lncRNAKB – A comprehensive knowledgebase of long non-coding RNAs

A team led by researchers at the National Heart, Lung, and Blood Institute has assembled the most comprehensive long non-coding RNA knowledgebase (lncRNAKB) by methodically integrating widely used lncRNAs resources. It presents the largest annotation of 77,199 human lncRNAs (224,286 transcripts) including the latest CHESS, FANTOM, LNCipedia, and NONCOD resources. In addition, the researchers employed the Genotype-Tissue Expression (GTEx) project to provide tissue-specific expression profiles and tissue-specificity scores for these lncRNAs in 31 solid organ human tissues. They also performed Weighted Gene Co-expression Network Analysis (WGCNA) to identify co-expressed lncRNA-mRNA that were then subjected to pathway enrichment analysis to identify meaningful biological processes that lncRNAs could be potentially involved in, providing potential understanding on lncRNAs function. They created dynamic Cytoscape networks for exploration and visualization of each pathway. The lncRNAKB also incorporates coding potential and phylogenetic conservation. Furthermore, using whole genome sequencing data of 652 subjects from GTEx, the researchers calculated expression quantitative trait loci (cis-eQTL) regulated lncRNAs in all tissues. This will provide a strong foundation for integrative traits association analysis by linking a variety of trait related GWAS and our eQTL results.

rna-seq

Availability – The lncRNAKB is available at http://www.lncrnakb.org

Seifuddin F, Singh K, Suresh A, Chen YC, Chaitankar V, Tunc I,  Ruan X,  Li P, Chen Y, Cao H, Lee RS, Goes F, Zandi PP, M. Saleet Jafri MS, Pirooznia M. (2019)  lncRNAKB: A comprehensive knowledgebase of long non-coding RNAs. bioRXiv [Epub ahead of print]. [abstract]

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