In this section, you could construct your own methylation profile for your target lncRNA/protein-coding gene by the following steps:
Calculate the methylation value as the Beta value.
Input your target lncRNA/protein-coding gene.
Upload Illumina Infinium 450k DNA methylation array data with the same format as our example data.
Choose 'yes', if there is a missing value in your methylation profile (the missing methylation value = NA). The missing methylation value would be imputed by Lnc2Meth with the k-NN method automatically.
Click on the 'Submit' button, you can download the returned methylation profile of the lncRNA/PCG.

 Caculate methylation Beta value

Beta value (β) : estimate of methylation level using ratio of intensities between methylated and unmethylated alleles
β = Methylated allele intensity (M) / (Unmethylated allele intensity (U) + Methylated allele intensity (M) + 100)
or
β = Methylated allele intensity (M) / (Unmethylated allele intensity (U) + Methylated allele intensity (M))

Differential Methylation Site

Differential methylation site refers to a single differentially methylated CpG site.

Differential Methylation Element

Differential methylation element was defined as a differentially methylated functional element including TSS1500 (1.5 kb upstream to 200 bp upstream from the transcriptional start site), TSS200 (200 bp upstream from the transcriptional start site), 1_exon (the first exon), intron, and gene body (excluding the first exon).

Differential Methylation Region

Differential methylation region was taken as the longest differentially methylated region within one functional element that contained CpG sites with a consistent methylation orientation and extending 2kb outwards from the boundary CpG sites.