TY - JOUR
T1 - YHMI
T2 - A web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast
AU - Wu, Wei Sheng
AU - Tu, Hao Ping
AU - Chu, Yu Han
AU - Nordling, Torbjörn E.M.
AU - Tseng, Yan Yuan
AU - Liaw, Hung Jiun
N1 - Funding Information:
We thank the National Cheng Kung University (NCKU), MOST AI Biomedical Research Center at NCKU and Ministry of Science and Technology of Taiwan for their support.
Funding Information:
National Cheng Kung University and Ministry of Science and Technology of Taiwan [MOST-105-2221-E-006-203-MY2, MOST-106-2628-E-006-006-MY2, MOST-107-2221-E-006-225-MY3, MOST-107-2634-F-006-009]. Funding for open access charge: National Cheng Kung University and Ministry of Science and Technology of Taiwan.
Publisher Copyright:
© The Author(s) 2018. Published by Oxford University Press.
PY - 2018/1/1
Y1 - 2018/1/1
N2 - 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.
AB - 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.
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U2 - 10.1093/database/bay116
DO - 10.1093/database/bay116
M3 - Article
C2 - 30371756
AN - SCOPUS:85055612278
VL - 2018
JO - Database : the journal of biological databases and curation
JF - Database : the journal of biological databases and curation
SN - 1758-0463
IS - 2018
ER -