MethHC: a database of DNA methylation and gene expression in human cancer

Wei-Yun Huang; Sheng-Da Hsu; Hsi-Yuan Huang; Yi-Ming Sun; Chih-Hung Chou; Shun-Long Weng; Hsien-Da Huang

doi:10.1093/nar/gku1151

MethHC: a database of DNA methylation and gene expression in human cancer

Nucleic Acids Res. 2015 Jan;43(Database issue):D856-61. doi: 10.1093/nar/gku1151. Epub 2014 Nov 14.

Authors

Wei-Yun Huang¹, Sheng-Da Hsu², Hsi-Yuan Huang², Yi-Ming Sun², Chih-Hung Chou¹, Shun-Long Weng³, Hsien-Da Huang⁴

Affiliations

¹ Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.
² Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.
³ Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsin-Chu 300, Taiwan Mackay Medicine, Nursing and Management College, Taipei 112, Taiwan Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan.
⁴ Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsin-Chu 300, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan bryan@mail.nctu.edu.tw.

Abstract

We present MethHC (http://MethHC.mbc.nctu.edu.tw), a database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. DNA methylation is an important epigenetic regulator of gene transcription, and genes with high levels of DNA methylation in their promoter regions are transcriptionally silent. Increasing numbers of DNA methylation and mRNA/microRNA expression profiles are being published in different public repositories. These data can help researchers to identify epigenetic patterns that are important for carcinogenesis. MethHC integrates data such as DNA methylation, mRNA expression, DNA methylation of microRNA gene and microRNA expression to identify correlations between DNA methylation and mRNA/microRNA expression from TCGA (The Cancer Genome Atlas), which includes 18 human cancers in more than 6000 samples, 6548 microarrays and 12 567 RNA sequencing data.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Methylation*
Databases, Genetic*
Humans
Internet
MicroRNAs / metabolism
Neoplasms / genetics*
Neoplasms / metabolism
RNA, Messenger / metabolism
Transcriptome*

Substances

MicroRNAs
RNA, Messenger