Table 2

Online lncRNA resources

Database	Nomenclature	size	Description of key features	Provenance of lncRNAs	Reference
lncRBase	hsaLB_AN_74656	133 361	Comprehensive database categorising lncRNA according to genomic context. Integrates, coding potential, expression data, associated genomic elements and publications	lncRNAdb, Broad Institute, Ensembl, NONCODE, H-InvDB	13
lncipedia	lnc-SMUG1-7	113 513	Grouping of isoforms that share at least one exon. Integrates prediction of secondary structure, locus conservation and coding potential	lncRNAdb, Ensembl, Gencode, RefSeq, NONCODE, Broad Institute and two further RNA Seq publications	19
NONCODE	n343067/NONHSAT028510	95 135	ncRNA database with detailed information regarding provenance and expression	RefSeq, literature mining and specialised databases	17
lncRNASNP	lnc-SMUG1-7	32 108	Lists overlapping miRNA binding sites and SNPs, predicting the influence of SNPs on secondary structure and miRNA binding and providing corresponding miRNA expression data	lncipedia, dbSNP and stringency filtering	27
Ensembl	ENSG00000228630	23 498	Integrative database of genome annotation with detailed information regarding provenance	Computational prediction from ESTs and chromatin marks	28
Gencode	ENSG00000228630	15 877	Integrative database including information on DNA methylation, occupancy and chromatin state, along with RNA expression and binding	HAVANA manual annotation and Ensembl annotation pipeline, mostly validated	29
Havana	OTTHUMT 00000328662	14 396	Manual genomic annotation supported by transcriptional evidence	Manual annotation	29
Broad Institute	TCONS_00079054	14 353	Expression levels in 24 tissues and cell types, stringent set of 4662 lincRNA	RNA Seq in 24 tissues and cell types	16
ChIPBase	lncRNA2314-1	10 559	Integrates chromatin immunoprecipitation sequencing data with lncRNA occupancy	Ensembl, refseq, UCSC, lncRNAdb and various publications	30
RefSeq	NR_047517.1	6917	Non-redundant database of annotated sequences	Data submitted to the International Nucleotide Sequencing Database	31
lincPoly	XLOC_000000*	4662	Similar to lncRNASNP, with SNPs categorised according to phenotype and conservation data integrated in the place of miRNAs	Stringent set from Broad Institute	32
lncRNAdb	HOTAIR	166	Manually curated database ofexperimentally validated, functional lncRNAs	Literature mining	33

This selection of resources is not exhaustive, but presents a broad spectrum of available and up to date tools. Included is an example of the nomenclature preferred by each database, with all entries referring to the lncRNA HOTAIR.
*HOTAIR is not found in lincPoly.