|Yue Liu,Tian Tian,Kang Zhang, Wenying Xu and Zhen Su.PCSD: a plant chromatin state database.Nucleic Acids Research.DOI: 10.1093/nar/gkx919|
PCSD: a plant chromatin state database
Yue Liu, Tian Tian, Kang Zhang, Qi You, Hengyu Yan, Nannan Zhao, Xin Yi, Wenying Xu and Zhen Su
Nucleic Acids Research.
DOI: 10.1093/nar/gkx919 47，s201810632，Xu, WY 苏震.pdf
Genome-wide maps of chromatin states have become a powerful representation of genome annotation and regulatory activity. We collected public and in-house plant epigenomic data sets and applied a Hidden Markov Model to deﬁne chromatin states, which included 290 553 (36 chromatin states), 831 235 (38 chromatin states) and 3 936 844 (26 chromatin states) segments across the whole genome of Arabidopsis tha liana , Oryza sativa and Zeamays , respectively. We constructed a Plant Chromatin State Database (PCSD,http://systemsbiology.cau.edu.cn/ chromstates) to integrate detailed information about chromatinstates,including the features and distribution of states, segments in states and related genes withsegments.Theself-organization mapping(SOM) results for these different chromatin signatures and UCSC Genome Browser for visualization were also integrated into the PCSD database. We further provided differential SOM maps between two epigenetic marks for chromatin state comparison and custom tools for new data analysis. The segments and related genes in SOM maps can be searched and used for motif and GO analysis, respectively. In addition, multi-species integration can be used to discover conserved features at the epigenomic level. In summary, our PCSD database integrated the identiﬁed chromatin states with epigenetic features and maybe beneﬁcial for communities to discover causal functions hidden in plant chromatin.