About lncRNAKB



Citation:
Seifuddin F, Singh K, Suresh A, Judy JT, Chen YC, Chaitankar V, Tunc I, Ruan X, Li P, Chen Y,
Cao H, Lee RS, Goes FS, Zandi PP, Jafri MS, Pirooznia M. lncRNAKB, a knowledgebase of
tissue-specific functional annotation and trait association of long noncoding RNA.

Sci Data. 2020 Oct 5;7(1):326. doi: 10.1038/s41597-020-00659-z. PMID: 33020484. [DOI] [PubMed]





Abstract: Long non-coding RNA Knowledgebase (lncRNAKB) is an integrated resource for exploring lncRNA biology in the context of tissue-specificity and disease association. A systematic integration of annotations from six independent databases resulted in 77,199 human lncRNA (224,286 transcripts). The user-friendly knowledgebase covers a comprehensive breadth and depth of lncRNA annotation. lncRNAKB is a compendium of expression patterns, derived from analysis of RNA-seq data in thousands of samples across 31 solid human normal tissues (GTEx). Thousands of co-expression modules identified via network analysis and pathway enrichment to delineate lncRNA function are also accessible. Millions of expression quantitative trait loci (cis-eQTL) computed using whole genome sequence genotype data (GTEx) can be downloaded at lncRNAKB that also includes tissue-specificity, phylogenetic conservation and coding potential scores. Tissue-specific lncRNA-trait associations encompassing 323 GWAS (UK Biobank) are also provided.




Citation


Under review.

BioRxiv abstract:
lncRNAKB: A comprehensive knowledgebase of long non-coding RNAs
Fayaz Seifuddin, Komudi Singh, Abhilash Suresh, Yun-Ching Chen, Vijender Chaitankar, Ilker Tunc, Xiangbo Ruan, Ping Li, Yi Chen, Haiming Cao, Richard S. Lee, Fernando Goes, Peter P. Zandi, M. Saleet Jafri, Mehdi Pirooznia
bioRxiv 669994; doi: https://doi.org/10.1101/669994

Abstract: We 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). We employed Genotype-Tissue Expression (GTEx) project to provide tissue-specific expression profiles and tissue-specificity scores in 31 solid organ human tissues and performed network analysis to identify co-expressed mRNAs that would provide potential understanding on lncRNAs function. It also incorporates coding potential and phylogenetic conservation. Furthermore, using whole genome sequencing data of 652 subjects from GTEx, we calculated expression quantitative trait loci (cis-eQTL) regulated lncRNAs in all tissues. lncRNAKB is available at http://www.lncrnakb.org



Credits



National Heart, Lung, and Blood Institute (NHLBI / NIH)


Bioinformatics and Computational Biology

Ilker Tunc, Ph.D.
Mehdi Pirooznia, M.D., Ph.D.

Cardiovascular Branch

Yi Chen, B.S.,
Xiangbo Ruan, Ph.D.,
Ping Li, Ph.D.,
Haiming Cao, Ph.D.,



School of Medicine, Johns Hopkins University


Peter Zandi, Ph.D.,
Richard Lee, Ph.D.,




School of Systems Biology, George Mason University


Saleet Jafri, Ph.D.,

 





Disclaimer


We have made every attempt to make sure the data displayed in lncRNAKB are as accurate as possible. However, it is possible we have made mistakes in representing these data. We cannot provide any warranty for the data and do not take any responsibility for their accuracy, completeness or usefulness.