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Table 1 List of databases for lncRNA annotation and characterization

From: Long non-coding RNAs (lncRNAs) in spermatogenesis and male infertility

Database Description Organism Website Reference
CHIPBase v2.0 It explores the transcriptional regulatory networks of non-coding RNAs (ncRNAs) and protein coding genes (PCGs). Human and mouse Rna.sysu.edu.cn/chipbase/ [82]
DIANA-LncBase This database contains information for both predicted and experimentally verified miRNA-lncRNA interactions. Human and mouse Diana.imis.athena-innovation.gr [83]
LNCipedia It is a public database for long non-coding RNA (lncRNA) sequences and annotation. It contains 127,802 transcripts and 56,946 genes. Human www.lncipedia.org [84]
lncRNAdb v2.0 This database provides a comprehensive annotation of eukaryotic long non-coding RNAs. 71 different organisms www.lncrnadb.org [85]
lncRNADisease Database containing experimentally validated lncRNAs-disease associations. Human Cmbi.bjmu.edu.cn/lncrnadisease [86]
lncRNome Database containing comprehensive list of lncRNA in humans. It contains information for over 17,000 long non-coding RNAs in humans. Human Genome.igib.res.in/lncRNom [87]
Noncode v5.0 Integrated knowledge database of non-coding RNAs containing non-coding RNAs expressing in 17 different species. Human, mouse, rat, chicken, fruit fly, zebrafish, C. elegans, yeast, Arabidopsis, chimpanzee, gorilla, orangutan, rhesus macaque, opossum platypus and pig www.bioinfo.org/noncode/ [88]
The Functional lncRNA database Database having information of long non-protein-coding transcripts that have been experimentally shown to be both non-coding and functional. Currently the database contains lncRNAs from Human, Mouse and Rat. Human, mouse and rat www.valadkhanlab.org [89]
Encyclopedia of DNA Elements (ENCODE) project It contains comprehensive list of functional elements in the human genome, including elements that act at the protein and RNA levels. Human www.encode.project.org [90]
StarBase v3.0 Contains information of more than 1.1 million miRNA-ncRNA, 2.5 million miRNA-mRNA, 2.1 million RBP-RNA and 1.5 million RNA-RNA interactions from sequencing data. Human, mouse and C. elegans www.starbase.sysu.edu.cn [91]
RNA-Protein Interaction Prediction (RPI Seq) This database helps in predicting any possible interaction between lncRNA of known sequence and proteins. Human, mouse, yeast, fruit fly and E. coli Prisdb.gdcb.iastate.edu/RPISeq/ [92]
Lnc2Catlas It gives information about lncRNAs and their association with cancer risk. It provides association between 33 different cancers and 27,670 lncRNA transcripts. Human Lnc2catlas.bioinfotech.org [93]
LncRIsearch It is a web server which predicts human and mouse lncRNA-lncRNA and lncRNA-mRNA interactions. It uses RI blast to predict RNA-RNA interaction. It also provides information of tissue-specific expression and subcellular localization data for the lncRNAs. Human and mouse rtools.cbrc.jp/LncRRIsearch/ [94]
LncTarD It provides information about disease- related lncRNAs for humans. This database provides a comprehensive resource of 2822 key lncRNA-target regulations, lncRNA influenced functions, and lncRNA-mediated regulatory mechanisms in human diseases. Human Biocc.hrbmu.edu.cn/LncTarD/ [95]