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