Lnc2Meth – a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease

Lnc2Meth, an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform that effectively integrates tools for calculating and identifying the differentially methylated lncRNAs and protein-coding genes (PCGs) in diverse human diseases.

The resource provides:

(i) advanced search possibilities, e.g. retrieval of the database by searching the lncRNA symbol of interest, DNA methylation patterns, regulatory mechanisms and disease types;

(ii) abundant computationally calculated DNA methylation array profiles for the lncRNAs and PCGs;

(iii) the prognostic values for each hit transcript calculated from the patients clinical data;

(iv) a genome browser to display the DNA methylation landscape of the lncRNA transcripts for a specific type of disease;

(v) tools to re-annotate probes to lncRNA loci and identify the differential methylation patterns for lncRNAs and PCGs with user-supplied external datasets;

(vi) an R package (LncDM) to complete the differentially methylated lncRNAs identification and visualization with local computers.

Content and interface of Lnc2Meth

(A) Manually curated lncRNA-methylation associations in Lnc2Meth. (B) Predicted differential methylation patterns of lncRNAs and PCGs in Lnc2Meth. (C) Curation module for manually curated lncRNA-methylation associations. (D) Search module for predicted lncRNA/PCG methylation patterns. (E) DMBrowser module for illustrating methylation landscape of lncRNAs and PCGs. (F) LncDM, an R package for calculating methylation patterns of lncRNAs and PCGs on local computers. (G) Tools module for identifying the differential methylation patterns of lncRNAs and PCGs online.

Lnc2Meth provides a timely and valuable resource that can be applied to significantly expand our understanding of the regulatory relationships between lncRNAs and DNA methylation in various human diseases.

Availability – http://www.bio-bigdata.com/Lnc2Meth/