Welcome to RiceENCODE database V0.1 !

The application of Hi-C, ChIA-PET, and other chromosome conformation capture technologies in plants in recent years has have made a the research on the spatial structure of plant genomes more and more important. With the continuous increase of a large number of plant chromosome interaction data, how to query the epigenetic modification and interaction information efficiently and quickly has become a major problem.Here we combine the published three-dimensional interactive

data ChIA-PET, Hi-C and the epigenomic datasets (ChIP-seq, ATAC-seq,MNase-seq, FAIRE-seq, BS-seq, ncRNA-seq and RNA-seq) to construct a comprehensive rice Encyclopedia of DNA Elements database (riceENCODE). This database contains 972 datasets, which is the largest one for rice epigenomics up to our best knowledge, which can help us to outline the rice epigenome in a comprehensive way, and provide an important platform for studying rice molecular breeding, genetic mechanisms, tissue specificities and subgroup properties in epigenetic regulation.

<！--div style="background-image:url(images/EPI/epi_03.png); position:absolute; left:344px; top:117px; width:141px; height:15px;" title=""> histone modification

<！--div style="background-image:url(images/EPI/epi_07.png); position:absolute; left:206px; top:153px; width:84px; height:19px;" title=""> 3D Genome

chromatin accessibility

transcriptome

DNA methylation

chromatin state

Quick Search

Gene ID Search: Example: MH01g0710600; Ghd7; ZS01g0067500; OsDREB2A; LOC_Os03g11600; D3;

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Citations

Xie L, Liu M, Zhao L, Cao K, Wang P, Xu W, Sung WK, Li X, Li G. RiceENCODE: A comprehensive epigenomic database as a rice Encyclopedia of DNA Elements. Mol Plant. 2021 Oct 4;14(10):1604-1606. doi: 10.1016/j.molp.2021.08.018. Epub 2021 Aug 27. PMID: 34455096.

Guoliang's Bioinformatics Lab

Welcome to Guoliang's Lab Website of Bioinformatics at College of Informatics, Huazhong Agricultural University (HZAU).Our main research interests are in the field of three-dimensional (3D) Genomics.