lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA

• Published in: Scientific data Vol. 7; no. 1; p. 326
• Main Authors: Seifuddin, Fayaz, Singh, Komudi, Suresh, Abhilash, Judy, Jennifer T., Chen, Yun-Ching, Chaitankar, Vijender, Tunc, Ilker, Ruan, Xiangbo, Li, Ping, Chen, Yi, Cao, Haiming, Lee, Richard S., Goes, Fernando S., Zandi, Peter P., Jafri, M. Saleet, Pirooznia, Mehdi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 05.10.2020; Nature Publishing Group
• Subjects: 631/114/129/2043; 631/114/1314; 631/114/2401; 631/114/2404; Computer applications; Data Descriptor; Digital curation; Gene expression; Genomes; Genotypes; Humanities and Social Sciences; Humans; Knowledge Bases; Molecular Sequence Annotation; multidisciplinary; Non-coding RNA; Nucleotide sequence; Organ Specificity; Phylogeny; Quantitative Trait Loci; RNA, Long Noncoding - genetics; Science; Science (multidisciplinary)
• ISSN: 2052-4463; 2052-4463
• DOI: 10.1038/s41597-020-00659-z

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. LncRNAKB is accessible at http://www.lncrnakb.org/ , and the data are freely available through Open Science Framework ( https://doi.org/10.17605/OSF.IO/RU4D2 ). Measurement(s) regulation of gene expression • sequence feature annotation • lnc_RNA • tissue-specific expression of lncRNA • Expression Quantitative Trait Locus Technology Type(s) digital curation • computational modeling technique Sample Characteristic - Organism Homo sapiens Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.12827597