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Table 1 Cao et al 2006 top ChIP-on-chip predictions with CORE_TF

From: CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

A. MyoD ChIP-on-chip
C2C12 MyoD FAST p-val* C2C12 MyoD %GC p-val* MDER MyoD FAST p-val* MDER MyoD %GC p-val*
AP1_Q6_01 0 MYOGENIN_Q6 1.5E-06 AP1_Q6_01 0 AP4_Q5 0
E2F1DP1_01 0 AP4_Q5 2.3E-06 AP4_Q5 0 AP4_Q6 3.1E-06
E2F4DP2_01 0 E2A_Q2 2.7E-06 COUP_DR1_Q6 0 MYOGENIN_Q6 2.7E-05
E2F_Q4 0 AP4_Q6 8.8E-06 E2F1DP1_01 0 AP4_Q6_01 2.7E-04
E2F_Q6_01 0 MYOD_Q6 8.8E-06 E2F4DP2_01 0 AP4_01 1.2E-03
GATA3_01 0 AP4_Q6_01 5.1E-05 E2F_Q4 0 MYOD_Q6 4.5E-03
MAF_Q6_01 0 E47_01 1.1E-03 E2F_Q6_01 0 E2A_Q2 5.2E-03
NF1_Q6_01 0 E12_Q6 1.4E-03 MAF_Q6_01 0 LBP1_Q6 2.3E-02
NFE2_01 0 LBP1_Q6 4.0E-03 NF1_Q6_01 0 HEN1_02 7.6E-02
OSF2_Q6 0 E2A_Q6 4.6E-03 NFE2_01 0 TAL1BETAE47_01 7.6E-02
AP4_Q5 7.9E-09 SMAD_Q6_01 2.7E-02 NFKB_Q6 0 MYOD_Q6_01 1.7E-01
MYOGENIN_Q6 7.9E-09 MYOD_Q6_01 4.4E-02 OSF2_Q6 0 HEB_Q6 2.9E-01
LBP1_Q6 2.2E-08 AP1FJ_Q2 4.5E-02 AP4_Q6 3.5E-09 HELIOSA_01 2.9E-01
AP4_Q6 5.8E-08 AP1_Q4 5.8E-02 GATA3_01 3.5E-09 AP1_Q4 4.0E-01
AP4_Q6_01 6.2E-08 E47_02 9.4E-02 LBP1_Q6 6.5E-08 HNF4_01 4.0E-01
B. Myog ChIP-on-chip
C2C12 Myog FAST p-val* C2C12 Myog %GC p-val* MDER Myog FAST p-val* MDER Myog %GC p-val*
AP1_Q6_01 0 AP4_Q5 0 AP1_Q6_01 0 AP4_Q5 0
AP4_Q5 0 AP4_Q6 0 AP4_Q5 0 AP4_Q6 0
E2F1DP1_01 0 MYOD_Q6 5.0E-06 COUP_DR1_Q6 0 AP4_Q6_01 2.5E-06
MAF_Q6_01 0 AP4_Q6_01 1.1E-05 E2F1DP1_01 0 LBP1_Q6 8.0E-06
MYOGENIN_Q6 0 E2A_Q2 9.0E-04 E2F4DP2_01 0 MYOD_Q6 8.1E-06
NF1_Q6_01 0 AREB6_01 6.9E-03 E2F_Q4 0 E2A_Q2 7.1E-03
NFE2_01 0 MYOD_Q6_01 1.4E-02 E2F_Q6_01 0 MYOD_Q6_01 8.6E-03
OSF2_Q6 0 LBP1_Q6 1.4E-02 LBP1_Q6 0 CLOCKBMAL_Q6 4.5E-02
E2F4DP2_01 4.7E-09 AP4_01 1.9E-02 MAF_Q6_01 0 AP2ALPHA_01 5.7E-02
COUP_DR1_Q6 1.6E-07 AP1_Q4 2.2E-02 MYOGENIN_Q6 0 ZEC_01 5.8E-02
AP4_Q6_01 2.3E-07 ZEC_01 2.2E-02 NF1_Q6_01 0 AP2_Q6 7.7E-02
E2F_Q4 1.3E-06 E2A_Q6 7.1E-02 NFE2_01 0 AP4_01 1.1E-01
GATA3_01 6.5E-06 ATF6_01 8.0E-02 OSF2_Q6 0 PPARG_01 1.2E-01
MYOD_Q6 7.5E-06 E47_01 8.2E-02 AP4_Q6_01 6.4E-09 CMYC_02 1.2E-01
  1. CORE_TF predictions on Cao et al 2006 ChIP-on-chip data. Target TFBS are presented in bold. * = p-values are Benjamini & Hochberg corrected. Note: in the MyoD FAST runs MYOD_Q6 and MYOD_Q6_01 had p-values < 0.05 but were not in the top 15 significant TFBS.