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Table 2 NFATc1 target gene regulation prediction based on the regulation prediction using SVM, NN and log2FC only

From: Predicting the targets of IRF8 and NFATc1 during osteoclast differentiation using the machine learning method framework cTAP

Model

Up regulation

Down regulation

Log2FC only

ABCB4, ACADM, ACADS, ACADVL, ACAT1, ACBD6, ACO2, AK2, ALDH4A1, AP1G2, APBA3, ATP5E, ATP5G1, ATP5G2, ATP5G3, ATP5J, ATP5L, ATP6V0B, ATP6V1C1, ATP6V1D, ATP6V1H, BCAT2, BCL2L13, BSG, C1QBP, CIAPIN1, COMTD1, COQ6, COX15, COX5B, COX7A2, COX7A2L, CS, CTTN, CYC1, CYCS, DLAT, DLST, ECSIT, ETFA, ETFDH, EXT1, FAHD1, FASTK, FDXR, GNB1L, GPX4, GSS, GTF2H3, HAGH, HINT3, IDH3A, IDH3B, IK, IMMT, KIF13A, LETM1, LRPPRC, MANBAL, MCAT, MCRS1, MDH1, MDH2, MFN2, MRPL1, MRPL14, MRPL34, MRPL36, MRPL38, MRPL46, MRPL48, MRPL51, MRPL9, MRPS25, MRPS34, MRPS35, MTX2, NDUFA10, NDUFA4, NDUFA5, NDUFA6, NDUFAB1, NDUFAF1, NDUFB10, NDUFB3, NDUFB5, NDUFB6, NDUFB7, NDUFC1, NDUFS3, NDUFS7, NDUFS8, NHEJ1, NSMAF, NUDT8, OGDH, OPA1, OXNAD1, PABPC4, PGAM5, PGLS, PIGO, PIP5K1B, PITPNM1, PPA2, PPARGC1B, PTGES2, PTPN12, PTPN9, RABGEF1, RELB, REPIN1, RREB1, SDHD, SLC25A11, SLC25A19, SLC25A3, SLC25A39, SLC25A5, SLC30A6, SLC39A13, SOD2, ST5, STARD7, TANK, TARBP2, TAX1BP3, TBC1D10B, TBRG4, TCIRG1, TERF2IP, TFRC, TIMM17A, TIMM44, TMEM60, TNFAIP3, TTC19, TUFM, UBE2G1, UBLCP1, UQCRC1, UQCRC2, UQCRH, USP4, VDAC1, VTI1B

CD164, CD48, CHST12, CNR2, CORO1A, EBI3, EPS15, FLI1, GCA, GNG2, IER3, IL10RA, IRF8, LAMP1, LSP1, MARCKS, NEDD9, NUCB2, P2RY6, PKIB, POU2F2, PRKD2, RASSF5, RB1, RBM43, RNASE4, RPS6KA3, SSBP2, TLE3, TLR6, TNFSF9, TPD52, WSB1, ZFP90

SVM

ABCB4, ACAD10, ACADS, AP1G2, ATP5L, CIAPIN1, CNIH4, COX15, COX7A2, CYC1, DLAT, DNAJA3, DUS3L, EXT1, FAHD1, FDXR, FEM1A, HAGH, HINT3, IDH3A, IMMT, LRPPRC, MANBAL, MCAT, MCRS1, MRPL36, MRPL38, MRPL9, MRPS34, MRPS35, NDUFB10, NDUFB5, NDUFB6, NDUFS3, NDUFS7, NSMAF, PABPC4, PEX16, PGLS, PIGQ, PIP5K1B, PPARGC1B, PRDX3, PTGES2, PTPN12, SEMA7A, SLC25A19, SLC39A13, SSNA1, ST5, TIMM44, TTC19, TUFM, USP4

ANXA6, ATF3, CCL3, CD48, CDC42EP3, CHST12, CPEB2, DCK, EBI3, FLI1, GNG2, IRF5, IRF8, LSP1, LXN, MAP4K2, PIK3CG, SLC15A3, SLC9A3R1, SP100, TEX2, TLR6, TNFSF9, ZFP90

NN

ABCB4, ACAD10, ACADS, AK2, AP1G2, ATP5G3, ATP5L, BCAT2, CIAPIN1, COG8, COQ6, COX15, COX17, CYC1, DLAT, DNAJA3, DUS3L, ECSIT, ETFDH, EXT1, FASTK, FDXR, GSS, HAGH, HINT2, HINT3, IDH3A, LRPPRC, MANBAL, MBTPS1, MCRS1, MRPL12, MRPL38, MRPL9, MRPS25, MRPS34, MRPS35, NDUFB10, NDUFC1, NDUFS3, NDUFS7, NSMAF, NUDT8, OXNAD1, PABPC4, PIP5K1B, PITPNM1, PPARGC1B, PRDX3, PTDSS2, PTGES2, RABGEF1, RELB, SLC39A13, STARD7, TANK, TAX1BP3, TBRG4, TCF12, TTC19, TUFM, UBE2G1, UBLCP1, UMPS, USP4

ADAM15, CCL3, CD48, CHST12, CPEB2, EBI3, FLI1, GNG2, IL10RA, IRF8, LSP1, LXN, MAP4K2, MARCKS, MS4A7, NAB2, NOTCH1, NUCB2, P2RY6, POU2F2, RB1, RNASE4, RPS6KA3, SLC15A3, SLC9A3R1, SNAP29, TEX2, TMBIM1, TNFSF9

Gaussian NB

ACO2, ACSL1, DLAT, DNAJA3, FDXR, GSS, MCRS1, NFKB2, NFKBIE, NUDT8, OTUD7B, OXNAD1, PPARGC1B, PTGES2, SARS2, SDC1, SEMA7A, SLC25A39, SLC39A13, TARBP2, TBRG4, TRAF1

CCR5, CDC42EP3, CNR2, ECE1, GSTK1, ICAM2, NAB2, PIAS3, SORL1, TLR6, TNFSF9

LR

ABCB4, ACAD10, AK2, AP1G2, ATOX1, ATP5G2, BCAT2, DNAJA3, DUS3L, EXT1, FAHD1, FASTK, FDXR, IDH3A, IVNS1ABP, MCRS1, MFN2, NDUFS3, NFKBIE, NSMAF, OTUD7B, OXNAD1, PABPC4, PPARGC1B, PTGES2, PTPN12, REPIN1, SDC1, SEMA7A, SERPINB8, SLC39A13, ST5, STARD7, TANK, TARBP2, TBRG4, XRCC5

GSTK1, HSPA2, ICAM2, NFKBIZ, PARVG, RASSF5, RBM43, SORL1, TNFSF9