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

From: Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation

TFBS p-value
CONFAC
Target genes
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
  1. In BDNF, TFBSs were found in promoters (p), exons or 3'UTR of the gene. In the correlated genes, TFBSs were searched for and discovered mostly in promoters (unless indicated otherwise). P-values are given for the TFBSs discovered using CONFAC. NA - not applicable for the TFBSs discovered using DiRE [see Additional files 10 and 11 for TFBS importance score].