CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines. Database (Oxford) 2023 May 18;2023
Date
05/19/2023Pubmed ID
37207350Pubmed Central ID
PMC10198702DOI
10.1093/database/baad022Scopus ID
2-s2.0-85159723701 (requires institutional sign-in at Scopus site) 6 CitationsAbstract
Enhancers, which are key tumorigenic factors with wide applications for subtyping, diagnosis and treatment of cancer, are attracting increasing attention in the cancer research. However, systematic analysis of cancer enhancers poses a challenge due to the lack of integrative data resources, especially those from tumor primary tissues. To provide a comprehensive enhancer profile across cancer types, we developed a cancer enhancer database CenhANCER by curating public resources including all the public H3K27ac ChIP-Seq data from 805 primary tissue samples and 671 cell line samples across 41 cancer types. In total, 57 029 408 typical enhancers, 978 411 super-enhancers and 226 726 enriched transcription factors were identified. We annotated the super-enhancers with chromatin accessibility regions, cancer expression quantitative trait loci (eQTLs), genotype-tissue expression eQTLs and genome-wide association study risk single nucleotide polymorphisms (SNPs) for further functional analysis. The identified enhancers were highly consistent with accessible chromatin regions in the corresponding cancer types, and all the 10 super-enhancer regions identified from one colorectal cancer study were recapitulated in our CenhANCER, both of which testified the high quality of our data. CenhANCER with high-quality cancer enhancer candidates and transcription factors that are potential therapeutic targets across multiple cancer types provides a credible resource for single cancer analysis and for comparative studies of various cancer types. Database URL http://cenhancer.chenzxlab.cn/.
Author List
Luo ZH, Shi MW, Zhang Y, Wang DY, Tong YB, Pan XL, Cheng SAuthor
Jake Luo Ph.D. Associate Professor; Director, Center for Biomedical Data and Language Processing (BioDLP) in the Health Informatics & Administration department at University of Wisconsin - MilwaukeeMESH terms used to index this publication - Major topics in bold
Cell LineChromatin
Enhancer Elements, Genetic
Genome-Wide Association Study
Humans
Neoplasms
Transcription Factors
