Table 3.
Comparison among the proposed miRTissue ce database and other 7 ceRNA interactions databases, in terms of their main features
| Features | miRTissue ce | miRTarBase | ceRDB | lnCeDB | miRSponge | LncACTdb | miRcode | starBase v2.0 |
|---|---|---|---|---|---|---|---|---|
| ceRNA interaction data sources | miRTarBase | HMDD | TargetScan | TargetScan | TarBase | miRTarBase | TargetScan | miRBase |
| miRCode | NCBI | StarBase | miRTarBase | miRanda | refSeq | |||
| LncACTdb 2.0 | RefSeq | miRCode | miRanda | TarBase | Ensembl database | |||
| miRSponge | miRBase | miRecord | TargetScan | |||||
| miRanda | Pictar2, miRanda | |||||||
| TargetScan | PITA, RNA22 | |||||||
| ceRNA classes | miRNA-mRNA | miRNA-mRNA | miRNA-mRNA | miRNA-mRNA | miRNA-mRNA | miRNA-mRNA | miRNA-mRNA | miRNA-mRNA |
| miRNA-lncRNA | miRNA-lncRNA | miRNA-lncRNA | miRNA-lncRNA | miRNA-lncRNA | miRNA-lncRNA | |||
| miRNA-Pseudogenes | miRNA-Pseudogenes | miRNA-Pseudogenes | miRNA-Pseudogenes | miRNA-Pseudogenes | ||||
| miRNA-circRNA | miRNA-circRNA | miRNA-circRNA | ||||||
| RBP-ncRNA | ||||||||
| RBP-mRNA | ||||||||
| ceRNA network | hypergeometric test | N/A | N/A | hypergeometric test | hypergeometric test | hypergeometric test | N/A | hypergeometric test |
| prediction algorithm | + | + | ||||||
| global test | Pearson correlation | |||||||
| + | ||||||||
| SPONGE | ||||||||
| TCGA expression profiles | Yes | No | No | No | No | Yes | No | Yes |
| for ceRNA interactions | ||||||||
| p-value on | Yes | No | No | No | No | No | No | No |
| ceRNA interaction score | ||||||||
| Multiple ceRNA analysis | Yes | No | No | No | No | No | No | No |
| Multiple tissue selection | Yes | No | No | No | No | No | No | Yes |
| References | N/A | [17] | [25] | [27] | [30] | [34] | [29] | [28] |