S.ScerTFYeast transcription factor database Aaron Spivak
← All factors / TF RECORD

CBF1

YJR060W, CPF1, CEP1

View at SGD ↗

Helix-loop-helix protein that binds the motif CACRTG, which is present at several sites including MET gene promoters and centromere DNA element I (CDEI); required for nucleosome positioning at this motif; targets Isw1p to DNA

01 / RECOMMENDED MATRIX

Best-performing DNA-binding model.

RecommendedSource: Macisaac et. al
Fisher’s P-value1.27e-162
Information content14.18
Max PWM score11.38
Recommended cutoff7.88
View and copy the recommended matrices ↘
Position frequency matrix (PFM)
A | 0.245 0.029 0.011 0.985 0.004 0.018 0.017 0.001 
C | 0.002 0.003 0.978 0.001 0.938 0.018 0.008 0.007 
G | 0.737 0.081 0.005 0.012 0.006 0.961 0.004 0.984 
T | 0.016 0.887 0.006 0.002 0.052 0.003 0.971 0.008
Position count matrix (PCM)
A |  24   2   1  98   0   1   1   0 
C |   0   0  97   0  93   1   0   0 
G |  73   8   0   1   0  96   0  98 
T |   1  88   0   0   5   0  97   0
Position weight matrix (PWM)
A | -0.27 -2.40 -3.37  1.12 -4.38 -2.88 -2.94 -5.77 
C | -4.50 -4.09  1.69 -5.19  1.65 -2.30 -3.11 -3.25 
G |  1.41 -0.80 -3.58 -2.71 -3.40  1.68 -3.81  1.70 
T | -3.00  1.02 -3.98 -5.08 -1.82 -4.67  1.11 -3.69
02 / COMPARATIVE BENCHMARKS

Alternative candidate matrices 12

Historical matrix candidates from the original ScerTF database. Expand a source to inspect its original logo, scores, and matrix values.

CBF1Badis et. al.P = 3.64e-147View matrix ↘
Sequence logo for CBF1
Fisher’s P-value3.64e-147
Information content12.37
Max PWM score10.78
Recommended cutoff8.31
Position frequency matrix (PFM)
A | 0.19 0.03 0.97 0.01 0.01 0.01 0.01 0.71 
C | 0.08 0.91 0.01 0.97 0.01 0.01 0.01 0.17 
G | 0.54 0.03 0.01 0.01 0.97 0.01 0.97 0.06 
T | 0.19 0.03 0.01 0.01 0.01 0.97 0.01 0.06
Position count matrix (PCM)
A |  19   3  97   1   1   1   1  71 
C |   8  91   1  97   1   1   1  17 
G |  54   3   1   1  97   1  97   6 
T |  19   3   1   1   1  97   1   6
Position weight matrix (PWM)
A | -0.52 -2.37  1.11 -3.47 -3.47 -3.47 -3.47  0.80 
C | -0.81  1.62 -2.89  1.68 -2.89 -2.89 -2.89 -0.06 
G |  1.10 -1.79 -2.89 -2.89  1.68 -2.89  1.68 -1.10 
T | -0.52 -2.37 -3.47 -3.47 -3.47  1.11 -3.47 -1.67
Badis et. al.
CBF1_AFoat et. al.P = 1.51e-144View matrix ↘
Sequence logo for CBF1_A
Fisher’s P-value1.51e-144
Information content10.47
Max PWM score8.7
Recommended cutoff8.7
Position frequency matrix (PFM)
A | 0.01 0.91 0.01 0.04 0.01 0.01 
C | 0.97 0.01 0.88 0.01 0.01 0.01 
G | 0.01 0.05 0.01 0.94 0.05 0.95 
T | 0.01 0.03 0.10 0.01 0.93 0.03
Position count matrix (PCM)
A |   1  91   1   4   1   1 
C |  97   1  88   1   1   1 
G |   1   5   1  94   5  95 
T |   1   3  10   1  93   3
Position weight matrix (PWM)
A | -3.47  1.05 -3.47 -2.08 -3.47 -3.47 
C |  1.68 -2.89  1.59 -2.89 -2.89 -2.89 
G | -2.89 -1.28 -2.89  1.65 -1.28  1.66 
T | -3.47 -2.37 -1.16 -3.47  1.07 -2.37
Foat et. al.
CBF1_BFoat et. al.P = 1.51e-144View matrix ↘
Sequence logo for CBF1_B
Fisher’s P-value1.51e-144
Information content10.66
Max PWM score8.75
Recommended cutoff8.75
Position frequency matrix (PFM)
A | 0.01 0.93 0.01 0.05 0.02 0.01 
C | 0.97 0.04 0.88 0.02 0.01 0.01 
G | 0.01 0.01 0.01 0.92 0.01 0.97 
T | 0.01 0.03 0.10 0.01 0.96 0.01
Position count matrix (PCM)
A |   1  93   1   5   2   1 
C |  97   4  88   2   1   1 
G |   1   1   1  92   1  97 
T |   1   3  10   1  96   1
Position weight matrix (PWM)
A | -3.47  1.07 -3.47 -1.86 -2.77 -3.47 
C |  1.68 -1.50  1.59 -2.20 -2.89 -2.89 
G | -2.89 -2.89 -2.89  1.63 -2.89  1.68 
T | -3.47 -2.37 -1.16 -3.47  1.10 -3.47
Foat et. al.
CBF1_AFordyce et. al.P = 3.46e-150View matrix ↘
Fisher’s P-value3.46e-150
Information content6.708
Max PWM score8.34
Recommended cutoff7.33
Position frequency matrix (PFM)
A | 0.41 0.15 0.05 0.84 0.01 0.18 0.14 0.03 
C | 0.13 0.34 0.93 0.04 0.69 0.15 0.11 0.06 
G | 0.17 0.22 0.01 0.05 0.06 0.66 0.05 0.73 
T | 0.28 0.30 0.01 0.07 0.24 0.01 0.71 0.17
Position count matrix (PCM)
A |  41  15   5  84   1  18  14   3 
C |  13  34  93   4  69  15  11   6 
G |  17  22   1   5   6  66   5  73 
T |  28  30   1   7  24   1  71  17
Position weight matrix (PWM)
A |  0.25 -0.76 -1.86  0.97 -3.47 -0.58 -0.83 -2.37 
C | -0.33  0.64  1.64 -1.50  1.34 -0.18 -0.49 -1.10 
G | -0.06  0.20 -2.89 -1.28 -1.10  1.30 -1.28  1.40 
T | -0.13 -0.06 -3.47 -1.52 -0.29 -3.47  0.80 -0.63
Fordyce et. al.
CBF1_BFordyce et. al.P = 9.37e-144View matrix ↘
Fisher’s P-value9.37e-144
Information content6.891
Max PWM score8.39
Recommended cutoff7.22
Position frequency matrix (PFM)
A | 0.16 0.05 0.85 0.01 0.18 0.14 0.03 0.39 
C | 0.35 0.93 0.04 0.71 0.15 0.10 0.07 0.15 
G | 0.23 0.01 0.04 0.05 0.67 0.04 0.75 0.16 
T | 0.26 0.01 0.07 0.24 0.01 0.71 0.16 0.29
Position count matrix (PCM)
A |  16   5  85   1  18  14   3  39 
C |  35  93   4  71  15  10   7  15 
G |  23   1   4   5  67   4  75  16 
T |  26   1   7  24   1  71  16  28
Position weight matrix (PWM)
A | -0.69 -1.86  0.98 -3.47 -0.58 -0.83 -2.37  0.20 
C |  0.66  1.64 -1.50  1.37 -0.18 -0.59 -0.94 -0.18 
G |  0.25 -2.89 -1.50 -1.28  1.31 -1.50  1.43 -0.12 
T | -0.21 -3.47 -1.52 -0.29 -3.47  0.80 -0.69 -0.10
Fordyce et. al.
CBF1_CFordyce et. al.P = 1.48e-112View matrix ↘
Fisher’s P-value1.48e-112
Information content7.575
Max PWM score8.48
Recommended cutoff6.66
Position frequency matrix (PFM)
A | 0.19 0.06 0.88 0.01 0.15 0.18 0.02 
C | 0.38 0.93 0.03 0.78 0.11 0.07 0.07 
G | 0.33 0.01 0.03 0.02 0.73 0.05 0.75 
T | 0.11 0.01 0.06 0.19 0.01 0.70 0.16
Position count matrix (PCM)
A |  19   6  88   1  15  18   2 
C |  38  93   3  78  11   7   7 
G |  33   1   3   2  73   5  75 
T |  11   1   6  19   1  70  16
Position weight matrix (PWM)
A | -0.52 -1.67  1.01 -3.47 -0.76 -0.58 -2.77 
C |  0.75  1.64 -1.79  1.47 -0.49 -0.94 -0.94 
G |  0.61 -2.89 -1.79 -2.20  1.40 -1.28  1.43 
T | -1.07 -3.47 -1.67 -0.52 -3.47  0.78 -0.69
Fordyce et. al.
CBF1Harbison et. al.P = 3.64e-147View matrix ↘
Sequence logo for CBF1
Fisher’s P-value3.64e-147
Information content12.17
Max PWM score9.76
Recommended cutoff8.82
Position frequency matrix (PFM)
A | 0.041 0.014 0.985 0.005 0.019 0.016 0.022 
C | 0.077 0.962 0.003 0.975 0.005 0.014 0.012 
G | 0.160 0.009 0.006 0.004 0.971 0.008 0.942 
T | 0.723 0.015 0.006 0.015 0.005 0.962 0.024
Position count matrix (PCM)
A |   4   1  98   0   1   1   2 
C |   7  96   0  97   0   1   1 
G |  16   0   0   0  97   0  94 
T |  72   1   0   1   0  96   2
Position weight matrix (PWM)
A | -2.05 -3.13  1.12 -4.16 -2.82 -3.00 -2.68 
C | -0.85  1.68 -4.09  1.69 -3.58 -2.55 -2.71 
G | -0.12 -3.00 -3.40 -3.81  1.69 -3.11  1.66 
T |  0.82 -3.06 -3.98 -3.06 -4.16  1.10 -2.59
Harbison et. al.
CBF1_AMorozov et. al.P = 1.51e-144View matrix ↘
Sequence logo for CBF1_A
Fisher’s P-value1.51e-144
Information content12.55
Max PWM score9.9
Recommended cutoff7.03
Position frequency matrix (PFM)
A | 0.047 0.009 0.986 0.003 0.019 0.001 0.034 
C | 0.079 0.960 0.006 0.992 0.006 0.004 0.018 
G | 0.048 0.011 0.004 0.002 0.972 0.003 0.914 
T | 0.826 0.019 0.004 0.003 0.004 0.992 0.033
Position count matrix (PCM)
A |   4   0  98   0   1   0   3 
C |   7  96   0  99   0   0   1 
G |   4   1   0   0  97   0  91 
T |  82   1   0   0   0  99   3
Position weight matrix (PWM)
A | -1.92 -3.57  1.13 -4.67 -2.82 -5.77 -2.24 
C | -0.82  1.67 -3.40  1.71 -3.40 -3.81 -2.30 
G | -1.32 -2.80 -3.81 -4.50  1.69 -4.09  1.62 
T |  0.95 -2.82 -4.38 -4.67 -4.38  1.13 -2.27
Morozov et. al.
CBF1_BMorozov et. al.P = 6.41e-150View matrix ↘
Sequence logo for CBF1_B
Fisher’s P-value6.41e-150
Information content12.5
Max PWM score11.94
Recommended cutoff8.12
Position frequency matrix (PFM)
A | 0.193 0.028 0.020 0.947 0.005 0.009 0.031 0.017 0.538 0.192 
C | 0.097 0.051 0.897 0.022 0.951 0.002 0.018 0.063 0.301 0.107 
G | 0.545 0.084 0.055 0.018 0.005 0.986 0.034 0.888 0.107 0.091 
T | 0.165 0.837 0.029 0.013 0.039 0.003 0.917 0.032 0.053 0.611
Position count matrix (PCM)
A |  19   2   2  94   0   0   3   1  53  19 
C |   9   5  89   2  95   0   1   6  30  10 
G |  54   8   5   1   0  98   3  88  10   9 
T |  16  83   2   1   3   0  91   3   5  61
Position weight matrix (PWM)
A | -0.51 -2.44 -2.77  1.08 -4.16 -3.57 -2.33 -2.94  0.52 -0.51 
C | -0.62 -1.26  1.61 -2.10  1.66 -4.50 -2.30 -1.05  0.51 -0.52 
G |  1.11 -0.76 -1.19 -2.30 -3.58  1.70 -1.67  1.60 -0.52 -0.68 
T | -0.66  0.96 -2.40 -3.20 -2.10 -4.67  1.05 -2.30 -1.80  0.65
Morozov et. al.
CBF1Pachkov et alP = 3.64e-147View matrix ↘
Sequence logo for CBF1
Fisher’s P-value3.64e-147
Information content13.34
Max PWM score9.95
Recommended cutoff8.88
Position frequency matrix (PFM)
A | 0.003 0.001 0.997 0.001 0.070 0.001 0.001 
C | 0.033 1.000 0.001 0.980 0.001 0.006 0.003 
G | 0.157 0.001 0.003 0.003 0.930 0.001 0.997 
T | 0.807 0.001 0.001 0.017 0.001 0.994 0.001
Position count matrix (PCM)
A |   0   0  99   0   7   0   0 
C |   3 100   0  98   0   0   0 
G |  15   0   0   0  93   0  99 
T |  80   0   0   1   0  99   0
Position weight matrix (PWM)
A | -4.67 -5.77  1.14 -5.77 -1.52 -5.77 -5.77 
C | -1.70  1.71 -5.19  1.69 -5.19 -3.40 -4.09 
G | -0.14 -5.19 -4.09 -4.09  1.64 -5.19  1.71 
T |  0.93 -5.77 -5.77 -2.94 -5.77  1.13 -5.77
Pachkov et al
CBF1Zhu et. al.P = 2.03e-147View matrix ↘
Sequence logo for CBF1
Fisher’s P-value2.03e-147
Information content12.21
Max PWM score11.95
Recommended cutoff7.64
Position frequency matrix (PFM)
A | 0.16 0.13 0.03 0.97 0.01 0.06 0.01 0.01 0.47 0.17 
C | 0.10 0.18 0.95 0.01 0.92 0.01 0.01 0.01 0.24 0.56 
G | 0.56 0.30 0.01 0.01 0.01 0.92 0.01 0.95 0.14 0.10 
T | 0.17 0.39 0.01 0.01 0.06 0.01 0.97 0.03 0.15 0.16
Position count matrix (PCM)
A |  16  13   3  97   1   6   1   1  47  17 
C |  10  18  95   1  92   1   1   1  24  56 
G |  56  30   1   1   1  92   1  95  14  10 
T |  17  39   1   1   6   1  97   3  15  16
Position weight matrix (PWM)
A | -0.69 -0.90 -2.37  1.11 -3.47 -1.67 -3.47 -3.47  0.38 -0.63 
C | -0.59  0.00  1.66 -2.89  1.63 -2.89 -2.89 -2.89  0.29  1.13 
G |  1.13  0.51 -2.89 -2.89 -2.89  1.63 -2.89  1.66 -0.25 -0.59 
T | -0.63  0.20 -3.47 -3.47 -1.67 -3.47  1.11 -2.37 -0.76 -0.69
Zhu et. al.
CBF1Zhao and StormoP = 1.37e-155View matrix ↘
Sequence logo for CBF1
Fisher’s P-value1.37e-155
Information content12.68
Max PWM score11.5
Recommended cutoff7.14
Position frequency matrix (PFM)
A | 0.329 0.137 0.010 0.963 0.001 0.023 0.013 0.002 0.514 0.126 
C | 0.142 0.165 0.986 0.014 0.965 0.011 0.010 0.003 0.184 0.402 
G | 0.402 0.184 0.003 0.010 0.011 0.965 0.014 0.986 0.165 0.142 
T | 0.126 0.514 0.002 0.013 0.023 0.001 0.963 0.010 0.137 0.329
Position count matrix (PCM)
A |  32  13   1  96   0   2   1   0  51  12 
C |  14  16  98   1  96   1   1   0  18  40 
G |  40  18   0   1   1  96   1  98  16  14 
T |  12  51   0   1   2   0  96   1  13  32
Position weight matrix (PWM)
A |  0.03 -0.85 -3.47  1.10 -5.77 -2.63 -3.20 -5.08  0.47 -0.93 
C | -0.24 -0.09  1.70 -2.55  1.68 -2.80 -2.89 -4.09  0.02  0.80 
G |  0.80  0.02 -4.09 -2.89 -2.80  1.68 -2.55  1.70 -0.09 -0.24 
T | -0.93  0.47 -5.08 -3.20 -2.63 -5.77  1.10 -3.47 -0.85  0.03
Zhao and Stormo
03 / EXPERIMENTAL CONTEXT

Gene-level annotations and interactions.

Genes bound in ChIP-chip experiments 112 genes

YAL026C, YAL053W, YAL054C, YBR049C, YBR051W, YBR089C-A, YBR090C, YBR222C, YBR224W, YBR225W, YBR249C, YBR250W, YCR092C, YCR093W, YDL020C, YDL058W, YDL059C, YDR508C, YDR510W, YEL024W, YEL025C, YEL043W, YER017C, YER060w-A, YER092W, YER094C, YER095W, YER099C, YER100W, YER111C, YER112W, YER114C, YER124C, YER125W, YFL017W-A, YFL018C, YFR018C, YFR019W, YFR030W, YGL252C, YGR116W, YGR204W, YGR223C, YGR224W, YHR089C, YHR098C, YHR099W, YHR136C, YHR137W, YIL074C, YIL088C, YIL126W, YIL127C, YIR017C, YIR018W, YJL115W, YJL116C, YJL117W, YJL119C, YJL133W, YJL167W, YJL168C, YJL209W, YJL211C, YJR009C, YJR010W, YJR095W, YKL007W, YKL008C, YKL015W, YKL016C, YKL191W, YKL192C, YLL008W, YLL009C, YLL010C, YLL055W, YLL056C, YLR081W, YLR092W, YLR139C, YLR142W, YLR149C, YLR150W, YLR155C, YLR156W, YLR157C, YLR160C, YLR174W, YNL036W, YNL037C, YNL094W, YNL095C, YNL220W, YNL221C, YNL277W, YNL282W, YNL283C, YNR033W, YOR038C, YOR039W, YOR064C, YOR065W, YOR327C, YOR328W, YPL068C, YPL093W, YPL094C, YPL096W, YPL204W, YPL206C, YPL221W

Genes affected by TF deletion 300 genes

YGL171W, YHL048W, YIL116W, YJR016C, YNR059W, YOR193W, YBR187W, YBR189W, YDL131W, YDR222W, YGL039W, YGL009C, YJL115W, YLR058C, YOR033C, YOR377W, YPL049C, YBR005W, YKR072C, YML113W, YNL051W, YOL011W, YOL048C, YOR220W, YMR198W, YAL034C, YBR186W, YEL011W, YJL048C, YJL116C, YKL110C, YLR405W, YMR189W, YMR191W, YNL274C, YPL014W, YPL016W, YBR126C, YJR116W, YJR147W, YKL016C, YMR103C, YMR105C, YNL111C, YOR289W, YPR048W, YOR359W, YPL235W, YBR287W, YER053C, YER055C, YGR248W, YGR250C, YLR120C, YLR156W, YBR093C, YGR032W, YJL017W, YMR070W, YMR104C, YNL174W, YNL116W, YNL180C, YPL267W, YPR017C, YBL058W, YDR281C, YER029C, YER057C, YGR211W, YHR209W, YIL051C, YJL148W, YLR119W, YLR181C, YLR121C, YLR183C, YML082W, YMR251W-A, YNL332W, YNL336W, YCR048W, YCR050C, YCR021C, YDR074W, YHR001W-A, YLR282C, YLR257W, YML123C, YNL058C, YOL052C-A, YOR201C, YOR203W, YPL245W, YPL250C, YNL040W, YAR015W, YBR169C, YGL053W, YKL051W, YKL113C, YLR410W, YLR439W, YMR170C, YMR173W, YOR043W, YOR385W, YPL057C, YCR047C, YCL064C, YDR077W, YER150W, YIL119C, YNL027W, YOL052C, YOR202W, YPL212C, YJR148W, YML100W, YEL051W, YJL060W, YMR169C, YNL282W, YOR046C, YOR384W, YBR104W, YDR502C, YHR089C, YLR348C, YLR350W, YMR145C, YOL144W, YBR265W, YDL198C, YDL234C, YER036C, YER063W, YGL111W, YIL022W, YHR215W, YJL217W, YLR130C, YLR194C, YML093W, YPL086C, YPL090C, YPL122C, YPL154C, YPL092W, YFL014W, YGR008C, YHR030C, YLL039C, YLR349W, YMR144W, YOL115W, YAR071W, YDR348C, YER064C, YHR214W-A, YJL158C, YKL150W, YLR159W, YLR161W, YMR319C, YNR001C, YPL087W, YKR061W, YKR093W, YMR061W, YNL036W, YOL029C, YOL064C, YPL252C, YPL223C, YPL227C, YIL114C, YBR177C, YBR241C, YGR138C, YJL101C, YLR414C, YLR449W, YMR236W, YNL259C, YDR023W, YER158C, YGR295C, YIL127C, YKR025W, YLR258W, YML128C, YML132W, YNL096C, YNL037C, YPL251W, YPL190C, YMR008C, YAR018C, YAR027W, YDR235W, YGR139W, YGR110W, YJL134W, YKL120W, YMR173W-A, YMR235C, YMR175W, YMR239C, YOR052C, YPL063W, YDL048C, YFL030W, YGR079W, YGR049W, YHR097C, YIR044C, YMR120C, YOL156W, YBL070C, YGR234W, YJL167W, YLR142W, YMR300C, YMR304C-A, YNL319W, YDR174W, YDR115W, YFR022W, YGR078C, YIR043C, YJR158W, YLR321C, YLR355C, YNL160W, YNL192W, YOL119C, YOL153C, YOL093W, YOR360C, YBR302C, YMR301C, YNR009W, YNR044W, YER091C, YBR054W, YBR056W, YIL170W, YJR074W, YLR297W, YLR270W, YNL109W, YDL124W, YGR144W, YGR146C, YDR027C, YDR055W, YFL004W, YHL033C, YMR001C, YMR034C, YMR007W, YMR038C, YNL108C, YOL007C, YBR214W, YEL037C, YJL142C, YMR215W, YMR246W, YMR250W, YFR028C, YGR055W, YLL026W, YMR093W, YOR309C, YCL040W, YCL042W, YDL182W, YDL216C, YGR208W, YLR178C, YMR305C, YMR310C, YDR121W, YFL062W, YHR104W, YKL034W, YLR327C, YLR359W, YOL097C, YOR342C, YPR069C, YBL077W, YBL018C, YJL200C, YLR149C, YNL009W, YNR050C, YPL171C

Genes supported by both experiments 12 genes

YHR089C, YIL127C, YJL115W, YJL116C, YJL167W, YKL016C, YLR142W, YLR149C, YLR156W, YNL036W, YNL037C, YNL282W

Predicted TF–TF partners 6 genes

GCN4, HMS1, INO2, MET32, MET4, YDR026C

Explore 6 original interaction plots →