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

ROX1

YPR065W, REO1

View at SGD ↗

Heme-dependent repressor of hypoxic genes; contains an HMG domain that is responsible for DNA bending activity

01 / RECOMMENDED MATRIX

Best-performing DNA-binding model.

RecommendedSource: Fordyce et. al.
Fisher’s P-value0.001137
Information content7.572
Max PWM score7.81
Recommended cutoff4.5
View and copy the recommended matrices ↘
Position frequency matrix (PFM)
A | 0.95 0.01 0.96 0.96 0.11 0.55 0.26 0.25 
C | 0.01 0.88 0.02 0.01 0.01 0.10 0.28 0.33 
G | 0.01 0.06 0.01 0.01 0.01 0.22 0.39 0.28 
T | 0.03 0.05 0.02 0.02 0.87 0.12 0.07 0.13
Position count matrix (PCM)
A |  95   1  96  96  11  55  26  25 
C |   1  88   2   1   1  10  28  33 
G |   1   6   1   1   1  22  39  28 
T |   3   5   2   2  87  12   7  13
Position weight matrix (PWM)
A |  1.09 -3.47  1.10  1.10 -1.07  0.54 -0.21 -0.25 
C | -2.89  1.59 -2.20 -2.89 -2.89 -0.59  0.44  0.61 
G | -2.89 -1.10 -2.89 -2.89 -2.89  0.20  0.77  0.44 
T | -2.37 -1.86 -2.77 -2.77  1.00 -0.98 -1.52 -0.90
02 / COMPARATIVE BENCHMARKS

Alternative candidate matrices 11

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

ROX1Badis et. al.P = 0.07122View matrix ↘
Sequence logo for ROX1
Fisher’s P-value0.07122
Information content7.889
Max PWM score6.12
Recommended cutoff6.12
Position frequency matrix (PFM)
A | 0.97 0.01 0.97 0.97 0.01 
C | 0.01 0.97 0.01 0.01 0.01 
G | 0.01 0.01 0.01 0.01 0.01 
T | 0.01 0.01 0.01 0.01 0.97
Position count matrix (PCM)
A |  97   1  97  97   1 
C |   1  97   1   1   1 
G |   1   1   1   1   1 
T |   1   1   1   1  97
Position weight matrix (PWM)
A |  1.11 -3.47  1.11  1.11 -3.47 
C | -2.89  1.68 -2.89 -2.89 -2.89 
G | -2.89 -2.89 -2.89 -2.89 -2.89 
T | -3.47 -3.47 -3.47 -3.47  1.11
Badis et. al.
ROX1_AFoat et. al.P = 0.0003137View matrix ↘
Sequence logo for ROX1_A
Fisher’s P-value0.0003137
Information content16.64
Max PWM score16.84
Recommended cutoff9.3
Position frequency matrix (PFM)
A | 0.01 0.27 0.05 0.01 0.01 0.01 0.01 0.62 0.01 0.30 0.39 0.05 0.17 0.69 0.93 0.61 
C | 0.36 0.34 0.30 0.93 0.93 0.05 0.10 0.06 0.94 0.35 0.27 0.12 0.38 0.01 0.05 0.27 
G | 0.53 0.01 0.31 0.04 0.04 0.93 0.85 0.06 0.04 0.31 0.33 0.59 0.42 0.30 0.02 0.12 
T | 0.10 0.39 0.33 0.02 0.02 0.01 0.05 0.26 0.01 0.04 0.01 0.24 0.04 0.01 0.01 0.01
Position count matrix (PCM)
A |   1  27   5   1   1   1   1  62   1  30  39   5  17  69  93  61 
C |  36  34  30  93  93   5  10   6  94  35  27  12  38   1   5  27 
G |  53   1  31   4   4  93  85   6   4  31  33  59  42  30   2  12 
T |  10  39  33   2   2   1   5  26   1   4   1  24   4   1   1   1
Position weight matrix (PWM)
A | -3.47 -0.17 -1.86 -3.47 -3.47 -3.47 -3.47  0.66 -3.47 -0.06  0.20 -1.86 -0.63  0.77  1.07  0.65 
C |  0.69  0.64  0.51  1.64  1.64 -1.28 -0.59 -1.10  1.65  0.66  0.41 -0.41  0.75 -2.89 -1.28  0.41 
G |  1.08 -2.89  0.54 -1.50 -1.50  1.64  1.55 -1.10 -1.50  0.54  0.61  1.19  0.85  0.51 -2.20 -0.41 
T | -1.16  0.20  0.03 -2.77 -2.77 -3.47 -1.86 -0.21 -3.47 -2.08 -3.47 -0.29 -2.08 -3.47 -3.47 -3.47
Foat et. al.
ROX1_BFoat et. al.P = 2.10e-07View matrix ↘
Sequence logo for ROX1_B
Fisher’s P-value2.10e-07
Information content16.22
Max PWM score15.08
Recommended cutoff10.48
Position frequency matrix (PFM)
A | 0.01 0.22 0.02 0.96 0.01 0.01 0.01 0.97 0.06 0.26 0.34 0.09 
C | 0.04 0.26 0.43 0.01 0.01 0.01 0.96 0.01 0.92 0.04 0.12 0.01 
G | 0.77 0.01 0.51 0.02 0.81 0.97 0.02 0.01 0.01 0.69 0.53 0.02 
T | 0.18 0.51 0.04 0.01 0.17 0.01 0.01 0.01 0.01 0.01 0.01 0.88
Position count matrix (PCM)
A |   1  22   2  96   1   1   1  97   6  26  34   9 
C |   4  26  43   1   1   1  96   1  92   4  12   1 
G |  77   1  51   2  81  97   2   1   1  69  53   2 
T |  18  51   4   1  17   1   1   1   1   1   1  88
Position weight matrix (PWM)
A | -3.47 -0.37 -2.77  1.10 -3.47 -3.47 -3.47  1.11 -1.67 -0.21  0.06 -1.27 
C | -1.50  0.37  0.87 -2.89 -2.89 -2.89  1.67 -2.89  1.63 -1.50 -0.41 -2.89 
G |  1.45 -2.89  1.04 -2.20  1.50  1.68 -2.20 -2.89 -2.89  1.34  1.08 -2.20 
T | -0.58  0.47 -2.08 -3.47 -0.63 -3.47 -3.47 -3.47 -3.47 -3.47 -3.47  1.01
Foat et. al.
ROX1_CFoat et. al.P = 4.31e-05View matrix ↘
Sequence logo for ROX1_C
Fisher’s P-value4.31e-05
Information content10.27
Max PWM score11.23
Recommended cutoff7.61
Position frequency matrix (PFM)
A | 0.01 0.48 0.10 0.01 0.17 0.97 0.57 0.87 0.93 0.12 0.01 0.21 
C | 0.23 0.01 0.10 0.01 0.64 0.01 0.41 0.01 0.03 0.27 0.37 0.12 
G | 0.50 0.18 0.48 0.97 0.01 0.01 0.01 0.11 0.01 0.20 0.11 0.01 
T | 0.27 0.33 0.32 0.01 0.19 0.01 0.01 0.01 0.03 0.41 0.52 0.67
Position count matrix (PCM)
A |   1  48  10   1  17  97  56  87  93  12   1  21 
C |  23   1  10   1  64   1  41   1   3  27  37  12 
G |  50  18  48  97   1   1   1  11   1  20  11   1 
T |  27  33  32   1  19   1   1   1   3  41  52  67
Position weight matrix (PWM)
A | -3.47  0.41 -1.16 -3.47 -0.63  1.11  0.58  1.00  1.07 -0.98 -3.47 -0.42 
C |  0.25 -2.89 -0.59 -2.89  1.27 -2.89  0.82 -2.89 -1.79  0.41  0.72 -0.41 
G |  1.02  0.00  0.98  1.68 -2.89 -2.89 -2.89 -0.49 -2.89  0.11 -0.49 -2.89 
T | -0.17  0.03  0.00 -3.47 -0.52 -3.47 -3.47 -3.47 -2.37  0.25  0.49  0.74
Foat et. al.
ROX1_BFordyce et. al.P = 0.001847View matrix ↘
Fisher’s P-value0.001847
Information content7.296
Max PWM score7.78
Recommended cutoff4.6
Position frequency matrix (PFM)
A | 0.55 0.24 0.34 0.90 0.01 0.96 0.95 0.12 
C | 0.11 0.23 0.23 0.01 0.86 0.02 0.01 0.01 
G | 0.23 0.47 0.30 0.01 0.07 0.01 0.01 0.01 
T | 0.11 0.06 0.13 0.09 0.07 0.01 0.03 0.86
Position count matrix (PCM)
A |  55  24  34  90   1  96  95  12 
C |  11  23  23   1  86   2   1   1 
G |  23  47  30   1   7   1   1   1 
T |  11   6  13   9   7   1   3  86
Position weight matrix (PWM)
A |  0.54 -0.29  0.06  1.03 -3.47  1.10  1.09 -0.98 
C | -0.49  0.25  0.25 -2.89  1.56 -2.20 -2.89 -2.89 
G |  0.25  0.96  0.51 -2.89 -0.94 -2.89 -2.89 -2.89 
T | -1.07 -1.67 -0.90 -1.27 -1.52 -3.47 -2.37  0.99
Fordyce et. al.
ROX1_CFordyce et. al.P = 0.002449View matrix ↘
Fisher’s P-value0.002449
Information content7.51
Max PWM score7.78
Recommended cutoff6.38
Position frequency matrix (PFM)
A | 0.28 0.95 0.01 0.96 0.96 0.11 0.54 0.28 
C | 0.33 0.01 0.86 0.02 0.01 0.01 0.12 0.25 
G | 0.26 0.01 0.07 0.01 0.01 0.01 0.23 0.40 
T | 0.14 0.03 0.06 0.01 0.02 0.87 0.11 0.07
Position count matrix (PCM)
A |  28  95   1  96  96  11  54  28 
C |  33   1  86   2   1   1  12  25 
G |  26   1   7   1   1   1  23  40 
T |  14   3   6   1   2  87  11   7
Position weight matrix (PWM)
A | -0.13  1.09 -3.47  1.10  1.10 -1.07  0.52 -0.13 
C |  0.61 -2.89  1.56 -2.20 -2.89 -2.89 -0.41  0.33 
G |  0.37 -2.89 -0.94 -2.89 -2.89 -2.89  0.25  0.80 
T | -0.83 -2.37 -1.67 -3.47 -2.77  1.00 -1.07 -1.52
Fordyce et. al.
ROX1Harbison et. al.P = 0.00599View matrix ↘
Sequence logo for ROX1
Fisher’s P-value0.00599
Information content12.17
Max PWM score10.18
Recommended cutoff5.22
Position frequency matrix (PFM)
A | 0.012 0.012 0.012 0.964 0.012 0.012 0.012 0.012 0.012 
C | 0.488 0.488 0.488 0.012 0.012 0.012 0.012 0.012 0.012 
G | 0.012 0.488 0.012 0.012 0.012 0.012 0.965 0.012 0.012 
T | 0.488 0.012 0.488 0.012 0.964 0.964 0.012 0.964 0.964
Position count matrix (PCM)
A |   1   1   1  96   1   1   1   1   1 
C |  48  48  48   1   1   1   1   1   1 
G |   1  48   1   1   1   1  96   1   1 
T |  48   1  48   1  96  96   1  96  96
Position weight matrix (PWM)
A | -3.28 -3.28 -3.28  1.10 -3.28 -3.28 -3.28 -3.28 -3.28 
C |  1.00  1.00  1.00 -2.71 -2.71 -2.71 -2.71 -2.71 -2.71 
G | -2.71  1.00 -2.71 -2.71 -2.71 -2.71  1.68 -2.71 -2.71 
T |  0.42 -3.28  0.42 -3.28  1.10  1.10 -3.28  1.10  1.10
Harbison et. al.
ROX1Macisaac et. alP = 2.16e-09View matrix ↘
Sequence logo for ROX1
Fisher’s P-value2.16e-09
Information content9.413
Max PWM score10.16
Recommended cutoff8.47
Position frequency matrix (PFM)
A | 0.541 0.440 0.681 0.822 0.001 0.224 0.232 0.001 0.054 0.229 
C | 0.007 0.002 0.315 0.001 0.465 0.774 0.678 0.843 0.136 0.499 
G | 0.171 0.223 0.001 0.173 0.497 0.001 0.051 0.001 0.621 0.233 
T | 0.281 0.334 0.003 0.004 0.038 0.001 0.039 0.155 0.189 0.040
Position count matrix (PCM)
A |  54  44  68  82   0  22  23   0   5  22 
C |   0   0  31   0  46  77  67  84  13  49 
G |  17  22   0  17  49   0   5   0  62  23 
T |  28  33   0   0   3   0   3  15  18   4
Position weight matrix (PWM)
A |  0.53  0.32  0.76  0.94 -5.77 -0.36 -0.32 -5.77 -1.78 -0.33 
C | -3.25 -4.50  0.56 -5.19  0.95  1.46  1.33  1.54 -0.28  1.02 
G | -0.05  0.21 -5.19 -0.04  1.02 -5.19 -1.26 -5.19  1.24  0.26 
T | -0.13  0.04 -4.67 -4.38 -2.13 -5.77 -2.10 -0.72 -0.53 -2.08
Macisaac et. al
ROX1Morozov et. al.P = 0.009598View matrix ↘
Sequence logo for ROX1
Fisher’s P-value0.009598
Information content7.022
Max PWM score7.54
Recommended cutoff5.31
Position frequency matrix (PFM)
A | 0.127 0.809 0.045 0.819 0.428 0.967 0.010 
C | 0.561 0.074 0.762 0.068 0.202 0.003 0.971 
G | 0.097 0.070 0.106 0.078 0.087 0.012 0.005 
T | 0.215 0.047 0.088 0.036 0.283 0.018 0.014
Position count matrix (PCM)
A |  12  80   4  81  42  96   1 
C |  56   7  76   6  20   0  97 
G |   9   7  10   7   8   1   0 
T |  21   4   8   3  28   1   1
Position weight matrix (PWM)
A | -0.92  0.93 -1.96  0.94  0.29  1.11 -3.47 
C |  1.14 -0.89  1.44 -0.97  0.12 -4.09  1.69 
G | -0.62 -0.94 -0.53 -0.84 -0.73 -2.71 -3.58 
T | -0.40 -1.92 -1.29 -2.18 -0.12 -2.88 -3.13
Morozov et. al.
ROX1Pachkov et alP = 0.01692View matrix ↘
Sequence logo for ROX1
Fisher’s P-value0.01692
Information content16.28
Max PWM score13.93
Recommended cutoff8.43
Position frequency matrix (PFM)
A | 0.097 0.001 0.001 0.839 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 
C | 0.409 0.891 0.549 0.001 0.001 0.001 0.001 0.001 0.059 0.684 0.058 0.550 
G | 0.001 0.001 0.001 0.001 0.001 0.001 1.000 0.001 0.001 0.198 0.258 0.001 
T | 0.494 0.109 0.451 0.161 1.000 1.000 0.001 1.000 0.941 0.118 0.684 0.450
Position count matrix (PCM)
A |   9   0   0  83   0   0   0   0   0   0   0   0 
C |  40  89  54   0   0   0   0   0   5  68   5  55 
G |   0   0   0   0   0   0 100   0   0  19  25   0 
T |  49  10  45  16 100 100   0 100  94  11  68  45
Position weight matrix (PWM)
A | -1.19 -5.77 -5.77  0.96 -5.77 -5.77 -5.77 -5.77 -5.77 -5.77 -5.77 -5.77 
C |  0.82  1.60  1.12 -5.19 -5.19 -5.19 -5.19 -5.19 -1.12  1.34 -1.13  1.12 
G | -5.19 -5.19 -5.19 -5.19 -5.19 -5.19  1.71 -5.19 -5.19  0.10  0.36 -5.19 
T |  0.43 -1.08  0.34 -0.69  1.14  1.14 -5.77  1.14  1.08 -1.00  0.76  0.34
Pachkov et al
ROX1Zhu J and MQ ZhangP = 0.0001483View matrix ↘
Sequence logo for ROX1
Fisher’s P-value0.0001483
Information content6.299
Max PWM score10.96
Recommended cutoff5.9
Position frequency matrix (PFM)
A | 0.08 0.08 0.25 0.67 0.08 0.08 0.08 0.08 0.08 0.08 0.17 0.08 
C | 0.42 0.58 0.42 0.17 0.08 0.08 0.08 0.08 0.08 0.50 0.08 0.50 
G | 0.08 0.08 0.08 0.08 0.08 0.17 0.75 0.08 0.08 0.17 0.17 0.25 
T | 0.42 0.25 0.25 0.08 0.75 0.67 0.08 0.75 0.75 0.25 0.58 0.17
Position count matrix (PCM)
A |   8   8  25  67   8   8   8   8   8   8  17   8 
C |  42  57  42  17   8   8   8   8   8  50   8  50 
G |   8   8   8   8   8  17  75   8   8  17  17  25 
T |  42  25  25   8  75  67   8  75  75  25  57  17
Position weight matrix (PWM)
A | -1.39 -1.39 -0.25  0.74 -1.39 -1.39 -1.39 -1.39 -1.39 -1.39 -0.63 -1.39 
C |  0.85  1.17  0.85 -0.06 -0.81 -0.81 -0.81 -0.81 -0.81  1.02 -0.81  1.02 
G | -0.81 -0.81 -0.81 -0.81 -0.81 -0.06  1.43 -0.81 -0.81 -0.06 -0.06  0.33 
T |  0.27 -0.25 -0.25 -1.39  0.85  0.74 -1.39  0.85  0.85 -0.25  0.59 -0.63
Zhu J and MQ Zhang
03 / EXPERIMENTAL CONTEXT

Gene-level annotations and interactions.

Genes bound in ChIP-chip experiments 172 genes

YAL033W, YAL034C, YAR009C, YAR023C, YAR068W, YBL029W, YBL074C, YBL098W, YBL099W, YBL100C, YBR230C, YCR024C, YCR063W, YCR064C, YCR065W, YCR073C, YDL024C, YDL045W-A, YDL060W, YDL061C, YDL147W, YDL148C, YDL184C, YDL245C, YDL246C, YDR023W, YDR042C, YDR064W, YDR077W, YDR085C, YDR151C, YDR152W, YDR259C, YDR278C, YDR306C, YDR339C, YDR340W, YDR343C, YDR362C, YDR363W, YDR372C, YDR373W, YDR441C, YDR442W, YDR470C, YDR471W, YDR472W, YDR524C, YDR525W, YEL040W, YEL047C, YEL055C, YEL059W, YEL060C, YEL070W, YER007C-A, YER011W, YER045C, YER056C-A, YER074W, YER075C, YER097W, YER098W, YER101C, YER102W, YER137C, YER158C, YFL039C, YFR016C, YFR039C, YFR040W, YGL005C, YGL012W, YGL013C, YGL029W, YGL123W, YGL124C, YGL134W, YGL135W, YGL136C, YGL195W, YGL234W, YGL236C, YGR027C, YGR084C, YGR124W, YGR190C, YGR221C, YGR256W, YHL034C, YHR185C, YHR193C, YHR194W, YIL014W, YIL015C-A, YIL056W, YIL099W, YIL102C, YIL119C, YIL135C, YIR020C, YJL039C, YJL045W, YJL048C, YJL105W, YJL148W, YJL219W, YJL221C, YJR094C, YJR100C, YJR158W, YJR159W, YKL044W, YKL057C, YKL127W, YKR073C, YKR102W, YLL027W, YLR034C, YLR035C-A, YLR043C, YLR074C, YLR075W, YLR105C, YLR255C, YLR256W, YLR256W-A, YLR328W, YLR354C, YLR368W, YLR406C, YLR407W, YML055W, YML056C, YML071C, YML102W, YML103C, YML124C, YMR014W, YMR017W, YMR135C, YMR136W, YMR193C-A, YMR319C, YNL034W, YNL097C, YNL111C, YNL288W, YNR050C, YOL026C, YOL121C, YOL155C, YOL156W, YOL157C, YOR042W, YOR223W, YOR236W, YOR272W, YOR277C, YOR278W, YOR315W, YPL018W, YPL019C, YPL130W, YPL143W, YPL198W, YPL220W, YPL230W, YPR010C, YPR013C, YPR109W, YPR160W

Genes affected by TF deletion 96 genes

YBL113C, YDR038C, YER145C, YJR048W, YOR225W, YDR222W, YCL051W, YDR371W, YIL111W, YJR047C, YOR226C, YPL240C, YDR039C, YEL047C, YHR179W, YPL016W, YER011W, YMR135W-A, YNL111C, YPL283C, YGR180C, YML058W-A, YMR252C, YNL339C, YBR067C, YCR077C, YDL034W, YFR006W, YGR060W, YKR106W, YLR337C, YPR015C, YGR213C, YDR044W, YGL177W, YHL050C, YML121W, YOR229W, YER002W, YGL053W, YJR148W, YOR010C, YJL026W, YLR348C, YBR291C, YMR320W, YJR150C, YLR349W, YPR065W, YMR319C, YMR263W, YJR070C, YAR028W, YNL261W, YMR058W, YNL094W, YDR116C, YGR049W, YOL096C, YOR333C, YHR219W, YIL066C, YLR142W, YMR272C, YGR018C, YDR297W, YER044C, YGL164C, YGL197W, YLR297W, YMR037C, YEL065W, YGL001C, YHR136C, YMR186W, YPL041C, YPR159W, YGL255W, YJR071W, YNL104C, YAR031W, YBR244W, YGR175C, YHR137W, YNL264C, YDR040C, YBR085W, YHR048W, YKL008C, YOR034C, YIL011W, YNR018W, YDL053C, YFL068W, YGR050C, YOR306C

Genes supported by both experiments 4 genes

YEL047C, YER011W, YMR319C, YNL111C