5
1Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, P.R. China.
A new database, CenhANCER, catalogs millions of cancer enhancers and transcription factors from primary tumor tissues. This resource aids in cancer subtyping, diagnosis, and identifying potential therapeutic targets across various cancer types.
Area of Science:
- Genomics
- Cancer Biology
- Bioinformatics
Background:
- Enhancers are crucial in cancer development and have therapeutic potential.
- Analyzing cancer enhancers is challenging due to limited integrated data, especially from primary tissues.
Purpose of the Study:
- To create a comprehensive cancer enhancer profile across diverse cancer types.
- To develop an integrated database, CenhANCER, for cancer enhancer research.
Main Methods:
- Curated public H3K27ac ChIP-Seq data from 805 primary tumor tissues and 671 cell lines across 41 cancer types.
- Identified typical enhancers, super-enhancers, and enriched transcription factors.
- Annotated super-enhancers with chromatin accessibility, eQTLs, and GWAS SNPs.
Main Results:
- Identified over 57 million typical enhancers, 978,000 super-enhancers, and 226,000 transcription factors.
- Enhancers identified were consistent with accessible chromatin regions.
- Database validation confirmed high data quality, recapitulating known super-enhancers.
Conclusions:
- CenhANCER provides a high-quality resource for cancer enhancer and transcription factor analysis.
- The database facilitates single cancer analysis and comparative studies.
- Offers potential therapeutic targets for multiple cancer types.
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