Table 3.
Summary of the revised miRNA functional enrichment analysis tools.
| Tool | Annotation/Bias Handling | Method | Targets | Sources of Annotations | Organism |
|---|---|---|---|---|---|
| miRNet | Indirect, Direct/Empirical sampling | SEA | Validated, predicted | GO, KEGG, Reactome, TAM [58] | H. sapiens, M. musculus, R. norvegicus, B. taurus, Sus scrofa, G. gallus, D. melanogaster, C. elegans, D. rerio, Schistosoma mansoni |
| GeneCodis | Indirect/Empirical sampling, co-annotation | MEA, SEA | Validated | DoRothEA [59], miRTarBase, GO, KEGG Pathways, MGI [60], Panther, Reactome, WikiPathways, CTD [61], HPO, LINCS [62], OMIM, PharmGKB [63] | D. melanogaster, D. rerio, H. sapiens, M. musculus, R. norvegicus. |
| miEAA | Indirect, Direct/None | SEA, GSEA | Validated, redicted | GO, HMDD, KEGG, miRandola [64], miRBase, miRPathDB, miRTarBase, miRWalk [65], MNDR, NPInter [66], RNALocate [67], SM2miR, TAM, TissueAtlas [68], TransmiR [69], Literature | H. sapiens, M. musculus. R. norvegicus, Arabidopsis thaliana, B. taurus, C. elegans, D. melanogaster, D. rerio, G. gallus, S. scrofa |
| MIENTURNET | Indirect/None | SEA | Validated, predicted | KEGG, Reactome, WikiPathways, Disease Ontology | H sapiens, M. musculus, R. norvegicus, C. elegans, D. melanogaster, D. rerio |
| TAM | Direct/Mask cancer and unspecific terms | SEA | - | Literature | H. sapiens |
| miTALOS | Indirect/Background specificity | SEA | Validated, predicted | KEGG, WikiPathways, Reactome | H. sapiens, M. musculus |
| miRSystem | Indirect/Empirical sampling | SEA | Validated, predicted | KEGG, GO, BioCarta [70], Pathway Interaction Database [71], Reactome. | H. sapiens, M. musculus |
| DIANA miRPath | Indirect/Empirical sampling | SEA | Validated, predicted | GO, KEGG | H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, G. gallus, D. rerio. |