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

YAP1

YML007W, SNQ3, PAR1

View at SGD ↗

Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium

01 / RECOMMENDED MATRIX

Best-performing DNA-binding model.

RecommendedSource: Pachkov et al
Fisher’s P-value2.25e-17
Information content13.95
Max PWM score12.13
Recommended cutoff10.25
View and copy the recommended matrices ↘
Position frequency matrix (PFM)
A | 0.032 0.009 0.001 0.001 0.001 0.934 0.003 0.152 0.996 0.982 0.131 
C | 0.288 0.057 0.901 0.001 0.001 0.003 0.949 0.001 0.001 0.006 0.001 
G | 0.053 0.591 0.037 0.001 0.455 0.055 0.039 0.007 0.004 0.004 0.262 
T | 0.626 0.344 0.062 1.000 0.545 0.009 0.009 0.840 0.001 0.009 0.607
Position count matrix (PCM)
A |   3   0   0   0   0  93   0  15  99  98  13 
C |  28   5  90   0   0   0  94   0   0   0   0 
G |   5  59   3   0  45   5   3   0   0   0  26 
T |  62  34   6 100  54   0   0  84   0   0  60
Position weight matrix (PWM)
A | -2.30 -3.57 -5.77 -5.77 -5.77  1.07 -4.67 -0.74  1.14  1.12 -0.89 
C |  0.47 -1.15  1.61 -5.19 -5.19 -4.09  1.66 -5.19 -5.19 -3.40 -5.19 
G | -1.22  1.19 -1.58 -5.19  0.93 -1.19 -1.53 -3.25 -3.81 -3.81  0.38 
T |  0.67  0.07 -1.64  1.14  0.53 -3.57 -3.57  0.97 -5.77 -3.57  0.64
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.

YAP1_AFoat et. al.P = 1View matrix ↘
Sequence logo for YAP1_A
Fisher’s P-value1
Information content20.77
Max PWM score23.47
Recommended cutoff17.6
Position frequency matrix (PFM)
A | 0.18 0.58 0.25 0.97 0.01 0.05 0.15 0.29 0.10 0.15 0.20 0.03 0.05 0.17 0.26 0.01 0.03 0.01 0.01 0.04 0.34 0.33 0.10 
C | 0.25 0.01 0.28 0.01 0.97 0.07 0.04 0.25 0.34 0.57 0.01 0.61 0.30 0.25 0.05 0.01 0.02 0.02 0.01 0.72 0.44 0.06 0.01 
G | 0.01 0.09 0.01 0.01 0.01 0.01 0.23 0.19 0.51 0.01 0.51 0.05 0.58 0.36 0.08 0.94 0.83 0.01 0.97 0.24 0.15 0.10 0.82 
T | 0.56 0.33 0.46 0.02 0.01 0.87 0.58 0.26 0.04 0.28 0.29 0.32 0.06 0.21 0.60 0.04 0.12 0.96 0.01 0.01 0.08 0.51 0.06
Position count matrix (PCM)
A |  18  57  25  97   1   5  15  28  10  15  20   3   5  17  26   1   3   1   1   4  34  33  10 
C |  25   1  28   1  97   7   4  25  34  56   1  61  30  25   5   1   2   2   1  72  44   6   1 
G |   1   9   1   1   1   1  23  19  51   1  51   5  57  36   8  94  83   1  97  24  15  10  82 
T |  56  33  46   2   1  87  57  26   4  28  28  32   6  21  60   4  12  96   1   1   8  51   6
Position weight matrix (PWM)
A | -0.58  0.59 -0.25  1.11 -3.47 -1.86 -0.76 -0.10 -1.16 -0.76 -0.47 -2.37 -1.86 -0.63 -0.21 -3.47 -2.37 -3.47 -3.47 -2.08  0.06  0.03 -1.16 
C |  0.33 -2.89  0.44 -2.89  1.68 -0.94 -1.50  0.33  0.64  1.15 -2.89  1.22  0.51  0.33 -1.28 -2.89 -2.20 -2.20 -2.89  1.39  0.89 -1.10 -2.89 
G | -2.89 -0.69 -2.89 -2.89 -2.89 -2.89  0.25  0.05  1.04 -2.89  1.04 -1.28  1.17  0.69 -0.81  1.65  1.53 -2.89  1.68  0.29 -0.18 -0.59  1.52 
T |  0.56  0.03  0.36 -2.77 -3.47  1.00  0.59 -0.21 -2.08 -0.13 -0.10  0.00 -1.67 -0.42  0.63 -2.08 -0.98  1.10 -3.47 -3.47 -1.39  0.47 -1.67
Foat et. al.
YAP1_BFoat et. al.P = 1.05e-14View matrix ↘
Sequence logo for YAP1_B
Fisher’s P-value1.05e-14
Information content10.33
Max PWM score10.41
Recommended cutoff9.58
Position frequency matrix (PFM)
A | 0.01 0.05 0.76 0.03 0.02 0.43 0.96 0.01 0.11 
C | 0.10 0.05 0.01 0.17 0.01 0.56 0.01 0.01 0.73 
G | 0.01 0.16 0.02 0.79 0.01 0.01 0.02 0.79 0.13 
T | 0.88 0.75 0.20 0.01 0.96 0.01 0.01 0.19 0.03
Position count matrix (PCM)
A |   1   5  76   3   2  43  96   1  11 
C |  10   5   1  17   1  56   1   1  73 
G |   1  16   2  79   1   1   2  79  13 
T |  88  75  20   1  96   1   1  19   3
Position weight matrix (PWM)
A | -3.47 -1.86  0.86 -2.37 -2.77  0.30  1.10 -3.47 -1.07 
C | -0.59 -1.28 -2.89 -0.06 -2.89  1.13 -2.89 -2.89  1.40 
G | -2.89 -0.12 -2.20  1.48 -2.89 -2.89 -2.20  1.48 -0.33 
T |  1.01  0.85 -0.47 -3.47  1.10 -3.47 -3.47 -0.52 -2.37
Foat et. al.
YAP1_CFoat et. al.P = 1View matrix ↘
Sequence logo for YAP1_C
Fisher’s P-value1
Information content19.95
Max PWM score21.52
Recommended cutoff16.14
Position frequency matrix (PFM)
A | 0.96 0.59 0.02 0.97 0.01 0.01 0.35 0.01 0.40 0.33 0.26 0.63 0.07 0.61 0.53 0.97 0.24 0.03 0.04 0.01 0.22 
C | 0.01 0.01 0.65 0.01 0.96 0.85 0.55 0.58 0.09 0.09 0.03 0.24 0.68 0.11 0.17 0.01 0.01 0.15 0.42 0.70 0.05 
G | 0.02 0.36 0.29 0.01 0.02 0.13 0.01 0.01 0.07 0.57 0.01 0.10 0.01 0.28 0.04 0.01 0.74 0.01 0.06 0.11 0.04 
T | 0.02 0.05 0.05 0.01 0.01 0.01 0.10 0.40 0.44 0.01 0.69 0.04 0.24 0.01 0.26 0.01 0.01 0.81 0.48 0.19 0.69
Position count matrix (PCM)
A |  96  59   2  97   1   1  35   1  40  33  26  63   7  61  53  97  24   3   4   1  22 
C |   1   1  65   1  96  85  55  57   9   9   3  24  68  11  17   1   1  15  42  70   5 
G |   2  36  28   1   2  13   1   1   7  56   1  10   1  28   4   1  74   1   6  11   4 
T |   2   5   5   1   1   1  10  40  44   1  69   4  24   1  26   1   1  81  48  19  69
Position weight matrix (PWM)
A |  1.10  0.61 -2.77  1.11 -3.47 -3.47  0.09 -3.47  0.22  0.03 -0.21  0.68 -1.52  0.65  0.50  1.11 -0.29 -2.37 -2.08 -3.47 -0.37 
C | -2.89 -2.89  1.28 -2.89  1.67  1.55  1.12  1.17 -0.69 -0.69 -1.79  0.29  1.33 -0.49 -0.06 -2.89 -2.89 -0.18  0.85  1.36 -1.28 
G | -2.20  0.69  0.48 -2.89 -2.20 -0.33 -2.89 -2.89 -0.94  1.15 -2.89 -0.59 -2.89  0.44 -1.50 -2.89  1.41 -2.89 -1.10 -0.49 -1.50 
T | -2.77 -1.86 -1.86 -3.47 -3.47 -3.47 -1.16  0.22  0.32 -3.47  0.77 -2.08 -0.29 -3.47 -0.21 -3.47 -3.47  0.93  0.41 -0.52  0.77
Foat et. al.
YAP1_DFoat et. al.P = 1.44e-15View matrix ↘
Sequence logo for YAP1_D
Fisher’s P-value1.44e-15
Information content10.1
Max PWM score9.81
Recommended cutoff7.42
Position frequency matrix (PFM)
A | 0.30 0.11 0.01 0.97 0.02 0.12 0.97 0.88 0.15 
C | 0.69 0.01 0.01 0.01 0.92 0.01 0.01 0.08 0.07 
G | 0.01 0.06 0.58 0.01 0.01 0.01 0.01 0.01 0.25 
T | 0.01 0.82 0.40 0.01 0.04 0.87 0.01 0.03 0.53
Position count matrix (PCM)
A |  30  11   1  97   2  12  97  88  15 
C |  69   1   1   1  92   1   1   8   7 
G |   1   6  57   1   1   1   1   1  25 
T |   1  82  40   1   4  87   1   3  53
Position weight matrix (PWM)
A | -0.06 -1.07 -3.47  1.11 -2.77 -0.98  1.11  1.01 -0.76 
C |  1.34 -2.89 -2.89 -2.89  1.63 -2.89 -2.89 -0.81 -0.94 
G | -2.89 -1.10  1.17 -2.89 -2.89 -2.89 -2.89 -2.89  0.33 
T | -3.47  0.94  0.22 -3.47 -2.08  1.00 -3.47 -2.37  0.50
Foat et. al.
YAP1_AFordyce et. al.P = 0.0004362View matrix ↘
Fisher’s P-value0.0004362
Information content8.667
Max PWM score7.95
Recommended cutoff5.19
Position frequency matrix (PFM)
A | 0.01 0.19 0.03 0.75 0.97 0.02 0.02 0.42 
C | 0.45 0.07 0.01 0.07 0.01 0.01 0.01 0.26 
G | 0.46 0.72 0.01 0.18 0.01 0.01 0.01 0.26 
T | 0.09 0.01 0.96 0.01 0.01 0.95 0.96 0.06
Position count matrix (PCM)
A |   1  19   3  75  97   2   2  42 
C |  45   7   1   7   1   1   1  26 
G |  46  72   1  18   1   1   1  26 
T |   9   1  96   1   1  95  96   6
Position weight matrix (PWM)
A | -3.47 -0.52 -2.37  0.85  1.11 -2.77 -2.77  0.27 
C |  0.92 -0.94 -2.89 -0.94 -2.89 -2.89 -2.89  0.37 
G |  0.94  1.39 -2.89  0.00 -2.89 -2.89 -2.89  0.37 
T | -1.27 -3.47  1.10 -3.47 -3.47  1.09  1.10 -1.67
Fordyce et. al.
YAP1_BFordyce et. al.P = 0.002881View matrix ↘
Fisher’s P-value0.002881
Information content8.771
Max PWM score8.01
Recommended cutoff4.02
Position frequency matrix (PFM)
A | 0.46 0.01 0.20 0.03 0.75 0.97 0.02 0.02 
C | 0.26 0.43 0.07 0.01 0.07 0.01 0.01 0.01 
G | 0.23 0.48 0.73 0.01 0.18 0.01 0.01 0.01 
T | 0.05 0.09 0.01 0.95 0.01 0.01 0.96 0.97
Position count matrix (PCM)
A |  46   1  20   3  75  97   2   2 
C |  26  43   7   1   7   1   1   1 
G |  23  48  73   1  18   1   1   1 
T |   5   9   1  95   1   1  96  97
Position weight matrix (PWM)
A |  0.36 -3.47 -0.47 -2.37  0.85  1.11 -2.77 -2.77 
C |  0.37  0.87 -0.94 -2.89 -0.94 -2.89 -2.89 -2.89 
G |  0.25  0.98  1.40 -2.89  0.00 -2.89 -2.89 -2.89 
T | -1.86 -1.27 -3.47  1.09 -3.47 -3.47  1.10  1.11
Fordyce et. al.
YAP1_CFordyce et. al.P = 0.0002793View matrix ↘
Fisher’s P-value0.0002793
Information content8.894
Max PWM score8.57
Recommended cutoff4.37
Position frequency matrix (PFM)
A | 0.01 0.01 0.95 0.01 0.08 0.05 0.97 0.97 
C | 0.01 0.19 0.01 0.67 0.31 0.10 0.02 0.01 
G | 0.01 0.08 0.01 0.07 0.59 0.10 0.01 0.01 
T | 0.97 0.72 0.03 0.25 0.02 0.74 0.01 0.01
Position count matrix (PCM)
A |   1   1  95   1   8   5  97  97 
C |   1  19   1  67  31  10   2   1 
G |   1   8   1   7  59  10   1   1 
T |  97  72   3  25   2  74   1   1
Position weight matrix (PWM)
A | -3.47 -3.47  1.09 -3.47 -1.39 -1.86  1.11  1.11 
C | -2.89  0.05 -2.89  1.31  0.54 -0.59 -2.20 -2.89 
G | -2.89 -0.81 -2.89 -0.94  1.19 -0.59 -2.89 -2.89 
T |  1.11  0.81 -2.37 -0.25 -2.77  0.84 -3.47 -3.47
Fordyce et. al.
YAP1Harbison et. al.P = 4.94e-16View matrix ↘
Sequence logo for YAP1
Fisher’s P-value4.94e-16
Information content11.6
Max PWM score10.74
Recommended cutoff9.38
Position frequency matrix (PFM)
A | 0.034 0.006 0.711 0.046 0.008 0.437 0.939 0.007 0.281 
C | 0.010 0.010 0.011 0.018 0.005 0.541 0.051 0.011 0.618 
G | 0.005 0.065 0.013 0.912 0.005 0.010 0.004 0.929 0.036 
T | 0.951 0.920 0.265 0.025 0.981 0.013 0.006 0.052 0.065
Position count matrix (PCM)
A |   3   0  71   4   0  43  93   0  28 
C |   1   1   1   1   0  54   5   1  61 
G |   0   6   1  91   0   1   0  92   3 
T |  95  92  26   2  98   1   0   5   6
Position weight matrix (PWM)
A | -2.24 -3.98  0.80 -1.94 -3.69  0.31  1.08 -3.82 -0.13 
C | -2.89 -2.89 -2.80 -2.30 -3.58  1.10 -1.26 -2.80  1.23 
G | -3.58 -1.02 -2.63  1.62 -3.58 -2.89 -3.81  1.64 -1.61 
T |  1.09  1.06 -0.19 -2.55  1.12 -3.20 -3.98 -1.82 -1.59
Harbison et. al.
YAP1Macisaac et. alP = 4.68e-15View matrix ↘
Sequence logo for YAP1
Fisher’s P-value4.68e-15
Information content9.863
Max PWM score11.22
Recommended cutoff9.01
Position frequency matrix (PFM)
A | 0.185 0.073 0.126 0.001 0.105 0.908 0.166 0.043 0.849 0.940 0.334 
C | 0.174 0.064 0.756 0.077 0.027 0.010 0.769 0.002 0.041 0.001 0.103 
G | 0.142 0.679 0.013 0.037 0.569 0.018 0.023 0.049 0.109 0.001 0.150 
T | 0.499 0.184 0.105 0.885 0.299 0.064 0.042 0.906 0.001 0.058 0.412
Position count matrix (PCM)
A |  18   7  12   0  10  90  16   4  84  94  33 
C |  17   6  75   7   2   1  76   0   4   0  10 
G |  14  67   1   3  56   1   2   4  10   0  15 
T |  49  18  10  88  29   6   4  90   0   5  41
Position weight matrix (PWM)
A | -0.55 -1.48 -0.93 -5.77 -1.11  1.04 -0.66 -2.01  0.98  1.08  0.04 
C | -0.03 -1.03  1.44 -0.85 -1.90 -2.89  1.45 -4.50 -1.48 -5.19 -0.56 
G | -0.24  1.33 -2.63 -1.58  1.15 -2.30 -2.06 -1.30 -0.50 -5.19 -0.18 
T |  0.44 -0.55 -1.11  1.02 -0.07 -1.61 -2.03  1.04 -5.77 -1.71  0.25
Macisaac et. al
YAP1Morozov et. al.P = 6.66e-15View matrix ↘
Sequence logo for YAP1
Fisher’s P-value6.66e-15
Information content9.995
Max PWM score10.69
Recommended cutoff8.95
Position frequency matrix (PFM)
A | 0.140 0.113 0.010 0.008 0.908 0.022 0.118 0.890 0.947 0.066 
C | 0.114 0.727 0.011 0.016 0.025 0.895 0.039 0.088 0.017 0.178 
G | 0.611 0.065 0.142 0.172 0.048 0.060 0.060 0.007 0.012 0.197 
T | 0.135 0.095 0.836 0.804 0.019 0.024 0.783 0.015 0.024 0.559
Position count matrix (PCM)
A |  14  11   1   0  90   2  11  89  94   6 
C |  11  72   1   1   2  89   3   8   1  17 
G |  61   6  14  17   4   6   6   0   1  19 
T |  13   9  83  80   1   2  78   1   2  55
Position weight matrix (PWM)
A | -0.83 -1.04 -3.47 -3.69  1.04 -2.68 -1.00  1.02  1.08 -1.58 
C | -0.46  1.40 -2.80 -2.42 -1.97  1.60 -1.53 -0.72 -2.36 -0.01 
G |  1.22 -1.02 -0.24 -0.05 -1.32 -1.10 -1.10 -3.25 -2.71  0.09 
T | -0.86 -1.21  0.96  0.92 -2.82 -2.59  0.89 -3.06 -2.59  0.56
Morozov et. al.
YAP1Zhu et. al.P = 3.79e-05View matrix ↘
Sequence logo for YAP1
Fisher’s P-value3.79e-05
Information content13.6
Max PWM score12
Recommended cutoff10.35
Position frequency matrix (PFM)
A | 0.40 0.01 0.01 0.97 0.01 0.06 0.01 0.97 0.97 0.04 
C | 0.53 0.01 0.01 0.01 0.89 0.04 0.01 0.01 0.01 0.03 
G | 0.05 0.01 0.01 0.01 0.04 0.89 0.01 0.01 0.01 0.52 
T | 0.02 0.97 0.97 0.01 0.06 0.01 0.97 0.01 0.01 0.42
Position count matrix (PCM)
A |  40   1   1  97   1   6   1  97  97   4 
C |  53   1   1   1  89   4   1   1   1   3 
G |   5   1   1   1   4  89   1   1   1  52 
T |   2  97  97   1   6   1  97   1   1  42
Position weight matrix (PWM)
A |  0.22 -3.47 -3.47  1.11 -3.47 -1.67 -3.47  1.11  1.11 -2.08 
C |  1.08 -2.89 -2.89 -2.89  1.60 -1.50 -2.89 -2.89 -2.89 -1.79 
G | -1.28 -2.89 -2.89 -2.89 -1.50  1.60 -2.89 -2.89 -2.89  1.06 
T | -2.77  1.11  1.11 -3.47 -1.67 -3.47  1.11 -3.47 -3.47  0.27
Zhu et. al.
YAP1Zhao and StormoP = 1.13e-05View matrix ↘
Sequence logo for YAP1
Fisher’s P-value1.13e-05
Information content3.784
Max PWM score4.43
Recommended cutoff4.29
Position frequency matrix (PFM)
A | 0.183 0.106 0.641 0.930 0.107 
C | 0.257 0.065 0.312 0.033 0.112 
G | 0.513 0.001 0.044 0.001 0.353 
T | 0.047 0.828 0.002 0.036 0.427
Position count matrix (PCM)
A |  18  10  64  93  10 
C |  25   6  31   3  11 
G |  51   0   4   0  35 
T |   4  82   0   3  42
Position weight matrix (PWM)
A | -0.56 -1.10  0.69  1.07 -1.10 
C |  0.36 -1.02  0.55 -1.70 -0.47 
G |  1.05 -5.19 -1.41 -5.19  0.67 
T | -1.92  0.95 -5.08 -2.18  0.29
Zhao and Stormo
03 / EXPERIMENTAL CONTEXT

Gene-level annotations and interactions.

Genes bound in ChIP-chip experiments 156 genes

YAL003W, YAL005C, YAL037W, YBL018C, YBL032W, YBL033C, YBL087C, YBR068C, YBR190W, YBR191W, YBR200W, YCR028C, YDL013W, YDL017W, YDL018C, YDL020C, YDL133W, YDL170W, YDL171C, YDL179W, YDL182W, YDL183C, YDR010C, YDR011W, YDR013W, YDR059C, YDR060W, YDR132C, YDR164C, YDR165W, YDR224C, YDR225W, YDR259C, YDR261C, YDR307W, YDR308C, YDR316W-A, YDR316W-B, YDR500C, YDR501W, YDR533C, YEL042W, YEL044W, YEL045C, YEL046C, YER012W, YER044C, YER078C, YER079W, YER138C, YFL034W, YFL056C, YFL057C, YFR017C, YFR023W, YGL114W, YGL134W, YGL135W, YGL136C, YGL202W, YGR009C, YGR010W, YGR011W, YGR027C, YGR060W, YGR162W, YGR191W, YGR192C, YGR194C, YGR195W, YGR234W, YHR048W, YHR179W, YJL048C, YJL060W, YJL095W, YJL098W, YJL100W, YJL101C, YJL148W, YJR104C, YJR105W, YJR109C, YJR110W, YJR122W, YJR123W, YKL071W, YKL150W, YKL151C, YKR052C, YKR054C, YKR055W, YKR058W, YKR071C, YKR076W, YLL024C, YLL058W, YLL059C, YLL060C, YLL063C, YLR074C, YLR075W, YLR105C, YLR108C, YLR109W, YLR302C, YLR367W, YLR369W, YLR439W, YLR460C, YML028W, YML115C, YML116W, YML130C, YML131W, YMR037C, YMR038C, YMR144W, YMR231W, YNL025C, YNL087W, YNL134C, YNL231C, YNL238W, YNR018W, YNR061C, YOL034W, YOL115W, YOL117W, YOL118C, YOL119C, YOL123W, YOL124C, YOL151W, YOR018W, YOR043W, YOR044W, YOR074C, YOR075W, YOR128C, YOR162C, YOR163W, YOR180C, YOR181W, YOR236W, YOR273C, YOR274W, YOR315W, YOR335C, YOR336W, YPL044C, YPL111W, YPL216W, YPL217C, YPR002C-A, YPR065W

Genes affected by TF deletion 56 genes

YOR225W, YDR135C, YOR226C, YPL016W, YMR105C, YNL111C, YML058W-A, YNL339C, YCR107W, YLR155C, YLR157C, YML028W, YGR296W, YMR173W, YMR023C, YNR066C, YLR099C, YJL026W, YOL150C, YLR160C, YPR065W, YGR294W, YJL101C, YKL096W, YLR108C, YNR076W, YKL120W, YLR109W, YMR173W-A, YGR019W, YDR353W, YHR219W, YDR481C, YJR162C, YOL119C, YOL151W, YDR297W, YER039C, YER067W, YER044C, YJR104C, YGL255W, YMR034C, YMR038C, YOL067C, YBR244W, YHR135C, YBR085W, YHR046C, YKL008C, YKL010C, YLR178C, YFL068W, YNL134C, YOR306C, YGR209C

Genes supported by both experiments 11 genes

YER044C, YJL101C, YJR104C, YLR108C, YLR109W, YML028W, YMR038C, YNL134C, YOL119C, YOL151W, YPR065W