YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast. (29th October 2018)

• Record Type: Journal Article
• Authors: Wu, Wei-Sheng; Tu, Hao-Ping; Chu, Yu-Han; Nordling, Torbjörn E M; Tseng, Yan-Yuan; Liaw, Hung-Jiun
• Is Part Of: Database. Volume 2018(2018)
• Publication Date: 2018-10-29
• Subjects: Biology -- Databases -- Periodicals; Bioinformatics -- Periodicals; 570.285
• DOI: 10.1093/database/bay116
• Languages: English
• ISSNs: 1758-0463

Abstract

Abstract: Post-translational modifications of histones (e.g. acetylation, methylation, phosphorylation and ubiquitination) play crucial roles in regulating gene expression by altering chromatin structures and creating docking sites for histone/chromatin regulators. However, the combination patterns of histone modifications, regulatory proteins and their corresponding target genes remain incompletely understood. Therefore, it is advantageous to have a tool for the enrichment/depletion analysis of histone modifications and histone/chromatin regulators from a gene list. Many ChIP-chip/ChIP-seq datasets of histone modifications and histone/chromatin regulators in yeast can be found in the literature. Knowing the needs and having the data motivate us to develop a web tool, called Yeast Histone Modifications Identifier (YHMI), which can identify the enriched/depleted histone modifications and the enriched histone/chromatin regulators from a list of yeast genes. Both tables and figures are provided to visualize the identification results. Finally, the high-quality and biological insight of the identification results are demonstrated by two case studies. We believe that YHMI is a valuable tool for yeast biologists to do epigenetics research.