Introduction to MDR

MDR (Methylation Database for Rosaceae) is an integrative database for storing, analyzing and visualizing of DNA 6mA and 4mC methylation based on single-molecule real-time (SMRT) sequencing data in Rosaceae. It provides a user-friendly interface to browse, search and download 6mA and 4mC profiling.


Home

MDR Home page provides three main functions: (1) Quick browse of methylation information in sample level; (2) Quick search of methylation in gene level. (3) About and news of MDR.


Browse page

A comprehensiv display about methylation information can be easily found through the Browse Page. The browse results can be accessed by clicking the Browse button in the menu with a selected species and methylation type.


Overview of meta data

Overview pane displays meta information of each sample. the Genome and Bio-Project are linked to the NCBI which provides detailed information. Article title directly links to the full text of related paper


Methylation density in chromosome

X-axis indicates chromosome name, and the corresponding density value of each chromosome is below the X-axis label. Y-axis indicates the value of methylation density. Density is calculated by dividing the number of total adenine (or cytimidine) into the number of related methylation sites, which can represent methylation level. Placing mouse pointer over a bar will show details.



Distribution of methylation sites in genomic feature

Different slices divided from pie chart indicate number (percentage) of methylation sites in different genomic feature. Move the pointer over each section of the pie chart to view details.


Methylation density in genomic feature

X-axis indicates the name of genomic feature. Y-axis indicates the value of methylation density.


Histogram of coverage of methylation sites

X-axis indicates the coverage of methylation sites in log2 scale. Y-axis indicates the number of methylation sites.


Histogram of modification score of methylation sites

The modification score is defined as phred-transformed p-value that a kinetic deviation exists at the position according to the PacBio manual. The higher score represent more reliable identified methylation site. X-axis indicates the modification score of methylation sites in log2 scale. Y-axis indicates the number of methylation sites.


DNA motif of methylation sites

MEME (version: 5.0.1) was used to detect enriched DNA methylation motifs. The top motif is list in this page, and the detailed results from MEME can be browsed by clicking “More motif info”.


Top gene methylation density

The top 200 highest methylation density genes are presented in this table, and the genomic features 5’UTR, CDS, 3’UTR, Intron of these genes are also be listed.


Gene Ontology enrichment analysis for high 6mA density genes

Alignments of amino acid sequences from the protein-coding genes of top 200 methylation density in every species onto protein in Arabidopsis thaliana were performed to acquire functional homologous genes. The results of Gene Ontology analysis of homologous genes group from DAVID(https://david.ncifcrf.gov), are used to illustrate the Gene Ontology enrichment of the high methylation density genes group in corresponding species.

Search page

This page provides two ways to query the database: (I) search by gene ; (II) search by position.



Download page

Download page provides an interface to achieve the 6mA and 4mC methylation files from SMRT sequencing datasets.


Processing pipeline



Contact

If you have any comments or suggestions, please contact

Shang-Qian Xie

sqianxie@hainu.edu.cn 

For technical support, please contact 

Zhaoyu Liu

zhaoyu_liu@foxmail.com

Address : Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China