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

PHO4

YFR034C, phoD

View at SGD ↗

Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability

01 / RECOMMENDED MATRIX

Best-performing DNA-binding model.

RecommendedSource: Morozov et. al.
Fisher’s P-value4.28e-16
Information content11.76
Max PWM score11.06
Recommended cutoff8.99
View and copy the recommended matrices ↘
Position frequency matrix (PFM)
A | 0.126 0.091 0.976 0.024 0.037 0.009 0.060 0.078 
C | 0.214 0.881 0.008 0.854 0.020 0.015 0.005 0.256 
G | 0.568 0.020 0.012 0.067 0.920 0.009 0.917 0.647 
T | 0.092 0.008 0.005 0.055 0.023 0.968 0.017 0.019
Position count matrix (PCM)
A |  12   9  97   2   3   0   6   7 
C |  21  88   0  85   2   1   0  25 
G |  56   2   1   6  92   0  91  64 
T |   9   0   0   5   2  96   1   1
Position weight matrix (PWM)
A | -0.93 -1.26  1.12 -2.59 -2.16 -3.57 -1.67 -1.41 
C |  0.17  1.59 -3.11  1.56 -2.20 -2.48 -3.58  0.35 
G |  1.15 -2.20 -2.71 -0.99  1.63 -3.00  1.63  1.28 
T | -1.25 -3.69 -4.16 -1.76 -2.63  1.11 -2.94 -2.82
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.

PHO4Badis et. al.P = 5.18e-07View matrix ↘
Sequence logo for PHO4
Fisher’s P-value5.18e-07
Information content8.681
Max PWM score9.33
Recommended cutoff7.79
Position frequency matrix (PFM)
A | 0.07 0.06 0.38 0.01 0.27 0.01 0.02 
C | 0.03 0.73 0.06 0.69 0.01 0.44 0.01 
G | 0.89 0.03 0.55 0.01 0.71 0.08 0.90 
T | 0.01 0.18 0.01 0.29 0.01 0.48 0.07
Position count matrix (PCM)
A |   7   6  38   1  27   1   2 
C |   3  73   6  69   1  44   1 
G |  89   3  55   1  71   8  90 
T |   1  18   1  28   1  48   7
Position weight matrix (PWM)
A | -1.52 -1.67  0.17 -3.47 -0.17 -3.47 -2.77 
C | -1.79  1.40 -1.10  1.34 -2.89  0.89 -2.89 
G |  1.60 -1.79  1.12 -2.89  1.37 -0.81  1.61 
T | -3.47 -0.58 -3.47 -0.10 -3.47  0.41 -1.52
Badis et. al.
PHO4_AFoat et. al.P = 8.84e-15View matrix ↘
Sequence logo for PHO4_A
Fisher’s P-value8.84e-15
Information content16.79
Max PWM score15.03
Recommended cutoff10.37
Position frequency matrix (PFM)
A | 0.58 0.02 0.01 0.01 0.97 0.01 0.03 0.02 0.01 0.04 0.01 0.08 
C | 0.01 0.34 0.71 0.96 0.01 0.97 0.01 0.01 0.01 0.50 0.79 0.35 
G | 0.12 0.50 0.27 0.02 0.01 0.01 0.95 0.01 0.96 0.03 0.17 0.02 
T | 0.29 0.14 0.01 0.01 0.01 0.01 0.01 0.96 0.02 0.44 0.03 0.55
Position count matrix (PCM)
A |  57   2   1   1  97   1   3   2   1   4   1   8 
C |   1  34  71  96   1  97   1   1   1  50  79  35 
G |  12  50  27   2   1   1  95   1  96   3  17   2 
T |  28  14   1   1   1   1   1  96   2  44   3  55
Position weight matrix (PWM)
A |  0.59 -2.77 -3.47 -3.47  1.11 -3.47 -2.37 -2.77 -3.47 -2.08 -3.47 -1.39 
C | -2.89  0.64  1.37  1.67 -2.89  1.68 -2.89 -2.89 -2.89  1.02  1.48  0.66 
G | -0.41  1.02  0.41 -2.20 -2.89 -2.89  1.66 -2.89  1.67 -1.79 -0.06 -2.20 
T | -0.10 -0.83 -3.47 -3.47 -3.47 -3.47 -3.47  1.10 -2.77  0.32 -2.37  0.54
Foat et. al.
PHO4_BFoat et. al.P = 1View matrix ↘
Sequence logo for PHO4_B
Fisher’s P-value1
Information content19.84
Max PWM score20.96
Recommended cutoff15.72
Position frequency matrix (PFM)
A | 0.38 0.04 0.42 0.97 0.01 0.02 0.70 0.36 0.34 0.11 0.26 0.02 0.12 0.08 0.12 0.01 0.01 0.97 0.08 0.38 0.45 
C | 0.08 0.01 0.01 0.01 0.05 0.96 0.03 0.30 0.32 0.03 0.19 0.51 0.02 0.57 0.02 0.01 0.97 0.01 0.01 0.01 0.36 
G | 0.01 0.77 0.49 0.01 0.93 0.01 0.01 0.31 0.01 0.85 0.05 0.11 0.38 0.06 0.42 0.01 0.01 0.01 0.35 0.01 0.13 
T | 0.54 0.17 0.08 0.01 0.01 0.01 0.27 0.03 0.33 0.01 0.49 0.36 0.48 0.30 0.44 0.97 0.01 0.01 0.56 0.61 0.05
Position count matrix (PCM)
A |  38   4  42  97   1   2  70  36  34  11  26   2  12   8  12   1   1  97   8  38  45 
C |   8   1   1   1   5  96   3  30  32   3  19  51   2  56   2   1  97   1   1   1  36 
G |   1  77  49   1  93   1   1  31   1  85   5  11  38   6  42   1   1   1  35   1  13 
T |  54  17   8   1   1   1  27   3  33   1  49  36  48  30  44  97   1   1  56  61   5
Position weight matrix (PWM)
A |  0.17 -2.08  0.27  1.11 -3.47 -2.77  0.78  0.12  0.06 -1.07 -0.21 -2.77 -0.98 -1.39 -0.98 -3.47 -3.47  1.11 -1.39  0.17  0.34 
C | -0.81 -2.89 -2.89 -2.89 -1.28  1.67 -1.79  0.51  0.58 -1.79  0.05  1.04 -2.20  1.15 -2.20 -2.89  1.68 -2.89 -2.89 -2.89  0.69 
G | -2.89  1.45  1.00 -2.89  1.64 -2.89 -2.89  0.54 -2.89  1.55 -1.28 -0.49  0.75 -1.10  0.85 -2.89 -2.89 -2.89  0.66 -2.89 -0.33 
T |  0.52 -0.63 -1.39 -3.47 -3.47 -3.47 -0.17 -2.37  0.03 -3.47  0.43  0.12  0.41 -0.06  0.32  1.11 -3.47 -3.47  0.56  0.65 -1.86
Foat et. al.
PHO4_AFordyce et. al.P = 5.20e-11View matrix ↘
Fisher’s P-value5.20e-11
Information content10.32
Max PWM score9.79
Recommended cutoff8.92
Position frequency matrix (PFM)
A | 0.14 0.92 0.01 0.06 0.05 0.01 0.06 0.24 
C | 0.85 0.02 0.94 0.01 0.06 0.01 0.30 0.33 
G | 0.01 0.01 0.01 0.92 0.02 0.84 0.16 0.42 
T | 0.01 0.05 0.04 0.01 0.87 0.13 0.48 0.01
Position count matrix (PCM)
A |  14  92   1   6   5   1   6  24 
C |  85   2  94   1   6   1  30  33 
G |   1   1   1  92   2  84  16  42 
T |   1   5   4   1  87  13  48   1
Position weight matrix (PWM)
A | -0.83  1.06 -3.47 -1.67 -1.86 -3.47 -1.67 -0.29 
C |  1.55 -2.20  1.65 -2.89 -1.10 -2.89  0.51  0.61 
G | -2.89 -2.89 -2.89  1.63 -2.20  1.54 -0.12  0.85 
T | -3.47 -1.86 -2.08 -3.47  1.00 -0.90  0.41 -3.47
Fordyce et. al.
PHO4_BFordyce et. al.P = 1.14e-10View matrix ↘
Fisher’s P-value1.14e-10
Information content8.403
Max PWM score8.65
Recommended cutoff6.8
Position frequency matrix (PFM)
A | 0.14 0.89 0.01 0.07 0.05 0.02 0.09 
C | 0.71 0.02 0.94 0.01 0.07 0.03 0.32 
G | 0.01 0.02 0.01 0.91 0.02 0.75 0.14 
T | 0.14 0.07 0.04 0.01 0.85 0.20 0.45
Position count matrix (PCM)
A |  14  89   1   7   5   2   9 
C |  71   2  94   1   7   3  32 
G |   1   2   1  91   2  75  14 
T |  14   7   4   1  85  20  45
Position weight matrix (PWM)
A | -0.83  1.02 -3.47 -1.52 -1.86 -2.77 -1.27 
C |  1.37 -2.20  1.65 -2.89 -0.94 -1.79  0.58 
G | -2.89 -2.20 -2.89  1.62 -2.20  1.43 -0.25 
T | -0.83 -1.52 -2.08 -3.47  0.98 -0.47  0.34
Fordyce et. al.
PHO4_CFordyce et. al.P = 4.54e-14View matrix ↘
Fisher’s P-value4.54e-14
Information content10.11
Max PWM score9.71
Recommended cutoff8.86
Position frequency matrix (PFM)
A | 0.23 0.13 0.92 0.01 0.06 0.05 0.01 0.09 
C | 0.35 0.86 0.02 0.94 0.01 0.06 0.02 0.29 
G | 0.42 0.01 0.01 0.01 0.92 0.02 0.79 0.15 
T | 0.01 0.01 0.05 0.04 0.01 0.87 0.18 0.46
Position count matrix (PCM)
A |  23  13  92   1   6   5   1   9 
C |  35  86   2  94   1   6   2  28 
G |  42   1   1   1  92   2  79  15 
T |   1   1   5   4   1  87  18  46
Position weight matrix (PWM)
A | -0.33 -0.90  1.06 -3.47 -1.67 -1.86 -3.47 -1.27 
C |  0.66  1.56 -2.20  1.65 -2.89 -1.10 -2.20  0.48 
G |  0.85 -2.89 -2.89 -2.89  1.63 -2.20  1.48 -0.18 
T | -3.47 -3.47 -1.86 -2.08 -3.47  1.00 -0.58  0.36
Fordyce et. al.
PHO4Harbison et. al.P = 3.79e-11View matrix ↘
Sequence logo for PHO4
Fisher’s P-value3.79e-11
Information content10.55
Max PWM score9.63
Recommended cutoff6.93
Position frequency matrix (PFM)
A | 0.067 0.945 0.025 0.049 0.014 0.024 0.060 
C | 0.864 0.013 0.915 0.022 0.013 0.011 0.360 
G | 0.022 0.016 0.019 0.895 0.006 0.905 0.503 
T | 0.047 0.026 0.041 0.035 0.967 0.060 0.078
Position count matrix (PCM)
A |   6  94   2   4   1   2   6 
C |  86   1  91   2   1   1  36 
G |   2   1   1  89   0  90  50 
T |   4   2   4   3  96   6   7
Position weight matrix (PWM)
A | -1.56  1.08 -2.55 -1.88 -3.13 -2.59 -1.67 
C |  1.57 -2.63  1.63 -2.10 -2.63 -2.80  0.69 
G | -2.10 -2.42 -2.25  1.60 -3.40  1.61  1.03 
T | -1.92 -2.51 -2.05 -2.21  1.11 -1.67 -1.41
Harbison et. al.
PHO4Macisaac et. alP = 2.23e-11View matrix ↘
Sequence logo for PHO4
Fisher’s P-value2.23e-11
Information content12.23
Max PWM score9.98
Recommended cutoff8.34
Position frequency matrix (PFM)
A | 0.001 0.982 0.029 0.018 0.001 0.029 0.177 
C | 0.983 0.001 0.938 0.001 0.045 0.001 0.145 
G | 0.001 0.016 0.001 0.980 0.001 0.969 0.516 
T | 0.015 0.001 0.032 0.001 0.953 0.001 0.162
Position count matrix (PCM)
A |   0  98   2   1   0   2  17 
C |  98   0  93   0   4   0  14 
G |   0   1   0  98   0  96  51 
T |   1   0   3   0  95   0  16
Position weight matrix (PWM)
A | -5.77  1.12 -2.40 -2.88 -5.77 -2.40 -0.59 
C |  1.70 -5.19  1.65 -5.19 -1.39 -5.19 -0.22 
G | -5.19 -2.42 -5.19  1.69 -5.19  1.68  1.05 
T | -3.06 -5.77 -2.30 -5.77  1.09 -5.77 -0.68
Macisaac et. al
PHO4Pachkov et alP = 2.23e-11View matrix ↘
Sequence logo for PHO4
Fisher’s P-value2.23e-11
Information content12.31
Max PWM score9.74
Recommended cutoff8
Position frequency matrix (PFM)
A | 0.001 0.001 1.000 0.001 0.002 0.021 0.034 
C | 0.466 0.998 0.001 0.986 0.002 0.030 0.003 
G | 0.389 0.001 0.001 0.001 0.996 0.015 0.777 
T | 0.145 0.002 0.001 0.014 0.001 0.934 0.186
Position count matrix (PCM)
A |   0   0 100   0   0   2   3 
C |  46  99   0  98   0   3   0 
G |  38   0   0   0  99   1  77 
T |  14   0   0   1   0  93  18
Position weight matrix (PWM)
A | -5.77 -5.77  1.14 -5.77 -5.08 -2.72 -2.24 
C |  0.95  1.71 -5.19  1.70 -4.50 -1.79 -4.09 
G |  0.77 -5.19 -5.19 -5.19  1.71 -2.48  1.46 
T | -0.79 -5.08 -5.77 -3.13 -5.77  1.07 -0.54
Pachkov et al
PHO4Zhu J and MQ ZhangP = 9.57e-14View matrix ↘
Sequence logo for PHO4
Fisher’s P-value9.57e-14
Information content7.09
Max PWM score10.36
Recommended cutoff8.4
Position frequency matrix (PFM)
A | 0.25 0.19 0.06 0.81 0.06 0.06 0.06 0.06 0.12 0.25 
C | 0.38 0.19 0.81 0.06 0.81 0.06 0.12 0.06 0.19 0.12 
G | 0.25 0.50 0.06 0.06 0.06 0.81 0.06 0.50 0.38 0.31 
T | 0.12 0.12 0.06 0.06 0.06 0.06 0.75 0.38 0.31 0.31
Position count matrix (PCM)
A |  25  19   6  81   6   6   6   6  12  25 
C |  38  19  81   6  81   6  12   6  19  12 
G |  25  50   6   6   6  81   6  50  38  31 
T |  12  12   6   6   6   6  75  38  31  31
Position weight matrix (PWM)
A | -0.25 -0.52 -1.67  0.93 -1.67 -1.67 -1.67 -1.67 -0.98 -0.25 
C |  0.75  0.05  1.50 -1.10  1.50 -1.10 -0.41 -1.10  0.05 -0.41 
G |  0.33  1.02 -1.10 -1.10 -1.10  1.50 -1.10  1.02  0.75  0.54 
T | -0.98 -0.98 -1.67 -1.67 -1.67 -1.67  0.85  0.17 -0.03 -0.03
Zhu J and MQ Zhang
PHO4Zhu et. al.P = 1.51e-14View matrix ↘
Sequence logo for PHO4
Fisher’s P-value1.51e-14
Information content11.75
Max PWM score10.62
Recommended cutoff8.08
Position frequency matrix (PFM)
A | 0.09 0.10 0.95 0.01 0.08 0.01 0.01 0.01 
C | 0.39 0.88 0.01 0.90 0.01 0.03 0.01 0.50 
G | 0.50 0.01 0.03 0.01 0.90 0.01 0.88 0.39 
T | 0.01 0.01 0.01 0.08 0.01 0.95 0.10 0.09
Position count matrix (PCM)
A |   9  10  95   1   8   1   1   1 
C |  39  88   1  90   1   3   1  50 
G |  50   1   3   1  90   1  88  39 
T |   1   1   1   8   1  95  10   9
Position weight matrix (PWM)
A | -1.27 -1.16  1.09 -3.47 -1.39 -3.47 -3.47 -3.47 
C |  0.77  1.59 -2.89  1.61 -2.89 -1.79 -2.89  1.02 
G |  1.02 -2.89 -1.79 -2.89  1.61 -2.89  1.59  0.77 
T | -3.47 -3.47 -3.47 -1.39 -3.47  1.09 -1.16 -1.27
Zhu et. al.
PHO4Zhao and StormoP = 1.51e-14View matrix ↘
Sequence logo for PHO4
Fisher’s P-value1.51e-14
Information content7.794
Max PWM score8.96
Recommended cutoff8.03
Position frequency matrix (PFM)
A | 0.226 0.161 0.742 0.002 0.097 0.093 0.039 0.133 
C | 0.321 0.773 0.068 0.889 0.013 0.097 0.027 0.321 
G | 0.321 0.027 0.097 0.013 0.889 0.068 0.773 0.321 
T | 0.133 0.039 0.093 0.097 0.002 0.742 0.161 0.226
Position count matrix (PCM)
A |  22  16  74   0   9   9   3  13 
C |  32  77   6  88   1   9   2  32 
G |  32   2   9   1  88   6  77  32 
T |  13   3   9   9   0  74  16  22
Position weight matrix (PWM)
A | -0.35 -0.69  0.84 -5.08 -1.19 -1.24 -2.10 -0.88 
C |  0.58  1.46 -0.97  1.60 -2.63 -0.62 -1.90  0.58 
G |  0.58 -1.90 -0.62 -2.63  1.60 -0.97  1.46  0.58 
T | -0.88 -2.10 -1.24 -1.19 -5.08  0.84 -0.69 -0.35
Zhao and Stormo
03 / EXPERIMENTAL CONTEXT

Gene-level annotations and interactions.

Genes bound in ChIP-chip experiments 165 genes

YAR014C, YAR015W, YAR019C, YBR065C, YBR152W, YBR193C, YBR194W, YCL034W, YCL035C, YCL063W, YCL064C, YCR066W, YDL004W, YDL005C, YDL013W, YDL179W, YDR070C, YDR164C, YDR165W, YDR281C, YDR283C, YDR294C, YDR411C, YDR412W, YDR440W, YDR534C, YEL001C, YEL026W, YER033C, YER034W, YER061C, YER078C, YER079W, YER085C, YER086W, YER129W, YER163C, YFL009W, YFL010C, YFL010W-A, YFR026C, YFR044C, YFR045W, YGL058W, YGL079W, YGL099W, YGL130W, YGL131C, YGL133W, YGL139W, YGL140C, YGL258W, YGR106C, YGR167W, YGR253C, YGR273C, YHR024C, YHR025W, YHR053C, YHR054C, YHR055C, YHR130C, YHR131C, YHR132W-A, YHR178W, YHR207C, YHR208W, YHR210C, YHR211W, YHR212C, YHR214W, YHR214W-A, YIL036W, YIL037C, YIL076W, YIL077C, YIL121W, YIL136W, YIL137C, YIL147C, YJL051W, YJL102W, YJL103C, YJL172W, YJL173C, YJL200C, YJR004C, YJR005W, YJR030C, YJR058C, YJR059W, YJR098C, YJR099W, YKL084W, YKL142W, YKL150W, YKL151C, YKR084C, YLR008C, YLR009W, YLR152C, YLR205C, YLR206W, YLR266C, YLR267W, YLR382C, YLR383W, YLR397C, YLR439W, YML029W, YML030W, YML032C, YML065W, YML066C, YML069W, YMR062C, YMR063W, YMR102C, YMR222C, YMR223W, YMR267W, YNL009W, YNL027W, YNL029C, YNL057W, YNL059C, YNL186W, YNL230C, YNL233W, YNL238W, YNL241C, YNL269W, YNL271C, YNL333W, YNL334C, YOL148C, YOL160W, YOR126C, YOR127W, YOR162C, YOR163W, YOR164C, YOR165W, YOR237W, YOR273C, YOR274W, YOR337W, YOR390W, YPL012W, YPL013C, YPL027W, YPL132W, YPL133C, YPL160W, YPL161C, YPL216W, YPL217C, YPL251W, YPL253C, YPR004C, YPR025C, YPR026W, YPR036W, YPR105C, YPR106W

Genes affected by TF deletion 237 genes

YDR372C, YGL173C, YKR043C, YLR244C, YLR216C, YNL052W, YNR061C, YOR191W, YBR189W, YDR220C, YHR178W, YJL053W, YLR406C, YMR224C, YMR194W, YOR377W, YOR381W, YGL231C, YHL015W, YHL047C, YKR013W, YOR220W, YOR258W, YJR078W, YBR218C, YGL038C, YFR033C, YMR189W, YPL018W, YOR382W, YBL034C, YFL013W-A, YKL016C, YKR105C, YLL034C, YOR317W, YBL021C, YDR314C, YLR156W, YBR067C, YGR034W, YJL019W, YMR072W, YMR136W, YOL073C, YOL139C, YPL265W, YGL076C, YNL300W, YNL302C, YPL079W, YPL081W, YIL092W, YIL124W, YLR287C-A, YMR020W, YMR022W, YOR203W, YPL245W, YPL247C, YAL011W, YLR066W, YDR411C, YLR225C, YLR285W, YOR196C, YOR198C, YPL249C-A, YML111W, YAL014C, YDL135C, YDL075W, YDR225W, YEL051W, YLR101C, YML001W, YDL041W, YHR063C, YLR344W, YOR298W, YPR028W, YPR060C, YBR265W, YHR215W, YBR071W, YDL012C, YDR538W, YJR123W, YMR142C, YOL111C, YOR352W, YOR298C-A, YPL273W, YAR075W, YGL148W, YJL158C, YLR161W, YML063W, YMR321C, YMR295C, YNL312W, YER137C, YIL064W, YBR052C, YDR418W, YDR450W, YER187W-A, YER131W, YHR010W, YHR012W, YIL098C, YJR038C, YKR057W, YLR293C, YLR264W, YLR295C, YNL067W, YNL069C, YOL031C, YOR209C, YPL225W, YLR042C, YBR047W, YDR447C, YDR417C, YGL214W, YHL001W, YHL031C, YLR292C, YLR294C, YNL031C, YNL096C, YAR027W, YDL111C, YDL081C, YDL143W, YDL083C, YDR209C, YGR137W, YJL102W, YLR075W, YLR448W, YMR173W-A, YPL004C, YBR140C, YBR299W, YBR108W, YBR080C, YBR082C, YBR112C, YBR144C, YDL021W, YDR110W, YDR173C, YDR543C, YDR545W, YGR081C, YJL036W, YKL001C, YLL017W, YMR119W, YNL191W, YOL120C, YOL122C, YOR331C, YOR367W, YOR383C, YGR266W, YJL167W, YMR304C-A, YDR174W, YDR509W, YLL045C, YLR351C, YLR325C, YMR146C, YMR119W-A, YNL162W, YOL121C, YDR297W, YKL156W, YLR167W, YML067C, YML073C, YNL322C, YPL131W, YPL163C, YBR022W, YBL107C, YBR026C, YDR396W, YHR018C, YIL102C, YLR268W, YNL109W, YEL027W, YBR181C, YDL120W, YEL065W, YPL074W, YCR005C, YDR033W, YER167W, YPL198W, YBR244W, YHR137W, YHR139C, YHR203C, YJL076W, YKL065C, YKL096W-A, YLR047C, YMR215W, YPL010W, YGR085C, YGR027C, YGR089W, YKL035W, YMR095C, YMR130W, YOR369C, YMR276W, YBR089W, YLL051C, YMR094W, YMR096W, YOR306C, YDR360W, YER102W, YGL158W, YGL100W, YGR267C, YGR273C, YIL041W, YIL043C, YKL197C, YMR307W

Genes supported by both experiments 4 genes

YDR411C, YGR273C, YHR178W, YJL102W

Predicted TF–TF partners 2 genes

HAC1, MET32

Explore 2 original interaction plots →