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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