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

RPH1

YER169W, KDM4

View at SGD ↗

JmjC domain-containing histone demethylase which can specifically demethylate H3K36 tri- and dimethyl modification states; transcriptional repressor of PHR1; Rph1p phosphorylation during DNA damage is under control of the MEC1-RAD53 pathway

01 / RECOMMENDED MATRIX

Best-performing DNA-binding model.

RecommendedSource: Aligned Matrix
Fisher’s P-value1.39e-08
Information content8.315
Max PWM score9.76
Recommended cutoff6.65
View and copy the recommended matrices ↘
Position frequency matrix (PFM)
A | 0.206 0.710 0.010 0.408 0.010 0.245 0.032 0.399 0.459 
C | 0.504 0.086 0.961 0.550 0.953 0.592 0.236 0.010 0.328 
G | 0.105 0.086 0.010 0.032 0.028 0.136 0.010 0.424 0.044 
T | 0.184 0.119 0.019 0.010 0.010 0.027 0.722 0.167 0.170
Position count matrix (PCM)
A |  20  71   1  40   1  24   3  39  45 
C |  50   8  96  55  95  59  23   1  32 
G |  10   8   1   3   2  13   1  42   4 
T |  18  11   1   1   1   2  72  16  17
Position weight matrix (PWM)
A | -0.44  0.80 -3.47  0.24 -3.47 -0.27 -2.30  0.22  0.36 
C |  1.03 -0.74  1.68  1.12  1.67  1.19  0.27 -2.89  0.60 
G | -0.54 -0.74 -2.89 -1.73 -1.86 -0.28 -2.89  0.86 -1.41 
T | -0.55 -0.99 -2.82 -3.47 -3.47 -2.47  0.81 -0.65 -0.63
02 / COMPARATIVE BENCHMARKS

Alternative candidate matrices 9

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

RPH1Badis et. al.P = 0.001065View matrix ↘
Sequence logo for RPH1
Fisher’s P-value0.001065
Information content11.23
Max PWM score9.33
Recommended cutoff5.76
Position frequency matrix (PFM)
A | 0.01 0.01 0.01 0.01 0.01 0.63 0.73 
C | 0.97 0.97 0.97 0.97 0.01 0.01 0.07 
G | 0.01 0.01 0.01 0.01 0.01 0.07 0.07 
T | 0.01 0.01 0.01 0.01 0.97 0.29 0.13
Position count matrix (PCM)
A |   1   1   1   1   1  63  73 
C |  97  97  97  97   1   1   7 
G |   1   1   1   1   1   7   7 
T |   1   1   1   1  97  28  13
Position weight matrix (PWM)
A | -3.47 -3.47 -3.47 -3.47 -3.47  0.68  0.82 
C |  1.68  1.68  1.68  1.68 -2.89 -2.89 -0.94 
G | -2.89 -2.89 -2.89 -2.89 -2.89 -0.94 -0.94 
T | -3.47 -3.47 -3.47 -3.47  1.11 -0.10 -0.90
Badis et. al.
RPH1_AFoat et. al.P = 7.77e-08View matrix ↘
Sequence logo for RPH1_A
Fisher’s P-value7.77e-08
Information content14.34
Max PWM score13.6
Recommended cutoff10.26
Position frequency matrix (PFM)
A | 0.10 0.01 0.44 0.06 0.97 0.01 0.92 0.01 0.55 0.06 0.09 0.11 
C | 0.01 0.28 0.24 0.92 0.01 0.95 0.01 0.93 0.11 0.53 0.01 0.66 
G | 0.19 0.01 0.27 0.01 0.01 0.01 0.06 0.05 0.30 0.01 0.88 0.01 
T | 0.70 0.71 0.05 0.01 0.01 0.03 0.01 0.01 0.05 0.41 0.02 0.22
Position count matrix (PCM)
A |  10   1  44   6  97   1  92   1  55   6   9  11 
C |   1  28  24  92   1  95   1  93  11  53   1  66 
G |  19   1  27   1   1   1   6   5  30   1  88   1 
T |  70  71   5   1   1   3   1   1   5  41   2  22
Position weight matrix (PWM)
A | -1.16 -3.47  0.32 -1.67  1.11 -3.47  1.06 -3.47  0.54 -1.67 -1.27 -1.07 
C | -2.89  0.44  0.29  1.63 -2.89  1.66 -2.89  1.64 -0.49  1.08 -2.89  1.30 
G |  0.05 -2.89  0.41 -2.89 -2.89 -2.89 -1.10 -1.28  0.51 -2.89  1.59 -2.89 
T |  0.78  0.80 -1.86 -3.47 -3.47 -2.37 -3.47 -3.47 -1.86  0.25 -2.77 -0.37
Foat et. al.
RPH1_BFoat et. al.P = 0.2069View matrix ↘
Sequence logo for RPH1_B
Fisher’s P-value0.2069
Information content15.53
Max PWM score13.85
Recommended cutoff9.02
Position frequency matrix (PFM)
A | 0.02 0.01 0.36 0.56 0.01 0.01 0.01 0.01 0.01 0.96 0.01 0.45 0.02 
C | 0.01 0.01 0.53 0.41 0.29 0.08 0.19 0.01 0.02 0.02 0.95 0.01 0.01 
G | 0.01 0.06 0.10 0.01 0.70 0.01 0.33 0.01 0.96 0.01 0.04 0.07 0.24 
T | 0.96 0.92 0.01 0.03 0.01 0.90 0.47 0.97 0.01 0.01 0.01 0.48 0.74
Position count matrix (PCM)
A |   2   1  36  56   1   1   1   1   1  96   1  45   2 
C |   1   1  53  41  28   8  19   1   2   2  95   1   1 
G |   1   6  10   1  70   1  33   1  96   1   4   7  24 
T |  96  92   1   3   1  90  47  97   1   1   1  48  74
Position weight matrix (PWM)
A | -2.77 -3.47  0.12  0.56 -3.47 -3.47 -3.47 -3.47 -3.47  1.10 -3.47  0.34 -2.77 
C | -2.89 -2.89  1.08  0.82  0.48 -0.81  0.05 -2.89 -2.20 -2.20  1.66 -2.89 -2.89 
G | -2.89 -1.10 -0.59 -2.89  1.36 -2.89  0.61 -2.89  1.67 -2.89 -1.50 -0.94  0.29 
T |  1.10  1.06 -3.47 -2.37 -3.47  1.03  0.38  1.11 -3.47 -3.47 -3.47  0.41  0.84
Foat et. al.
RPH1_CFoat et. al.P = 0.2143View matrix ↘
Sequence logo for RPH1_C
Fisher’s P-value0.2143
Information content9.691
Max PWM score11.13
Recommended cutoff6.03
Position frequency matrix (PFM)
A | 0.01 0.29 0.35 0.01 0.45 0.71 0.03 0.01 0.74 0.10 0.46 0.21 
C | 0.10 0.47 0.03 0.89 0.30 0.01 0.01 0.01 0.16 0.50 0.18 0.12 
G | 0.35 0.06 0.25 0.09 0.01 0.25 0.96 0.01 0.09 0.07 0.30 0.55 
T | 0.54 0.17 0.37 0.01 0.25 0.03 0.01 0.97 0.01 0.33 0.06 0.12
Position count matrix (PCM)
A |   1  28  35   1  45  71   3   1  74  10  46  21 
C |  10  47   3  89  30   1   1   1  16  50  18  12 
G |  35   6  25   9   1  25  96   1   9   7  30  55 
T |  54  17  37   1  25   3   1  97   1  33   6  12
Position weight matrix (PWM)
A | -3.47 -0.10  0.09 -3.47  0.34  0.80 -2.37 -3.47  0.84 -1.16  0.36 -0.42 
C | -0.59  0.96 -1.79  1.60  0.51 -2.89 -2.89 -2.89 -0.12  1.02  0.00 -0.41 
G |  0.66 -1.10  0.33 -0.69 -2.89  0.33  1.67 -2.89 -0.69 -0.94  0.51  1.12 
T |  0.52 -0.63  0.15 -3.47 -0.25 -2.37 -3.47  1.11 -3.47  0.03 -1.67 -0.98
Foat et. al.
RPH1_DFoat et. al.P = 0.5853View matrix ↘
Sequence logo for RPH1_D
Fisher’s P-value0.5853
Information content14.66
Max PWM score15.95
Recommended cutoff9.86
Position frequency matrix (PFM)
A | 0.53 0.56 0.04 0.96 0.63 0.81 0.06 0.01 0.63 0.35 0.07 0.96 0.01 0.73 0.24 0.08 0.81 
C | 0.43 0.03 0.08 0.02 0.01 0.01 0.28 0.29 0.17 0.52 0.10 0.01 0.01 0.02 0.01 0.01 0.18 
G | 0.03 0.01 0.02 0.01 0.09 0.01 0.66 0.46 0.15 0.11 0.08 0.02 0.01 0.01 0.30 0.84 0.01 
T | 0.01 0.40 0.85 0.01 0.27 0.17 0.01 0.24 0.05 0.02 0.74 0.01 0.97 0.24 0.46 0.06 0.01
Position count matrix (PCM)
A |  53  56   4  96  63  81   6   1  63  35   7  96   1  73  24   8  81 
C |  43   3   8   2   1   1  28  28  17  52  10   1   1   2   1   1  18 
G |   3   1   2   1   9   1  66  46  15  11   8   2   1   1  30  84   1 
T |   1  40  85   1  27  17   1  24   5   2  74   1  97  24  46   6   1
Position weight matrix (PWM)
A |  0.50  0.56 -2.08  1.10  0.68  0.93 -1.67 -3.47  0.68  0.09 -1.52  1.10 -3.47  0.82 -0.29 -1.39  0.93 
C |  0.87 -1.79 -0.81 -2.20 -2.89 -2.89  0.44  0.48 -0.06  1.06 -0.59 -2.89 -2.89 -2.20 -2.89 -2.89  0.00 
G | -1.79 -2.89 -2.20 -2.89 -0.69 -2.89  1.30  0.94 -0.18 -0.49 -0.81 -2.20 -2.89 -2.89  0.51  1.54 -2.89 
T | -3.47  0.22  0.98 -3.47 -0.17 -0.63 -3.47 -0.29 -1.86 -2.77  0.84 -3.47  1.11 -0.29  0.36 -1.67 -3.47
Foat et. al.
RPH1Harbison et. al.P = 0.2294View matrix ↘
Sequence logo for RPH1
Fisher’s P-value0.2294
Information content18.61
Max PWM score14.48
Recommended cutoff10.67
Position frequency matrix (PFM)
A | 0.012 0.012 0.012 0.012 0.012 0.012 0.965 0.965 0.012 0.012 
C | 0.965 0.965 0.965 0.965 0.012 0.012 0.012 0.012 0.012 0.012 
G | 0.012 0.012 0.012 0.012 0.012 0.012 0.012 0.012 0.965 0.965 
T | 0.012 0.012 0.012 0.012 0.965 0.965 0.012 0.012 0.012 0.012
Position count matrix (PCM)
A |   1   1   1   1   1   1  96  96   1   1 
C |  96  96  96  96   1   1   1   1   1   1 
G |   1   1   1   1   1   1   1   1  96  96 
T |   1   1   1   1  96  96   1   1   1   1
Position weight matrix (PWM)
A | -3.28 -3.28 -3.28 -3.28 -3.28 -3.28  1.10  1.10 -3.28 -3.28 
C |  1.68  1.68  1.68  1.68 -2.71 -2.71 -2.71 -2.71 -2.71 -2.71 
G | -2.71 -2.71 -2.71 -2.71 -2.71 -2.71 -2.71 -2.71  1.68  1.68 
T | -3.28 -3.28 -3.28 -3.28  1.10  1.10 -3.28 -3.28 -3.28 -3.28
Harbison et. al.
RPH1Macisaac et. alP = 0.2294View matrix ↘
Sequence logo for RPH1
Fisher’s P-value0.2294
Information content18.57
Max PWM score14.48
Recommended cutoff10.67
Position frequency matrix (PFM)
A | 0.012 0.012 0.012 0.012 0.012 0.012 0.964 0.964 0.012 0.012 
C | 0.964 0.964 0.964 0.964 0.012 0.012 0.012 0.012 0.012 0.012 
G | 0.012 0.012 0.012 0.012 0.012 0.012 0.012 0.012 0.964 0.964 
T | 0.012 0.012 0.012 0.012 0.964 0.964 0.012 0.012 0.012 0.012
Position count matrix (PCM)
A |   1   1   1   1   1   1  96  96   1   1 
C |  96  96  96  96   1   1   1   1   1   1 
G |   1   1   1   1   1   1   1   1  96  96 
T |   1   1   1   1  96  96   1   1   1   1
Position weight matrix (PWM)
A | -3.28 -3.28 -3.28 -3.28 -3.28 -3.28  1.10  1.10 -3.28 -3.28 
C |  1.68  1.68  1.68  1.68 -2.71 -2.71 -2.71 -2.71 -2.71 -2.71 
G | -2.71 -2.71 -2.71 -2.71 -2.71 -2.71 -2.71 -2.71  1.68  1.68 
T | -3.28 -3.28 -3.28 -3.28  1.10  1.10 -3.28 -3.28 -3.28 -3.28
Macisaac et. al
RPH1Zhu et. al.P = 0.09329View matrix ↘
Sequence logo for RPH1
Fisher’s P-value0.09329
Information content11.37
Max PWM score11.03
Recommended cutoff6.6
Position frequency matrix (PFM)
A | 0.57 0.48 0.17 0.20 0.96 0.22 0.01 0.01 0.02 0.11 
C | 0.05 0.03 0.03 0.05 0.01 0.01 0.01 0.01 0.01 0.04 
G | 0.13 0.12 0.02 0.01 0.02 0.76 0.97 0.97 0.94 0.38 
T | 0.24 0.36 0.79 0.74 0.01 0.01 0.01 0.01 0.03 0.47
Position count matrix (PCM)
A |  56  48  17  20  96  22   1   1   2  11 
C |   5   3   3   5   1   1   1   1   1   4 
G |  13  12   2   1   2  76  97  97  94  38 
T |  24  36  79  74   1   1   1   1   3  47
Position weight matrix (PWM)
A |  0.58  0.41 -0.63 -0.47  1.10 -0.37 -3.47 -3.47 -2.77 -1.07 
C | -1.28 -1.79 -1.79 -1.28 -2.89 -2.89 -2.89 -2.89 -2.89 -1.50 
G | -0.33 -0.41 -2.20 -2.89 -2.20  1.44  1.68  1.68  1.65  0.75 
T | -0.29  0.12  0.90  0.84 -3.47 -3.47 -3.47 -3.47 -2.37  0.38
Zhu et. al.
RPH1Zhao and StormoP = 0.003682View matrix ↘
Sequence logo for RPH1
Fisher’s P-value0.003682
Information content3.468
Max PWM score5.64
Recommended cutoff5.64
Position frequency matrix (PFM)
A | 0.671 0.323 0.187 0.200 0.261 
C | 0.074 0.037 0.051 0.053 0.003 
G | 0.154 0.572 0.641 0.631 0.612 
T | 0.100 0.068 0.121 0.115 0.124
Position count matrix (PCM)
A |  67  32  18  20  26 
C |   7   3   5   5   0 
G |  15  57  64  63  61 
T |  10   6  12  11  12
Position weight matrix (PWM)
A |  0.74  0.01 -0.54 -0.47 -0.20 
C | -0.89 -1.58 -1.26 -1.22 -4.09 
G | -0.16  1.16  1.27  1.25  1.22 
T | -1.16 -1.55 -0.97 -1.02 -0.95
Zhao and Stormo
03 / EXPERIMENTAL CONTEXT

Gene-level annotations and interactions.

Genes bound in ChIP-chip experiments 24 genes

YBL022C, YBL072C, YBR033W, YBR036C, YBR056W, YBR126C, YCL057W, YCL058C, YCL074W, YDL120W, YDL121C, YDL191W, YDR098C, YDR428C, YDR449C, YDR450W, YFR009W, YHR136C, YHR137W, YKR062W, YLR336C, YLR338W, YOL026C, YOL121C

Genes affected by TF deletion 186 genes

YBR006W, YJR016C, YLR274W, YLR218C, YLR248W, YGL009C, YHR113W, YHR146W, YKL043W, YLR060W, YOR377W, YDR207C, YKR076W, YMR040W, YOL048C, YPL206C, YPL240C, YAL008W, YOR038C, YPL016W, YPR138C, YLR309C, YMR071C, YNL115C, YNL149C, YOR285W, YOR317W, YOR291W, YER028C, YER058W, YGR244C, YLR156W, YNL333W, YNL305C, YBR093C, YBR129C, YGR062C, YHR024C, YLR304C, YOL073C, YOL076W, YOL105C, YPR047W, YBL024W, YBR288C, YDR281C, YDR313C, YER057C, YGR211W, YLR155C, YLR157C, YNL332W, YNL306W, YIL156W, YML121W, YAL043C, YMR173W, YPL059W, YPL160W, YER119C, YIL085C, YNR066C, YOR228C, YOR260W, YOR198C, YPL246C, YAR002W, YBR166C, YGR131W, YKL087C, YLR099C, YMR171C, YNL214W, YPL054W, YIR036C, YLL009C, YLR346C, YDR347W, YHR215W, YKL149C, YPL122C, YPL154C, YBR101C, YBR105C, YDL040C, YGR012W, YIR037W, YIR010W, YJR156C, YLL041C, YMR083W, YNL184C, YOL083W, YOR292C, YBL065W, YBR264C, YER062C, YGL112C, YLR159W, YLR161W, YMR317W, YMR321C, YNR034W, YNR038W, YPL091W, YPL123C, YCR061W, YNL065W, YOR209C, YDR345C, YAL023C, YBR241C, YJL067W, YKL058W, YLR290C, YML130C, YNL037C, YAL049C, YJL066C, YJL068C, YKL120W, YPL032C, YDL021W, YFL059W, YGR019W, YLR324W, YLR356W, YOR383C, YGR232W, YLR136C, YPL132W, YDR115W, YNL160W, YOR330C, YPR067W, YER044C, YGR261C, YGR231C, YHL004W, YHR016C, YJR044C, YKR065C, YLR297W, YOR215C, YOR217W, YBR185C, YJL143W, YKL066W, YKL103C, YMR182C, YMR186W, YNL269W, YPR159W, YBR053C, YMR034C, YOL071W, YAL030W, YBR244W, YDR211W, YGL032C, YGR149W, YHR135C, YHR137W, YHR140W, YHR171W, YLR047C, YLR115W, YMR181C, YPL075W, YPR038W, YGR270W, YIL070C, YKL192C, YLR174W, YML110C, YPL172C, YMR157C, YNL200C, YOR306C, YPR037C, YJL200C, YKR001C, YLR173W, YNL007C, YMR307W, YNR017W

Genes supported by both experiments 1 genes

YHR137W

Predicted TF–TF partners 10 genes

GIS1, MIG1, MIG3, MSN2, MSN4, RGM1, RSF2, SUT1, USV1, YER184C

Explore 10 original interaction plots →