Table 1.
Databases for identifying lncRNAs and their basic properties or associations. Overview of active databases cataloguing various properties (sequence conservation, mutation, expression, localisation) or associations attributed to lncRNA genes or transcripts. A link to the hosting website is provided followed by the latest known version as well as the most recent publication describing the database.
| Database/Version/Ref. | Link | Conservation | Mutations | Expression | Localisation | Associations |
|---|---|---|---|---|---|---|
| LNCiPedia v5 (2019) [89] |
https://lncipedia.org/ (accessed on 8 March 2021) | H. sapiens, D. melanogaster, D. rerio, M. musculus, P. troglodytes | NA | NA | NA | Relevant references |
| lncATLAS (2017) [90] |
https://lncatlas.crg.eu/ (accessed on 8 March 2021) | NA | NA | GENCODE | GENCODE | NA |
| NONCODE v6 (2020) [88] |
http://www.noncode.org/ (accessed on 8 March 2021) | H. sapiens, M. musculus and 15 more | dbSNP | Human Body Map; NCBI GEO | NA | Gene Ontology |
| lncWiki/Book (2019) [91,92] |
https://bigd.big.ac.cn/lncrnawiki/index.php/Main_Page (accessed on 8 March 2021) https://bigd.big.ac.cn/lncbook/index (accessed on 8 March 2021) |
NA | ClinVar; COSMIC | HPA; GTEx; Methylation | NA | Gene Ontology; MeSH Ontology; miRNA Interaction Prediction; |
| Lnc2Cancer v3 (2020) [93] |
http://bio-bigdata.hrbmu.edu.cn/lnc2cancer/ (accessed on 8 March 2021) | NA | NA | Literature Mining | lncATLAS | Expression Correlation; Survival; TF Motif; lncBook |
| LncRNADisease v2 (2019) [94] |
http://www.rnanut.net/lncrnadisease/ (accessed on 8 March 2021) | NA | NA | NA | NA | Disease Ontology; MeSH Ontology; Predictive Associations |
| LncMAP v2 (2018) [95] |
http://bio-bigdata.hrbmu.edu.cn/LncMAP/ (accessed on 8 March 2021) | NA | NA | NA | NA | Associations with: TF, Genes, Drugs, Survival |
| TANRIC v2 (2019) [96] |
https://www.tanric.org (accessed on 8 March 2021) | NA | TCGA Somatic Mutations | TCGA | NA | TCGA/CCLE Correlations: Expression, Stage; Survival |
| MNDR v3.1 (2020) [97] |
https://www.rna-society.org/mndr/ (accessed on 8 March 2021) | NA | NA | Mammalian | NA | Evidenced disease associations and Predictor |
| lncRNASNP v2 (2018) [98] |
http://bioinfo.life.hust.edu.cn/lncRNASNP/#!/ (accessed on 8 March 2021) | NA | TCGA and COSMIC SNVs | NA | NA | miRNA binding & SNP effects; GWAS LD; Mutation effects |
| lncRNAMAP (2014) [99] |
https://lncrnamap.mbc.nctu.edu.tw (accessed on 8 March 2021) | NA | NA | NCBI GEO | NA | miRNA and endo-siRNA predictors |
| LncTarD (2020) [100] |
http://bio-bigdata.hrbmu.edu.cn/LncTarD/ (accessed on 8 March 2021) | NA | NA | NA | NA | Disease-related Target Prediction |
| EVLncRNAs (2017) [101] |
http://biophy.dzu.edu.cn/EVLncRNAs/ (accessed on 8 March 2021) | NA | NA | NA | NA | Manually curated disease association |
| LncSPA (2020) [102] |
http://bio-bigdata.hrbmu.edu.cn/LncSpA/ (accessed on 8 March 2021) | NA | NA | GTEx, HPA, HBM2, FANTOM, TCGA, TARGET | NA | Expression in diseased tissues |