An atlas of cell type specific long non-coding RNAs implicated in human diseases

Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Using FANTOM5 Cap Analysis of Gene Expression (CAGE) data we integrated multiple transcript collections to generate a comprehensive catalog of 27,919 high-confidence 5’ complete human lncRNA genes and their expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classifications of these lncRNAs revealed that most intergenic lncRNAs are derived from enhancer-like regions rather than from promoters. Incorporating genetic and expression data we showed that trait-associated SNPs enriched at lncRNA loci were specifically expressed in the relevant cell-types, suggesting their roles in numerous diseases. We further demonstrated that thousands of lncRNA loci overlapping eQTL-associated SNPs were co-expressed with the mRNA target of the eQTL. Combining these findings with conservation data allowed us to identify 19,175 potentially functional lncRNA loci in human. The functional evidence and annotations of our lncRNA catalog are summarized and available as a web resource.


  • FANTOM CAT - an web application allows users to browse genes, view their genomic loci through ZENBU, filter by their annotations, intersect them with their associated sample ontologies or traits, and download the relevant data

Zenbu Views

  • Minimal - displays minimal information, including CAGE signal, gene, transcripts and conservation
  • Main - displays essential information, e.g. expression, conservation and SNPs and more
  • Expression - focus on expression profile, e.g. expression levels, sample ontology enrichment, dynamic expression and more
  • Assembly - focus on assembly information, e.g. source transcripts, FANTOM CAT at other cutoffs and more
  • Epigenome - focus on epigenomic information, e.g. Roadmap chromHMM state and histone marks
  • Evolution View - focus on evolutionary information, e.g. RS score, orthlogous expression in other species
  • Extended - displays integrated information and users can turn on extra tracks for elaborated information


Direct link to this directory: /5/suppl/Hon_et_al_2016/data/

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