1. MethHC 2.0: information repository of DNA methylation and gene expression in human cancer
- Author
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Jia-Tong Xu, Pei-Yi Xu, Ying Zhou, Hsi-Yuan Huang, Xin-Yi Chen, Si-Yuan Ding, Yi-Gang Chen, Yun Tang, Hsien Da Huang, Si-yao Hu, Meng-Fan Luo, Xin Li, Hsiao Chin Hong, Hua-Li Zuo, Chen-Nan Jin, Yi-Xian Huang, Yue-Yang Xie, Yang-Chi-Dung Lin, Zhe-Yuan Zhou, Jing Li, and Le-Shan Zhao
- Subjects
DNA Copy Number Variations ,AcademicSubjects/SCI00010 ,Computational biology ,Biology ,Circulating Tumor DNA ,Epigenesis, Genetic ,03 medical and health sciences ,0302 clinical medicine ,Neoplasms ,Databases, Genetic ,Biomarkers, Tumor ,Genetics ,medicine ,Humans ,Database Issue ,Copy-number variation ,Epigenetics ,Gene ,030304 developmental biology ,Regulation of gene expression ,Internet ,0303 health sciences ,Microarray analysis techniques ,High-Throughput Nucleotide Sequencing ,Cancer ,Molecular Sequence Annotation ,Epigenome ,DNA Methylation ,Microarray Analysis ,medicine.disease ,Gene Expression Regulation, Neoplastic ,Enhancer Elements, Genetic ,030220 oncology & carcinogenesis ,Mutation ,DNA methylation ,Disease Progression ,Transcriptome ,Software - Abstract
DNA methylation is an important epigenetic regulator in gene expression and has several roles in cancer and disease progression. MethHC version 2.0 (MethHC 2.0) is an integrated and web-based resource focusing on the aberrant methylomes of human diseases, specifically cancer. This paper presents an updated implementation of MethHC 2.0 by incorporating additional DNA methylomes and transcriptomes from several public repositories, including 33 human cancers, over 50 118 microarray and RNA sequencing data from TCGA and GEO, and accumulating up to 3586 manually curated data from >7000 collected published literature with experimental evidence. MethHC 2.0 has also been equipped with enhanced data annotation functionality and a user-friendly web interface for data presentation, search, and visualization. Provided features include clinical-pathological data, mutation and copy number variation, multiplicity of information (gene regions, enhancer regions, and CGI regions), and circulating tumor DNA methylation profiles, available for research such as biomarker panel design, cancer comparison, diagnosis, prognosis, therapy study and identifying potential epigenetic biomarkers. MethHC 2.0 is now available at http://awi.cuhk.edu.cn/∼MethHC.
- Published
- 2020