tutorial arrow
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

Specific Methylation Analysis and Report Tool SMART

Detects the cell type-specific methylation marks by integrating multiple methylomes from human cell lines and tissues. SMART is an entropy-based framework focused on integrating of a large number of DNA methylomes for the de novo identification of cell type-specific MethyMarks. To facilitate the specific methylation analysis, this method dynamically integrates multiple methylomes and identifies the cell type-specific methylation marks.

User report

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Sort by:

1 user review

1 user review

Hongbo Liu's avatar image

Hongbo Liu

SMART2 is a newly developed tool for deep analysis of DNA methylation data detected by bisulfite sequencing platforms. This tool is focused on three main functions including de novo identification of differentially methylated regions (DMRs) (wikipedia) by genome segmentation, identification of DMRs from predefined regions of interest, and identification of differentially methylated CpG sites. It is known that DNA methylation plays important roles in the regulation of cell development and differentiation. DNA methylation/unmethylation mechanisms are common in all tissue/cell. However, different cell types with the same genome have different methylomes. Recently, high-throughput sequencing combining bisulfite treatment (Bisulfite-Seq) have been used to generate DNA methylomes from a wide range of human tissue/cell types at a genome-wide perspective. In order to de novo identify DMRs across different biological groups, entropy-based procedures facilitated the quantification of methylation specificity for each CpG and the determination of the Euclidean distance and similar entropy for each pair of neighboring CpGs. Subsequently, genome segmentation based on these quantified parameters segments the genome into primary segments comprising CpG sites with high methylation similarities across all groups. Further, the primary segments in close proximity and sharing similar methylation patterns were merged into larger segments of different types, including DMRs and non-DMRs which are identified based on methylation specificity and one-way ANOVA analysis. Eventually, the DMRs with specific hypo-/hypermethylation in the minority of groups, group-specific hypomethylation marks (HypoMarks) and the group-specific hypermethylation marks (HyperMarks), are identified using a statistical method. To facilitate the mining of methylation marks across cell types and species. In addition, SMART2 also supports the identification of DMRs from pre-defined regions of interest and differentially methylated CpG sites.

SMART forum

tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.

SMART versioning

tutorial arrow
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Version Operating System DOI Size Download Info
32/64 bits
865.84 Ko process validation...

SMART classification

SMART specifications

Software type:
Restrictions to use:
Academic or non-commercial use
Input format:
Output format:
Programming languages:
Computer skills:
Command line interface
Input data:
A methylation data matrix.
Output data:
DMR and related information.
Operating system:
Unix/Linux, Mac OS
GNU General Public License version 2.0

SMART support



tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.



College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; Department of Rehabilitation, the First Affiliated Hospital of Harbin Medical University, Harbin, China; School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China

Funding source(s)

Supported by National Natural Science Foundation of China [61403112, 31371334, 81573021, 61402139 and 31371478]; Natural Scientific Research Fund of Heilongjiang Provincial [ZD2015003].

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.