Table 3 Comparison of network-based analysis approaches considering internal knowledge bases
From: Analysis of miRNA, mRNA, and TF interactions through network-based methods
Tool | miRNA-mRNA | TF-genes | miRNA-TF |
|---|---|---|---|
dChip-GemiNi [42] | TargetScan and PicTar | TRANSFAC matrices v7.0 | miRBase - TRANSFAC |
MAGIA 2[44] | Microcosm, microrna.org, DIANA-microT, miRDB, PicTar, PITA, RNA22, and TargetScan | ECRbase | mirGen2.0 and TransmiR |
mirConnX [47] | PITA, miRANDA, TargetScan 5.0, RNAhybrid, and PicTar | JASPAR and TRANSFAC | CoreBoost_HM |
IntegraMiR [54] | mSigDB, mirTarBase, miRecords | TRANSFAC | TransMiR |