. Author manuscript; available in PMC: 2019 Apr 8.

Published in final edited form as: Nat Rev Genet. 2018 Sep;19(9):535–548. doi: 10.1038/s41576-018-0017-y

Table 1 |.

lncRNA annotations

name (version)	Reported size (gene loci)	Methods^a	comments	completeness	comprehensiveness^b	exhaustiveness^c
NONCODE (v5)	96,308	Integration of other databases	The most comprehensive resource	8.9%	67,276	2.3
MiTranscriptome (v2)	63,615	Assembly from short reads	Mainly cancer samples	4.4%	45,088	4.4
FANTOM CAT (v1)	27,919	Assembly, other annotations and CAGE evidence	Mapped 5′ ends using CAGE tags	15.8%	27,278	3.3
RefSeq (GCF_000001405.37_GRCh38.p11)	15,791	Manual (based on cDNA) and automated annotation (based on RNA-seq data)	The oldest annotation	11.0%	14,889	1.9
GENCODE (v27)	15,778	Manual annotation based on cDNA, ESTs and high-quality long-read data	Used by most consortia and integrated with Ensembl	13.5%	15,063	1.9
BIGTranscriptome (v1)	14,158	Assembly, with CAGE and 3 P-seq evidence	Full-length transcripts	27.7%	12,632	2.1
GENCODE+	13,434	Union of GENCODE (v20) and CLS lncRNAs with anchor-merged CLS transcript models	Extension of GENCODE by CLS	24.0%	13,434	3.3
CLS FL	807	lncRNAs from GENCODE+ with CAGE and poly(A) evidence	Full-length transcripts	71.7%	807	5.5
Protein-coding^d	19,502	GENCODE confident protein-coding transcripts	Not tagged mRNA_end_NF nor mRNA_start_NF in the original GENCODE v27 GTF file	53.8%	18,995	2.9

All numbers correct as of the end of 2017. MiTranscriptome, Functional Annotation of the Mammalian genome (FANTOM) cap analysis of gene expression (CAGE)-associated transcriptome (CAT) and BIGTranscriptome long non-coding RNA (lncRNA) catalogues were lifted over to the Genome Reference Consortium Human Build 38 (GRCh38) genome assembly. 3P-seq, poly(A)-position profiling by sequencing; CLS, capture long-read sequencing; EST, expressed sequence tag; RNA-seq, RNA sequencing.

Assembly in the Methods column refers to transcriptome assembly using short reads from RNA-seq.

Comprehensiveness is the total number of gene loci boundaries defined using buildLoci. To compare gene sets in a consistent way, the assembly patches were excluded, and the gene loci boundaries were redefined using buildLoci, which explains discrepancies between gene numbers presented here and those reported in original publications.

Exhaustiveness is the average number of isoforms per gene locus. Figures for completeness, comprehensiveness and exhaustiveness as presented in FIG. 3 are shown here.

A set of protein-coding transcripts was used as a reference.