Table 3.
Databases integrating computational and experimental sources for predicting lncRNA interactions. Databases are listed detailing the types of interactions they cover. A link to the hosting website is provided followed by the latest known version as well as the most recent publication describing the database. Most databases rely on a primary experimental (EXP) or computational (CPU) source, which are briefly explained. Any additional sources are also summarised.
| Database | Link | Interaction Type | Primary Source | Additional Sources |
|---|---|---|---|---|
| NPInter v4 (2019) [160] |
http://bigdata.ibp.ac.cn/npinter4 (accessed on 8 March 2021) | miRNA-RNA; ncRNA-DNA; ncRNA-Protein; circRNA | EXP: Re-processing and integration of experimental data (GEO; ENCODE; RISE) | CPU: miRNA binding (miRanda, TargetScan); Disease association (LncRNADisease, MNDR, eDGAR and circRNADisease)EXP: Literature mining |
| lncRRIsearch (2019) [163] |
http://rtools.cbrc.jp/LncRRIsearch/ (accessed on 8 March 2021) | lncRNA-mRNA | CPU: RIBlast | EXP: Tissue expression |
| DIANA-LncBase v3 (2020) [164] |
https://diana.e-ce.uth.gr/lncbasev3 (accessed on 8 March 2021) | miRNA-lncRNA | EXP: Re-processing and integration of experimental data (miRNA, AGO2-CLIP-Seq and CLIP-Seq) | CPU: Correlation with lncRNA expression |
| SPONGEdb v1 (2021) [165] |
https://exbio.wzw.tum.de/sponge/home (accessed on 8 March 2021) | miRNA-lncRNA | CPU: DIANA-LncBase, TargetScan, miRcode, miRTarBase | EXP: TCGA expression |
| LnCeVar v1 (2020) [166] |
http://www.bio-bigdata.net/LnCeVar/ (accessed on 8 March 2021) | miRNA-lncRNA | EXP: SNP and mutation data from TCGA, COSMIC, 1000 Genomes Project | CPU: Integration from miRanda, mirBase, miRTarBase, TargetScan |
| miRSponge v1 (2015) [167] |
http://bio-bigdata.hrbmu.edu.cn/miRSponge/ (accessed on 8 March 2021) | miRNA-lncRNA miRNA-circRNA |
EXP: Manual curation from literature | CPU: Integration from TarBase, miRTarBase, miRanda, miRecord |
| starBase/ENCORI v2 (2014/2021) [79] |
http://starbase.sysu.edu.cn/ (accessed on 8 March 2021) | miRNA-ncRNA; RBP-RNA;RNA-RNA | EXP: Re-processing and integration of experimental data (CLIP-Seq & variations) | CPU: Correlation of RBP somatic mutation with diseases EXP: Pan-Cancer networks from expression profiles (TCGA) |
| RAID v3/RNAInter (2020) [168] |
http://www.rna-society.org/raid/ (accessed on 8 March 2021) | RNA-Protein; RNA-RNA; RNA-Histone; RNA-Drug | EXP/CPU: Integration of literature sources and 35 databases. | EXP: Methylation, localisation and editing data from other databases. |
| RISE (2018) [161] |
http://rise.life.tsinghua.edu.cn/index.html (accessed on 8 March 2021) | RNA-RNA | EXP: Integration from sequencing based studies | CPU: Integration with several other databases (RAIN, RAID, NPInter) |
| LncRNA2Target v2 (2019) [169] |
http://123.59.132.21/lncrna2target/ (accessed on 8 March 2021) | lncRNA-RNA | EXP: Manual extraction of interaction associations from literature | EXP: Re-processing of lncRNA perturbation RNA-Seq datasets |
| LncExpDB (2020) [170] |
https://bigd.big.ac.cn/lncexpdb/interactions (accessed on 8 March 2021) | lncRNA-mRNA | CPU: Co-expression network analysis and prediction | EXP: Expression extracted from public repositories (GEO, SRA and ArrayExpress) |
| LncACTdb v2 (2019) [171] |
http://www.bio-bigdata.net/LncACTdb (accessed on 8 March 2021) | miRNA-lncRNA-mRNAmiRNA-circRNA | EXP: Manual curation from literature | CPU: Predictions from networks and integration with Pan-Cancer data (TCGA) |