Table 1.

Resources of human lncRNA annotation.

Database Name	Reference build	Annotation file name	URL
CHESS18	hg38	chess2.2.gtf	http://ccb.jhu.edu/chess/data/chess2.2.gtf.gz
LNCipedia19,20	hg19,hg38	lncipedia_5_2_hc_hg38.gtf	https://lncipedia.org/downloads/lncipedia_5_2/full-database/lncipedia_5_2_hg38.gtf
NONCODE21	hg19,hg38	NONCODEv5_human_hg38_lncRNA.gtf	http://www.noncode.org/datadownload/NONCODEv5_human_hg38_lncRNA.gtf.gz
FANTOM522	hg19	FANTOM_CAT.lv3_robust.only_lncRNA.gtf	https://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/data/assembly/lv3_robust/FANTOM_CAT.lv3_robust.only_lncRNA.gtf.gz
MiTranscriptome25	hg19	mitranscriptome.hg19.v2.gtf	http://mitranscriptome.org/download/mitranscriptome.gtf.tar.gz
BIGTranscriptome26	hg19	BIGTranscriptome_lncRNA_catalog.hg19.gtf	http://big.hanyang.ac.kr/UCSC/RNA-seq/hg19/CAFE/GTFs/BIGTranscriptome/BIGTranscriptome_lncRNA_catalog.gtf
deepBase23	hg19	hg19_allLncRNA.rnaFam.bed	http://rna.sysu.edu.cn/deepBase/Download/hg19_allLncRNA.rnaFam.bed
lncRNAdb17	hg38	under development	http://lncrnadb.org/
LncRNAWiki24	hg19	RawData.tar.gz	http://lncrna.big.ac.cn/data/RawData.tar.gz
LncBook27	hg19,hg38	LncBook_GENCODE_GRCh38_9.28.gtf.gz	ftp://download.big.ac.cn/lncbook/1-LncRNAs(GRCh37%7C38)/LncBook_GENCODE_GRCh38_9.28.gtf.gz
RNAcentral28	hg38	homo_sapiens.GRCh38.gff3.gz	ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/releases/14.0/genome_coordinates/gff3/homo_sapiens.GRCh38.gff3.gz
GENCODE29	hg19,hg38	gencode.v33.annotation.gtf.gz	ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/gencode.v33.annotation.gtf.gz
ENSEMBL30	hg19,hg38	Homo_sapiens.GRCh38.99.gtf.gz	ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz
RefSeq.31	hg19,hg38	GRCh38_latest_genomic.gtf.gz	ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gtf.gz