Lnc2meth: methylation sites on disease-related lncrna

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DNA Methylation is one of the most widely studied epigenetic markers , Its effect on gene expression is the basic content of research . With lncRNA Development of research , Scientists have set their sights on lncRNA Genetically DNA Methylation sites , adopt lncRNA Methylation sites on genes to find disease-related lncRNA, And explore lncRNA Role in disease .

Some scholars collect similar literature , And collated into a database ​​Ln2Meth​​, Address the following

​ ​http://bio-bigdata.hrbmu.edu.cn/Lnc2Meth/index.jsp​​

The database provides the following two retrieval methods

1. Disease-Centric
2. Transcript-Centric
   

Can be based on disease or lncRNA Search by name , The results are as follows

For methylation sites , The expression pattern in patients is given , These include the following

1. differential methylation
2. hypermethylation
3. hypomethylation
4. methylation
5. demethylation
   

about DNA Methylation sites and lncRNA The relationship between , The following 3 Kind of model

1. Cis-Methylated LncRNA(CML)

2. Trans-Methylation Due to LncRNAs(TMDL)

3. Trans-Methylation Regulated LncRNA(TMRL)

adopt ​​DMBrowser​​ function , You can view it in the genome browser lncRNA Methylation sites on , It is shown as follows

The site also provides two tools

1.  Probe Re-annotation

Yes illumina 450K The probe of the chip has been re annotated , The results are as follows

The corresponding lncRNA gene , The corresponding area of the probe is divided into the following 5 Types

1. TSS1500
2. TSS200
3. 1_exon
4. 5’UTR
5. 3’UTR
   

The schematic diagram is as follows

2. Differentail Methylation Patterns Identification

Input 450k Expression profile data of the chip , Sample grouping , Interested in lncRNA gene , The tool will perform variance analysis , Finally given lncRNA Difference analysis results of corresponding probe level , It is shown as follows

Corresponding to this online tool , One is also provided R package ​​LncDM​​, It achieves the same function , For specific usage, you can view the help document of the package .

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