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 | [82] | |
DIANA-LncBase | This database contains information for both predicted and experimentally verified miRNA-lncRNA interactions. | Human and mouse | [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 | [84] | |
lncRNAdb v2.0 | This database provides a comprehensive annotation of eukaryotic long non-coding RNAs. | 71 different organisms | [85] | |
lncRNADisease | Database containing experimentally validated lncRNAs-disease associations. | Human | [86] | |
lncRNome | Database containing comprehensive list of lncRNA in humans. It contains information for over 17,000 long non-coding RNAs in humans. | Human | [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 | [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 | [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 | [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 | [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 | [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 | [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 | [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 | [95] |