Welcome to Lnc2Meth
Long noncoding RNAs (lncRNAs) play an important role in modulating gene expression or participating in some essential epigenetic regulation processes, including chromatin modification or DNA methylation. DNA methylation is a fundamental feature of epigenomes that can affect the expression of protein-coding or non-coding transcripts. Here, we constructed Lnc2Meth, aimed to provide a comprehensive resource and web tool for clarifying the regulatory relationships between human lncRNAs and associated DNA methylation in diverse diseases.
LncRNA annotations are obtained from GENCODE and lncRNAdb v2.0.
In the curation module, we used 16271 lncRNA symbols, lncRNA aliases and 15693 Ensembl gene ID obtained from lncRNAdb v2.0 and GENCODE v27 as the lncRNA keywords in the text-mining process. In the search module, we re-annotated the CpG probes of Illumina Infinium 450k DNA methylation array and the CpG sites from Whole-Genome Bisulfite Sequencing data into seven lncRNA-associated functional regions (TSS10kb, TSS1500, TSS200, first_exon, genebody, intron and TTS10kb) with respect to the lncRNA annotation information from GNECODE v22.
Curation provides a unique dataset containing the experimentally verified regulatory relationships between human lncRNAs and DNA methylation manually curated from PubMed, users can retrieve it through Quick Search.
Search provides the Disease-Centric search, where users can identify the specific lncRNAs dysmethylated in a specific disease; and Transcript-Centric search, where users can obtain the diseases regulated by a specific lncRNA, including three types of differential DNA methylation patterns:
1.Differential methylation site refers to a single differentially methylated CpG site.
2.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).
3.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.
DMBrowser for navigating the transcript structure and visualizing the differential methylation patterns of a transcript in specific diseases.
Tools provide Illumina Infinium 450k DNA methylation array Probe Re-annotation and Differential Methylation Patterns Identification for lncRNAs and protein-coding genes with the user-supplied external datasets.
LncDM is an R package to identify differentially DNA methylated lncRNAs (and protein-coding genes) in the targeted control VS disease datasets.
Lnc2Meth allows the users to Download the profiles of differentially DNA methylated lncRNAs/protein-coding genes for each dataset at the site, region or element level.