HHMD: the human histone modification database

Nucleic Acids Res. 2010 Jan;38(Database issue):D149-54. doi: 10.1093/nar/gkp968. Epub 2009 Nov 5.


Histone modifications play important roles in chromatin remodeling, gene transcriptional regulation, stem cell maintenance and differentiation. Alterations in histone modifications may be linked to human diseases especially cancer. Histone modifications including methylation, acetylation and ubiquitylation probed by ChIP-seq, ChIP-chip and qChIP have become widely available. Mining and integration of histone modification data can be beneficial to novel biological discoveries. There has been no comprehensive data repository that is exclusive for human histone modifications. Therefore, we developed a relatively comprehensive database for human histone modifications. Human Histone Modification Database (HHMD, http://bioinfo.hrbmu.edu.cn/hhmd) focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. The latest release of HHMD incorporates 43 location-specific histone modifications in human. To facilitate data extraction, flexible search options are built in HHMD. It can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. HHMD also includes a user-friendly visualization tool named HisModView, by which genome-wide histone modification map can be shown. HisModView facilitates the acquisition and visualization of histone modifications. The database also has manually curated information of histone modification dysregulation in nine human cancers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromatin / chemistry
  • Chromatin Immunoprecipitation
  • Computational Biology / methods*
  • Computational Biology / trends
  • DNA Methylation
  • Databases, Genetic*
  • Databases, Protein*
  • Gene Expression Profiling / methods
  • Histones / chemistry*
  • Histones / metabolism
  • Humans
  • Information Storage and Retrieval / methods
  • Internet
  • Software


  • Chromatin
  • Histones