Supplementary table 4. Transcription factors significantly over-represented in the 500bp upstream sequences of analyzed groups of genes. The matrix ID and factor name are from the Transfac database.

Genes* / Transcription factor/ binding matrix ID / Number of genes containing the motif / Number of genes containing the motif in the control group (n=44236) § / FDR-adjusted p-value
Cluster A genes (n=372) / ETF/V$ETF_Q6 / 88 / 5911 / 0
Kid3/V$KID3_01 / 336 / 36299 / 0
RFX/V$RFX_Q6 / 128 / 8768 / 0
RFX1/V$RFX1_02 / 49 / 1918 / 0
Sp1/V$SP1_Q2_01 / 91 / 5329 / 0
ZF5/V$ZF5_B / 118 / 7490 / 0
v-Myb/V$VMYB_02 / 107 / 8273 / 0
KROX/V$KROX_Q6 / 57 / 3707 / 0.00001
MAZ/V$MAZ_Q6 / 81 / 5854 / 0.00001
c-Ets-1 p54/V$CETS1P54_03 / 56 / 3711 / 0.00001
CKROX/V$CKROX_Q2 / 58 / 4121 / 0.00007
AP-2/V$AP2_Q6_01 / 44 / 2918 / 0.00025
Pax-5/V$PAX5_02 / 26 / 1466 / 0.00032
HIC1/V$HIC1_02 / 26 / 1541 / 0.00066
Pax-3/V$PAX3_B / 60 / 4789 / 0.00105
Tax/CREB/V$TAXCREB_02 / 19 / 1072 / 0.002
WT1/V$WT1_Q6 / 79 / 7003 / 0.00319
GABP/V$GABP_B / 51 / 4161 / 0.00399
LRF/V$LRF_Q2 / 45 / 3678 / 0.00701
CP2/LBP-1c/LSF/V$CP2_02 / 67 / 5977 / 0.00788
ATF6/V$ATF6_01 / 22 / 1507 / 0.00906
NF-Y/V$NFY_Q6_01 / 15 / 910 / 0.0107
STAT1/V$STAT1_01 / 13 / 755 / 0.01214
ZNF219/V$ZNF219_01 / 7 / 247 / 0.01847
AP-2alpha/V$AP2ALPHA_01 / 27 / 2097 / 0.01896
SZF1-1/V$SZF11_01 / 64 / 5928 / 0.02
Tax/CREB/V$TAXCREB_01 / 16 / 1077 / 0.02076
c-Ets-1(p54)/V$CETS1P54_02 / 16 / 1131 / 0.03065
Sp3/V$SP3_Q3 / 12 / 785 / 0.03471
PPAR, HNF-4, COUP, RAR/V$DR1_Q3 / 11 / 706 / 0.03751
HIF1/V$HIF1_Q3 / 19 / 1381 / 0.0449
PPAR direct repeat 1/V$PPAR_DR1_Q2 / 21 / 1688 / 0.04839
c-Myc:Max/V$MYCMAX_03 / 40 / 3645 / 0.04932
Known cilia-related genes in cluster A (n=162) / RFX1/V$RFX1_02 / 26 / 1918 / 0
ZF5/V$ZF5_B / 56 / 7490 / 0
Sp1/V$SP1_Q2_01 / 46 / 5329 / 0
RFX/V$RFX_Q6 / 58 / 8768 / 0
ETF/V$ETF_Q6 / 43 / 5911 / 0.000318
CKROX/V$CKROX_Q2 / 31 / 4121 / 0.005565
v-Myb/V$VMYB_02 / 49 / 8273 / 0.005906
MAZ/V$MAZ_Q6 / 38 / 5854 / 0.01113
Kid3/V$KID3_01 / 147 / 36299 / 0.025793
ZNF219/V$ZNF219_01 / 5 / 247 / 0.032378
KROX/V$KROX_Q6 / 25 / 3678 / 0.032378
New ciliary genes prediction (n=210) / ZF5/V$ZF5_B / 62 / 7490 / 0
RFX/V$RFX_Q6 / 70 / 8768 / 0
RFX1/V$RFX1_02 / 23 / 1918 / 0.002173
Sp1/V$SP1_Q2_01 / 45 / 5329 / 0.002853
c-Ets-1 p54/V$CETS1P54_03 / 32 / 3711 / 0.015281
KROX/V$KROX_Q6 / 32 / 3707 / 0.015281
ETF/V$ETF_Q6 / 45 / 5911 / 0.015281
Kid3/V$KID3_01 / 189 / 36299 / 0.015281
v-Myb/V$VMYB_02 / 58 / 8273 / 0.015938
Pax-3/V$PAX3_B / 38 / 4789 / 0.016137
MAZ/V$MAZ_Q6 / 43 / 5854 / 0.030229
Motile Ciliome
(N=648) / AhR, Arnt, HIF-1/V$AHRHIF_Q6 / 28 / 1044 / 0.007381
AP-2/V$AP2_Q6 / 51 / 2918 / 0.006626
AP-2/V$AP2_Q6_01 / 58 / 2918 / 0.032471
AP-2alpha/V$AP2ALPHA_01 / 46 / 2097 / 0.014335
ATF6/V$ATF6_01 / 44 / 1507 / 8.71E-05
CBF (core binding factor)/V$CBF_02 / 11 / 285 / 0.014335
c-Ets-1 p54/V$CETS1P54_03 / 130 / 3711 / 0
c-Ets-1(p54)/V$CETS1P54_02 / 42 / 1131 / 0
CKROX/V$CKROX_Q2 / 90 / 4121 / 0.00025
c-Myc:Max/V$MYCMAX_03 / 94 / 3645 / 0
CP2/LBP-1c/LSF/V$CP2_02 / 137 / 5977 / 0
CREB/V$CREB_02 / 61 / 2403 / 8.71E-05
CREB/V$CREB_Q4_01 / 45 / 1710 / 0.000534
DEC/V$DEC_Q1 / 9 / 235 / 0.032471
E2F/V$E2F_03 / 37 / 1157 / 8.71E-05
E2F/V$E2F_Q6_01 / 21 / 726 / 0.01098
Ebox/V$EBOX_Q6_01 / 30 / 827 / 0
ETF/V$ETF_Q6 / 165 / 5911 / 0
GABP/V$GABP_B / 117 / 4161 / 0
HIC1/V$HIC1_02 / 39 / 1541 / 0.003006
HIF1/V$HIF1_Q3 / 38 / 1381 / 0.000805
Kid3/V$KID3_01 / 572 / 36299 / 0
KROX/V$KROX_Q6 / 100 / 3707 / 0
MAZ/V$MAZ_Q6 / 113 / 5854 / 0.003006
MyoD/V$MYOD_Q6_01 / 19 / 663 / 0.017311
NF-Y/V$NFY_01 / 37 / 1411 / 0.002323
Pax-3/V$PAX3_B / 106 / 4789 / 0
Pax-5/V$PAX5_02 / 44 / 1466 / 0
Pax-8/V$PAX8_01 / 51 / 2546 / 0.042045
RFX/V$RFX_Q6 / 172 / 8768 / 0
RFX1/V$RFX1_02 / 61 / 1918 / 0
Sp1/V$SP1_Q2_01 / 163 / 5329 / 0
STAT1/V$STAT1_01 / 26 / 755 / 0.000318
Stra13/V$STRA13_01 / 6 / 121 / 0.036097
Tax/CREB/V$TAXCREB_01 / 28 / 1077 / 0.010866
Tax/CREB/V$TAXCREB_02 / 28 / 1072 / 0.010508
Tel-2/V$TEL2_Q6 / 60 / 2912 / 0.014335
USF/V$USF_Q6_01 / 48 / 1280 / 0
v-Myb/V$VMYB_02 / 51 / 8273 / 0
WT1/V$WT1_Q6 / 143 / 7003 / 0
ZF5/V$ZF5_B / 216 / 7490 / 0

*Only the transcription factors that remained significant after multiple testing correction are shown. §All human promoters sequences in PAINT databases were used as reference set. FDR false-discovery rate.