LCLNCRdb

The lncRNAs in LCLNCRdb can be explored using LCLNCRdb’s three principal modules, the search module, the analysis module and the download module.

SEARCH MODULE

LCLNCRdb users can search for lncRNA of interest in two ways:
1) By entering lncRNA official GENE symbol or GENE id such as HGNC id, Entrez id, Ensemble id and NONCODE id
2) By entering the fasta sequence of lncRNA

The lncRNA ‘ABCA9-AS1’ was taken as an example to demonstrate the database.
The results page returns ‘General information ’ of lncRNA of interest, including gene symbol, Entrez ID, Ensembl ID, HGNC id, NONCODE id, Refseq accession, Lncipedia ID, Chromosome number, Map location, Source, Type and Expression pattern obtained from DEG analysis

The results page also includes the miRNA targets identified for the lncRNA and Survival Analysis.
The visual representation of lncRNA and their respective miRNA targets obtained from the Cytoscape platform can be viewed.

The Kaplan-Meier plot along with their respective p-value are added in the ‘Survival plot’ section.

Also, the FASTA sequence of lncRNA can be viewed by clicking the Refseq Id.

In Browse option under Search module the user can browse through the lncRNA and apply filters that provide a combined query functionality by using ‘Type’ and ‘Expression Patterns’ options. For example, users can do a combined query by selecting ‘LUAD and LUSC’ from Type and ‘Upregulated’ from the expression pattern find lncRNAs that are found in both LUAD and LUSC and upregulated.

ANALYSIS MODULE

LCLNCRdb provides two sections in Analysis namely Network Analysis and Survival Analysis.
In Network Analysis, the DElncRNA - DEmiRNA target network, DElncRNA - DemiRNA - DEmRNA target network and the ceRNA network of both LUAD and LUSC is available. The interactive network was constructed by modifying Cytoscape javascript (cytoscape.js). The summary statistics and the network properties (Closeness Centrality, Degree, Eccentricity, Betweenness Centrality, Topological Coefficient, Average Shortest PathLength) obtained from the Cytoscape platform were added.

In Survival Analysis, you can search for the Kaplan-Meier plot for the DElncRNA and miRNA/mRNA in ceRNA network.

Through Submit module, users can submit information relevant to lncRNAs or ask any queries by filling out the form.

DOWNLOAD MODULE

The download module allows users to download complete information present in LCLNCRdb. The files about general information and the predicted targets, and network analysis properties table can be downloaded in CSV format.