Table 3 Over-represented conserved TFBSs in human BDNF and in the BDNF-correlated genes as predicted by DiRE and CONFAC.

ARNT

0.012

BDNF pI-II, BDNF 3'UTR; PRKCE, USP2, CAMK2D, CCND2, NEUROD6, THRA, DUSP1, CBX6, ATP1B1, FREQ, ITF-2

POU3F2

(BRN2)

< 0.001

BDNF pII-V, BDNF exon II, IV, IX, BDNF3'UTR; USP2, CAMK2D, THRA, NFIA, PRSS23, CBX6, CUGBP2, EPHA5, EPHA7, BAIAP2, RKCE, CPD, EPHA4, IL6ST, CCND2, DUSP6, KCND2, MAN1A1, SCG2, GRIA3, COL11A1, TRPC4, FGF13, HN1, ANGPT1, TCF4, MYH9, PCSK1

CHOP

NA

BDNF I, COL11A1, CD44, BAIAP2, PPP3CA, IL6ST, NEUROD6, SCG2, CYR61, IGFBP5, THRA, NFIA, FGF13, ATP1A2, ANGPT1, DBC1, CUGBP2, EGR1

CREB

0.013

BDNF pI, IV, VI, BDNF exon I; BAIAP2, PRKCE, USP2, EPHA4, CAMK2D, CCND2, FGFR1, CYR61, GRIA3, THRA, DUSP1, PENK, PCSK1, PCSK2, HN1, ATP1B1, EGR1, COL4A5, KLF10, EPHA4, FGF13, CBX6, CUGBP2, EPHA5

ETS2

NA

BDNF pII, VIII; THRA, EPHA7, FGF13, BAIAP2 and NFIA promoters, and in COL11A1, PLAGL1, and XIAP intergenic regions

FOXO4

< 0.001

BDNF exon I, II, VIII, IX, BDNF pIII, IV, BDNF 3'UTR; CD44, TBX3, BAIAP2, PPP3CA, CPD, USP2, PRKCB, EPHA4, CORO1A, CAMK2D, NEUROD6, FGFR1, SCG2, CYR61, GRIA3, THRA, NFIA, COL11A1, DUSP1, TRPC4, PRSS23, PCSK2, ANGPT1, FREQ, PRKAG2, TCF4, MYH9, PCSK1, DBC1, CUGBP2, EGR1, EPHA5

GATA1

< 0.001

BDNF pI, III-V, BDNF exon I, II, VIII, IX, BDNF 3'UTR; CD44, TBX3, SNCA, PPP3CA, PRKCE, COL4A5, USP2, EPHA4, IL6ST, SLC4A7, CAMK2D, ATF3, CCND2, NEUROD6, DUSP6, KCND2, SCG2, CYR61, IGFBP5, THRA, NFIA, COL11A1, PENK, FGF13, PRSS23, ATP1B1, ATP1A2, ANGPT1, DBC1, CUGBP2, EGR1

GFI1

< 0.001

BDNF exon I, BDNF pII-VI, BDNF 3'UTR; SNCA, ATP1A2, MYH9, DBC1, CD44, BAIAP2, PPP3CA, PRKCE, COL4A5, CPD, USP2, EPHA4, IL6ST, SLC4A7, CAMK2D, CCND2, NEUROD6, KCND2, SCG2, CYR61, IGFBP5, THRA, NFIA, COL11A1, DUSP1, TRPC4, PENK, FGF13, PRSS23, PCSK2, ATP1B1, PTPRF, ANGPT1, TCF4, CUGBP2, EGR1, EPHA5, EPHA7

IK1 (ikaros)

< 0.001

BDNF pI, BDNF exon I-V, IX, BDNF 3'UTR; PRKCB, KLF10, KCND2, THRA, NFIA, COL11A1, FGF13, ATP1A2, MYH9, PCSK1, CUGBP2, EPHA7

KROX family

NA

BDNF pV, BDNF exon IV; PPP3CA, NFIA, DBN1, KCND2, IRS2, MAN1A2, CCND2, PVRL3, XIAP, DLGAP4, CYR61, ATP1B1, PURA, SMARCA4, MYH9, GRIA3, EPHA4, DUSP6, EGR1, COL4A5, TRPC4, PRKCB, NPTX1, PTGS2, EPHA5, FGFR1, CBX6, PRKCE, KLF10, THRA, ATP1A2, BAIAP2, CPD, CORO1A, CAMK2D, IGFBP5, DUSP1, PTPRF, FREQ, PRKAG2

MAZ

NA

BDNF pVh, BDNF exon III, IV; CD44, PPP3CA, PRKCE, COL4A5, USP2, PRKCB, KLF10, EPHA4, CAMK2D, CCND2, DUSP6, GRIA3, THRA, COL11A1, PENK, FGF13, CBX6, ATP1B1, PTPRF, ATP1A2, FREQ, DBN1, CUGBP2, EGR1, EPHA7

MEF2

NA

BDNF pII-V, BDNF exon II, IX, BDNF 3'UTR; CD44, TBX3, BAIAP2, PPP3CA, PRKCE, COL4A5, EPHA4, IL6ST, CAMK2D, CCND2, NEUROD6, DUSP6, MAN1A1, IGFBP5, COL11A1, TRPC4, PRSS23, ANGPT1, FREQ, PURA, MYH9, PCSK1, CUGBP2, EPHA7, SNCA, FGF13

MYC/MAX

NA

BDNF pI, II, IV; CD44, TBX3, PRKCE, USP2, CAMK2D, CCND2, NEUROD6, THRA, NFIA, DUSP1, CBX6, ATP1B1, FREQ, ITF-2, EGR1

MYCN

NA

BDNF pI, II; PRKCE, USP2, CAMK2D, CCND2, NEUROD6, THRA, DUSP1, CBX6, ATP1B1, FREQ, ITF-2

MYOD

< 0.001

BDNF exon I, IX; CD44, PRKCE, USP2, PRKCB, EPHA4, DUSP6, SCG2, SMARCA4, THRA, PRSS23, ATP1B1, CUGBP2

NFkB

< 0.001

BDNFI, BDNF 3'UTR; PPP3CA, KLF10, PCSK2, ATP1B1, ANGPT1, MYH9, USP2, DUSP6, FGF13, PURA, BAIAP2, CAMK2D, CCND2, FGFR1, CYR61, PCSK2, MYH9, CUGBP2, EGR1, EPHA7

NRSF

NA

BDNFII, EPHA4, IRS2, EPHA5, NPTX1, PRKCB, TRPC4, COL4A5

S8

< 0.001

BDNF pII-IV, BDNF exon II, IV, VIII, IX, BDNF 3'UTR; CD44, BAIAP2, PRKCE, NPTX1, EPHA4, CAMK2D, CCND2, NEUROD6, DUSP6, FGFR1, KCND2, MAN1A1, SCG2, THRA, NFIA, COL11A1, PENK, PCSK2, ANGPT1, PURA, ITF-2, MYH9, DBC1, CUGBP2, EGR1, EPHA5

SOX5

0.001

BDNF exon I, BDNF 3'UTR; EPHA4, THRA and PLAGL1 3'UTR; NFIA and OLFM1 promoters; SCG2 intergenic region; KCND2 intron

TAL1/TCF4

NA

BDNF pIV, BDNF exon I, BDNF 3'UTR; ATP1B1 3'UTR, MYH9 3'UTR and XIAP 3'UTR; SCG2, CD44, SERPINE1, SLC4A7, CCND2, NEUROD6, FGFR1, THRA, COL11A1, PCSK2, ANGPT1, DBC1, CUGBP2

WT1

NA

BDNF pI, BASP1, PPP3CA, NFIA, DBN1, EPHA7, BAIAP2, XIAP, DLGAP4, PURA, IRS2, ATP1B1, KCND2, GRIA3, HN1, EPHA4, EGR1, COL4A5, TRPC4, ATP1A2, PRKCB, NPTX1, DBC1, EPHA5