lncRNAKB: A comprehensive knowledgebase of long non-coding RNAs

Fayaz Seifuddin; Komudi Singh; Abhilash Suresh; Jennifer Judy; Yun-Ching Chen; Vijender Chaitankar; Ilker Tunc; Xiangbo Ruan; Ping Li; Yi Chen; Haiming Cao; Richard S. Lee; Fernando S. Goes; Peter P. Zandi; Mohsin Saleet Jafri; Mehdi Pirooznia

doi:10.1038/s41597-020-00659-z

BioinformaticsScientific DataOct 5, 2020

Peer-reviewed journal article

lncRNAKB: A comprehensive knowledgebase of long non-coding RNAs

Fayaz Seifuddin iD, Komudi Singh iD, Abhilash Suresh iD, Jennifer Judy iD, Yun-Ching Chen iD, Vijender Chaitankar, Ilker Tunc iD, Xiangbo Ruan iD, Ping Li iD, Yi Chen iD, Haiming Cao iD, Richard S. Lee iD, Fernando S. Goes iD, Peter P. Zandi iD, Mohsin Saleet Jafri iD, Mehdi Pirooznia iD

Abstract

We have assembled a comprehensive long non-coding RNA knowledgebase (lncRNAKB) of 77,199 annotated human lncRNAs (224,286 transcripts) by methodically integrating widely used lncRNAs resources. To facilitate functional characterization of lncRNAs, we employed Genotype-Tissue Expression (GTEx) project to provide tissue-specific gene expression profiles of lncRNAs in 31 solid organ tissues. Additional information includes network analysis to identify co-expressed gene modules to potentially delineate lncRNA function. Tissue-specificity, phylogenetic conservation scores and coding potential for lncRNAs are included. Finally, using whole genome sequencing data from GTEx, expression quantitative trait loci (cis-eQTL) regulated lncRNAs were calculated in all tissues. lncRNAKB is available at http://www.lncrnakb.org.

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