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

GCN4

YEL009C, AAS101, ARG9, AAS3

View at SGD ↗

Basic leucine zipper (bZIP) transcriptional activator of amino acid biosynthetic genes in response to amino acid starvation; expression is tightly regulated at both the transcriptional and translational levels

01 / RECOMMENDED MATRIX

Best-performing DNA-binding model.

RecommendedSource: Aligned Matrix
Fisher’s P-value1.50e-93
Information content11.38
Max PWM score10.22
Recommended cutoff6.69
View and copy the recommended matrices ↘
Position frequency matrix (PFM)
A | 0.547 0.012 0.011 0.964 0.009 0.015 0.073 0.915 0.038 
C | 0.059 0.010 0.026 0.012 0.657 0.010 0.891 0.022 0.352 
G | 0.363 0.011 0.889 0.013 0.323 0.014 0.024 0.016 0.060 
T | 0.031 0.968 0.075 0.012 0.010 0.962 0.013 0.046 0.550
Position count matrix (PCM)
A |  54   1   1  96   0   1   7  91   3 
C |   5   1   2   1  65   1  89   2  35 
G |  36   1  88   1  32   1   2   1   6 
T |   3  96   7   1   1  96   1   4  55
Position weight matrix (PWM)
A |  0.54 -3.28 -3.37  1.10 -3.57 -3.06 -1.48  1.05 -2.13 
C | -1.12 -2.89 -1.93 -2.71  1.29 -2.89  1.60 -2.10  0.67 
G |  0.70 -2.80  1.60 -2.63  0.58 -2.55 -2.01 -2.42 -1.10 
T | -2.33  1.11 -1.45 -3.28 -3.47  1.10 -3.20 -1.94  0.54
02 / COMPARATIVE BENCHMARKS

Alternative candidate matrices 13

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

GCN4_AFoat et. al.P = 2.46e-67View matrix ↘
Sequence logo for GCN4_A
Fisher’s P-value2.46e-67
Information content9.311
Max PWM score8.65
Recommended cutoff8.65
Position frequency matrix (PFM)
A | 0.14 0.01 0.85 0.01 0.01 0.06 0.97 
C | 0.10 0.06 0.06 0.05 0.01 0.92 0.01 
G | 0.06 0.73 0.01 0.93 0.01 0.01 0.01 
T | 0.70 0.20 0.09 0.01 0.97 0.01 0.01
Position count matrix (PCM)
A |  14   1  85   1   1   6  97 
C |  10   6   6   5   1  92   1 
G |   6  73   1  93   1   1   1 
T |  70  20   9   1  97   1   1
Position weight matrix (PWM)
A | -0.83 -3.47  0.98 -3.47 -3.47 -1.67  1.11 
C | -0.59 -1.10 -1.10 -1.28 -2.89  1.63 -2.89 
G | -1.10  1.40 -2.89  1.64 -2.89 -2.89 -2.89 
T |  0.78 -0.47 -1.27 -3.47  1.11 -3.47 -3.47
Foat et. al.
GCN4_BFoat et. al.P = 2.46e-67View matrix ↘
Sequence logo for GCN4_B
Fisher’s P-value2.46e-67
Information content9.703
Max PWM score8.71
Recommended cutoff8.71
Position frequency matrix (PFM)
A | 0.19 0.01 0.87 0.01 0.01 0.05 0.97 
C | 0.07 0.04 0.04 0.01 0.01 0.93 0.01 
G | 0.10 0.79 0.01 0.97 0.01 0.01 0.01 
T | 0.64 0.16 0.08 0.01 0.97 0.01 0.01
Position count matrix (PCM)
A |  19   1  87   1   1   5  97 
C |   7   4   4   1   1  93   1 
G |  10  79   1  97   1   1   1 
T |  64  16   8   1  97   1   1
Position weight matrix (PWM)
A | -0.52 -3.47  1.00 -3.47 -3.47 -1.86  1.11 
C | -0.94 -1.50 -1.50 -2.89 -2.89  1.64 -2.89 
G | -0.59  1.48 -2.89  1.68 -2.89 -2.89 -2.89 
T |  0.69 -0.69 -1.39 -3.47  1.11 -3.47 -3.47
Foat et. al.
GCN4_CFoat et. al.P = 1.95e-76View matrix ↘
Sequence logo for GCN4_C
Fisher’s P-value1.95e-76
Information content10.07
Max PWM score9.17
Recommended cutoff8.77
Position frequency matrix (PFM)
A | 0.72 0.08 0.01 0.96 0.02 0.04 0.11 0.87 
C | 0.01 0.01 0.01 0.01 0.50 0.01 0.85 0.01 
G | 0.27 0.01 0.87 0.02 0.45 0.01 0.04 0.04 
T | 0.01 0.90 0.11 0.01 0.03 0.94 0.01 0.07
Position count matrix (PCM)
A |  72   8   1  96   2   4  11  87 
C |   1   1   1   1  50   1  85   1 
G |  27   1  87   2  45   1   4   4 
T |   1  90  11   1   3  94   1   7
Position weight matrix (PWM)
A |  0.81 -1.39 -3.47  1.10 -2.77 -2.08 -1.07  1.00 
C | -2.89 -2.89 -2.89 -2.89  1.02 -2.89  1.55 -2.89 
G |  0.41 -2.89  1.58 -2.20  0.92 -2.89 -1.50 -1.50 
T | -3.47  1.03 -1.07 -3.47 -2.37  1.08 -3.47 -1.52
Foat et. al.
GCN4_AFordyce et. al.P = 1.31e-15View matrix ↘
Fisher’s P-value1.31e-15
Information content10.42
Max PWM score9.45
Recommended cutoff5.4
Position frequency matrix (PFM)
A | 0.88 0.01 0.01 0.02 0.97 0.01 0.06 0.01 
C | 0.01 0.12 0.01 0.96 0.01 0.34 0.16 0.12 
G | 0.03 0.86 0.01 0.01 0.01 0.20 0.01 0.78 
T | 0.08 0.01 0.97 0.01 0.01 0.46 0.77 0.09
Position count matrix (PCM)
A |  88   1   1   2  97   1   6   1 
C |   1  12   1  96   1  34  16  12 
G |   3  86   1   1   1  20   1  78 
T |   8   1  97   1   1  46  77   9
Position weight matrix (PWM)
A |  1.01 -3.47 -3.47 -2.77  1.11 -3.47 -1.67 -3.47 
C | -2.89 -0.41 -2.89  1.67 -2.89  0.64 -0.12 -0.41 
G | -1.79  1.56 -2.89 -2.89 -2.89  0.11 -2.89  1.47 
T | -1.39 -3.47  1.11 -3.47 -3.47  0.36  0.88 -1.27
Fordyce et. al.
GCN4_BFordyce et. al.P = 1.55e-69View matrix ↘
Fisher’s P-value1.55e-69
Information content10.66
Max PWM score9.13
Recommended cutoff8.46
Position frequency matrix (PFM)
A | 0.27 0.03 0.01 0.97 0.01 0.06 0.03 0.97 
C | 0.11 0.01 0.01 0.01 0.50 0.02 0.87 0.01 
G | 0.29 0.01 0.97 0.01 0.49 0.01 0.09 0.01 
T | 0.33 0.95 0.01 0.01 0.01 0.92 0.01 0.01
Position count matrix (PCM)
A |  27   3   1  97   1   6   3  97 
C |  11   1   1   1  50   2  87   1 
G |  28   1  97   1  49   1   9   1 
T |  33  95   1   1   1  92   1   1
Position weight matrix (PWM)
A | -0.17 -2.37 -3.47  1.11 -3.47 -1.67 -2.37  1.11 
C | -0.49 -2.89 -2.89 -2.89  1.02 -2.20  1.58 -2.89 
G |  0.48 -2.89  1.68 -2.89  1.00 -2.89 -0.69 -2.89 
T |  0.03  1.09 -3.47 -3.47 -3.47  1.06 -3.47 -3.47
Fordyce et. al.
GCN4_CFordyce et. al.P = 2.14e-76View matrix ↘
Fisher’s P-value2.14e-76
Information content10.63
Max PWM score9.48
Recommended cutoff8.35
Position frequency matrix (PFM)
A | 0.06 0.01 0.88 0.01 0.01 0.03 0.97 0.01 
C | 0.11 0.01 0.01 0.27 0.01 0.96 0.01 0.36 
G | 0.02 0.88 0.02 0.71 0.01 0.01 0.01 0.10 
T | 0.81 0.10 0.09 0.01 0.97 0.01 0.01 0.54
Position count matrix (PCM)
A |   6   1  88   1   1   3  97   1 
C |  11   1   1  27   1  96   1  36 
G |   2  88   2  71   1   1   1  10 
T |  81  10   9   1  97   1   1  54
Position weight matrix (PWM)
A | -1.67 -3.47  1.01 -3.47 -3.47 -2.37  1.11 -3.47 
C | -0.49 -2.89 -2.89  0.41 -2.89  1.67 -2.89  0.69 
G | -2.20  1.59 -2.20  1.37 -2.89 -2.89 -2.89 -0.59 
T |  0.93 -1.16 -1.27 -3.47  1.11 -3.47 -3.47  0.52
Fordyce et. al.
GCN4Harbison et. al.P = 8.20e-68View matrix ↘
Sequence logo for GCN4
Fisher’s P-value8.20e-68
Information content8.102
Max PWM score8.32
Recommended cutoff8.32
Position frequency matrix (PFM)
A | 0.059 0.036 0.927 0.029 0.044 0.101 0.697 
C | 0.017 0.022 0.008 0.662 0.027 0.827 0.043 
G | 0.015 0.866 0.012 0.251 0.018 0.029 0.045 
T | 0.908 0.077 0.054 0.058 0.911 0.043 0.214
Position count matrix (PCM)
A |   5   3  92   2   4  10  69 
C |   1   2   0  66   2  82   4 
G |   1  86   1  25   1   2   4 
T |  90   7   5   5  91   4  21
Position weight matrix (PWM)
A | -1.69 -2.18  1.06 -2.40 -1.98 -1.15  0.78 
C | -2.36 -2.10 -3.11  1.30 -1.90  1.52 -1.43 
G | -2.48  1.57 -2.71  0.33 -2.30 -1.83 -1.39 
T |  1.04 -1.42 -1.78 -1.71  1.05 -2.01 -0.40
Harbison et. al.
GCN4Macisaac et. alP = 1.60e-79View matrix ↘
Sequence logo for GCN4
Fisher’s P-value1.60e-79
Information content10.64
Max PWM score9.49
Recommended cutoff7.38
Position frequency matrix (PFM)
A | 0.642 0.003 0.008 0.995 0.011 0.042 0.218 0.735 
C | 0.050 0.021 0.025 0.001 0.875 0.021 0.729 0.029 
G | 0.274 0.001 0.957 0.003 0.106 0.001 0.009 0.056 
T | 0.034 0.975 0.010 0.001 0.008 0.936 0.044 0.180
Position count matrix (PCM)
A |  64   0   0  99   1   4  21  73 
C |   5   2   2   0  87   2  72   2 
G |  27   0  95   0  10   0   0   5 
T |   3  97   1   0   0  93   4  18
Position weight matrix (PWM)
A |  0.70 -4.67 -3.69  1.13 -3.37 -2.03 -0.38  0.83 
C | -1.28 -2.15 -1.97 -5.19  1.58 -2.15  1.40 -1.83 
G |  0.42 -5.19  1.67 -4.09 -0.53 -5.19 -3.00 -1.17 
T | -2.24  1.11 -3.47 -5.77 -3.69  1.07 -1.98 -0.58
Macisaac et. al
GCN4Morozov et. al.P = 1.72e-86View matrix ↘
Sequence logo for GCN4
Fisher’s P-value1.72e-86
Information content10.26
Max PWM score10.02
Recommended cutoff7.48
Position frequency matrix (PFM)
A | 0.587 0.015 0.014 0.949 0.007 0.028 0.112 0.753 0.095 
C | 0.116 0.010 0.073 0.016 0.980 0.007 0.802 0.057 0.187 
G | 0.231 0.012 0.793 0.019 0.001 0.023 0.065 0.034 0.123 
T | 0.066 0.962 0.120 0.016 0.012 0.942 0.020 0.155 0.595
Position count matrix (PCM)
A |  58   1   1  94   0   2  11  75   9 
C |  11   1   7   1  98   0  80   5  18 
G |  23   1  79   1   0   2   6   3  12 
T |   6  96  12   1   1  94   2  15  59
Position weight matrix (PWM)
A |  0.61 -3.06 -3.13  1.09 -3.82 -2.44 -1.05  0.86 -1.21 
C | -0.44 -2.89 -0.90 -2.42  1.69 -3.25  1.49 -1.15  0.04 
G |  0.25 -2.71  1.48 -2.25 -5.19 -2.06 -1.02 -1.67 -0.38 
T | -1.58  1.10 -0.98 -3.00 -3.28  1.08 -2.77 -0.72  0.62
Morozov et. al.
GCN4Pachkov et alP = 1.92e-55View matrix ↘
Sequence logo for GCN4
Fisher’s P-value1.92e-55
Information content10.29
Max PWM score8.68
Recommended cutoff7.17
Position frequency matrix (PFM)
A | 0.017 0.868 0.011 0.001 0.061 0.997 0.032 
C | 0.053 0.047 0.011 0.001 0.939 0.001 0.280 
G | 0.737 0.001 0.975 0.001 0.001 0.003 0.076 
T | 0.193 0.085 0.003 1.000 0.001 0.001 0.612
Position count matrix (PCM)
A |   1  86   1   0   6  99   3 
C |   5   4   1   0  93   0  28 
G |  73   0  97   0   0   0   7 
T |  19   8   0 100   0   0  61
Position weight matrix (PWM)
A | -2.94  1.00 -3.37 -5.77 -1.66  1.14 -2.30 
C | -1.22 -1.34 -2.80 -5.19  1.65 -5.19  0.44 
G |  1.41 -5.19  1.69 -5.19 -5.19 -4.09 -0.86 
T | -0.51 -1.33 -4.67  1.14 -5.77 -5.77  0.65
Pachkov et al
GCN4Zhu J and MQ ZhangP = 2.36e-55View matrix ↘
Sequence logo for GCN4
Fisher’s P-value2.36e-55
Information content5.772
Max PWM score6.91
Recommended cutoff6.91
Position frequency matrix (PFM)
A | 0.04 0.04 0.88 0.08 0.04 0.23 
C | 0.04 0.04 0.04 0.69 0.04 0.50 
G | 0.04 0.85 0.04 0.12 0.08 0.15 
T | 0.88 0.08 0.04 0.12 0.85 0.12
Position count matrix (PCM)
A |   4   4  88   8   4  23 
C |   4   4   4  69   4  50 
G |   4  85   4  12   8  15 
T |  88   8   4  12  85  12
Position weight matrix (PWM)
A | -2.08 -2.08  1.01 -1.39 -2.08 -0.33 
C | -1.50 -1.50 -1.50  1.34 -1.50  1.02 
G | -1.50  1.55 -1.50 -0.41 -0.81 -0.18 
T |  1.01 -1.39 -2.08 -0.98  0.98 -0.98
Zhu J and MQ Zhang
GCN4Zhu et. al.P = 1.31e-76View matrix ↘
Sequence logo for GCN4
Fisher’s P-value1.31e-76
Information content12.25
Max PWM score10.44
Recommended cutoff6.54
Position frequency matrix (PFM)
A | 0.54 0.01 0.01 0.96 0.01 0.01 0.06 0.97 0.02 
C | 0.04 0.01 0.01 0.01 0.43 0.01 0.92 0.01 0.41 
G | 0.41 0.01 0.92 0.01 0.55 0.01 0.01 0.01 0.04 
T | 0.02 0.97 0.06 0.01 0.01 0.96 0.01 0.01 0.54
Position count matrix (PCM)
A |  54   1   1  96   1   1   6  97   2 
C |   4   1   1   1  43   1  92   1  41 
G |  41   1  92   1  55   1   1   1   4 
T |   2  97   6   1   1  96   1   1  54
Position weight matrix (PWM)
A |  0.52 -3.47 -3.47  1.10 -3.47 -3.47 -1.67  1.11 -2.77 
C | -1.50 -2.89 -2.89 -2.89  0.87 -2.89  1.63 -2.89  0.82 
G |  0.82 -2.89  1.63 -2.89  1.12 -2.89 -2.89 -2.89 -1.50 
T | -2.77  1.11 -1.67 -3.47 -3.47  1.10 -3.47 -3.47  0.52
Zhu et. al.
GCN4Zhao and StormoP = 1.98e-46View matrix ↘
Sequence logo for GCN4
Fisher’s P-value1.98e-46
Information content6.334
Max PWM score7.05
Recommended cutoff6.72
Position frequency matrix (PFM)
A | 0.440 0.001 0.001 0.950 0.049 0.225 0.230 
C | 0.125 0.001 0.001 0.001 0.621 0.089 0.483 
G | 0.346 0.001 0.860 0.001 0.211 0.220 0.130 
T | 0.089 0.997 0.138 0.048 0.118 0.466 0.156
Position count matrix (PCM)
A |  44   0   0  95   4  22  23 
C |  12   0   0   0  62   8  48 
G |  34   0  86   0  21  22  13 
T |   8  99  13   4  11  46  15
Position weight matrix (PWM)
A |  0.32 -5.77 -5.77  1.09 -1.88 -0.35 -0.33 
C | -0.36 -5.19 -5.19 -5.19  1.24 -0.70  0.99 
G |  0.65 -5.19  1.56 -5.19  0.16  0.20 -0.33 
T | -1.28  1.14 -0.84 -1.90 -1.00  0.38 -0.72
Zhao and Stormo
03 / EXPERIMENTAL CONTEXT

Gene-level annotations and interactions.

Genes bound in ChIP-chip experiments 143 genes

YBL001C, YBL059W, YBL076C, YBR043C, YBR048W, YBR104W, YBR112C, YBR114W, YBR115C, YBR144C, YBR145W, YBR218C, YBR248C, YBR249C, YBR250W, YBR256C, YBR257W, YCL002C, YCL006C, YCL007C, YCL008C, YCL009C, YCL010C, YCL030C, YCR002C, YCR004C, YCR005C, YCR006C, YCR008W, YCR012W, YCR096C, YDL044C, YDL054C, YDL170W, YDL171C, YDL182W, YDL198C, YDR034C, YDR035W, YDR042C, YDR084C, YDR125C, YDR126W, YDR127W, YDR144C, YDR145W, YDR341C, YDR354W, YDR481C, YEL001C, YEL062W, YEL063C, YER052C, YER055C, YER069W, YER073W, YER085C, YER086W, YER089C, YER090W, YGL125W, YGL184C, YGL202W, YGL234W, YGL236C, YGR071C, YGR072W, YGR094W, YGR218W, YGR267C, YGR269W, YGR271W, YHR018C, YHR071W, YHR161C, YHR162W, YJL003W, YJL004C, YJL071W, YJL072C, YJL088W, YJL200C, YJR016C, YJR018W, YJR025C, YJR026W, YJR027W, YJR028W, YJR029W, YJR109C, YJR110W, YJR111C, YJR112W, YKL015W, YKL016C, YKL211C, YLL004W, YLL005C, YLR261C, YLR262C, YLR302C, YLR355C, YLR356W, YLR451W, YMR019W, YMR062C, YMR063W, YMR095C, YMR096W, YNL004W, YNL005C, YNL103W, YNL104C, YNL309W, YNL311C, YNL337W, YNR050C, YOL058W, YOL064C, YOL119C, YOL140W, YOL160W, YOR108W, YOR130C, YOR201C, YOR202W, YOR203W, YOR204W, YOR221C, YOR222W, YOR302W, YOR303W, YOR337W, YPL111W, YPL188W, YPL252C, YPL273W, YPR038W, YPR039W, YPR040W, YPR110C, YPR111W, YPR185W

Genes affected by TF deletion 113 genes

YCR040W, YDR068W, YGR280C, YOR225W, YDL131W, YGL009C, YPL019C, YDR035W, YMR044W, YOR226C, YHR143W-A, YJL052W, YOR382W, YGR063C, YOL142W, YOR285W, YOR287C, YOR351C, YPL187W, YDL222C, YER024W, YHR208W, YBR091C, YBR093C, YDR461W, YFR008W, YHR021C, YJR146W, YNL146W, YOR288C, YCL018W, YDR281C, YIL015W, YLR185W, YML055W, YMR287C, YER109C, YCL065W, YPL183W-A, YDL106C, YKL054C, YOR045W, YBR011C, YNL027W, YJR148W, YER001W, YLR348C, YOL144W, YBL062W, YGR192C, YKL209C, YKL178C, YLR343W, YLR349W, YNL150W, YOL143C, YKL177W, YLR234W, YOR239W, YKL058W, YLR040C, YLR420W, YNL259C, YOR393W, YCL066W, YHR005C-A, YOR210W, YDR235W, YKL120W, YLR041W, YOR020C, YOR054C, YFL026W, YFL059W, YFL030W, YHR072W-A, YLR388W, YNL195C, YOR383C, YDR322C-A, YGL089C, YBR145W, YNL162W, YPL281C, YBL042C, YGR233C, YJR004C, YKL216W, YDR056C, YHR018C, YLR303W, YAL033W, YER019C-A, YHR136C, YHR141C, YBR053C, YCR028C-A, YIL105C, YLR302C, YNL070W, YAR044W, YGL032C, YGL004C, YHR140W, YBR118W, YJR135W-A, YJR009C, YEL009C, YCL039W, YBR276C, YCL006C, YML081C-A, YOR182C

Genes supported by both experiments 5 genes

YBR145W, YCL006C, YDR035W, YHR018C, YLR302C

Predicted TF–TF partners 10 genes

ABF1, ACA1, ARG80, BAS1, CBF1, LEU3, RSC3, RTG3, STB3, TYE7

Explore 10 original interaction plots →