Skip to main content

Table 1 Performance of Virtual ChIP-seq for 36 chromatin factors on validation cell types. Each row displays median values ± standard deviation of several performance metrics for prediction of a chromatin factor across 4 chromosomes for each available validation cell type. MCC, Matthews correlation coefficient; auROC, area under the receiver operating characteristic curve; auPR, area under the precision-recall curve; N, number of validation cell types for 36 chromatin factors with MCC>0.3. We reported auROC and auPR across all the validation cell types across all posterior probability cutoffs. Black chromatin factors: we found the posterior probability cutoff which maximized MCC in H1-hESC, and then reported F1, accuracy, and MCC of the other validation cell types

From: Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome

Chromatin factor F1 Accuracy MCC auROC auPR N
ATF2 0.270±0.002 0.990±0.001 0.314±0.008 0.917±0.026 0.443±0.022 1
BHLHE40 0.334±0.021 0.997±0.000 0.356±0.010 0.974±0.002 0.382±0.010 1
CEBPB 0.510±0.091 0.992±0.002 0.515±0.072 0.964±0.017 0.534±0.073 3
CHD2 0.399±0.038 0.998±0.000 0.406±0.034 0.950±0.012 0.386±0.046 1
CREB1 0.362±0.131 0.997±0.002 0.371±0.121 0.868±0.135 0.335±0.174 2
CTCF 0.667±0.126 0.995±0.004 0.675±0.092 0.985±0.050 0.841±0.108 6
E2F1 0.256±0.097 0.998±0.002 0.314±0.078 0.978±0.019 0.291±0.105 2
ELF1 0.431±0.047 0.997±0.001 0.456±0.038 0.949±0.042 0.493±0.066 2
ELK1 0.430±0.069 1.000±0.000 0.465±0.054 0.991±0.009 0.420±0.054 2
ESR1 0.372±0.103 0.993±0.006 0.430±0.049 0.883±0.033 0.461±0.019 2
FOS 0.333±0.027 0.997±0.001 0.393±0.020 0.861±0.004 0.394±0.008 1
FOSL1 0.319±0.006 0.994±0.001 0.316±0.006 0.929±0.006 0.272±0.012 1
FOXA1 0.433±0.082 0.997±0.004 0.492±0.072 0.981±0.022 0.568±0.117 3
GABPA 0.298±0.049 0.994±0.002 0.393±0.036 0.986±0.012 0.496±0.036 3
GTF2F1 0.235±0.120 0.996±0.001 0.312±0.070 0.985±0.015 0.191±0.081 2
HCFC1 0.459±0.021 0.999±0.000 0.487±0.024 0.990±0.005 0.515±0.044 2
HDAC2 0.303±0.033 0.986±0.005 0.370±0.018 0.948±0.051 0.281±0.040 2
HSF1 0.350±0.149 1.000±0.000 0.378±0.145 0.999±0.012 0.309±0.240 1
JUN 0.218±0.127 0.998±0.001 0.311±0.153 0.983±0.009 0.456±0.257 2
JUND 0.341±0.163 0.993±0.002 0.386±0.135 0.979±0.019 0.326±0.161 4
MAFK 0.354±0.041 0.997±0.001 0.423±0.028 0.989±0.005 0.513±0.103 3
MAX 0.400±0.045 0.996±0.002 0.444±0.059 0.961±0.012 0.491±0.111 3
MAZ 0.370±0.025 0.997±0.001 0.422±0.019 0.987±0.005 0.493±0.070 2
MXI1 0.394±0.018 0.999±0.000 0.402±0.017 0.993±0.004 0.381±0.025 1
NRF1 0.658±0.042 1.000±0.000 0.664±0.038 0.994±0.014 0.720±0.051 3
RAD21 0.593±0.062 0.996±0.002 0.626±0.056 0.983±0.033 0.740±0.095 3
REST 0.482±0.120 0.999±0.001 0.493±0.091 0.985±0.008 0.567±0.095 3
SIN3A 0.389±0.048 0.998±0.002 0.394±0.029 0.966±0.004 0.411±0.037 3
SMC3 0.733±0.016 0.999±0.000 0.734±0.016 0.998±0.001 0.792±0.018 1
SRF 0.353±0.060 0.998±0.001 0.364±0.070 0.982±0.008 0.365±0.115 2
TAF1 0.378±0.073 0.999±0.001 0.437±0.097 0.987±0.009 0.490±0.168 3
TEAD4 0.344±0.061 0.990±0.002 0.385±0.020 0.967±0.023 0.343±0.019 2
TP53 0.275±0.103 1.000±0.000 0.382±0.086 1.000±0.008 0.660±0.222 1
USF1 0.353±0.047 0.993±0.001 0.382±0.040 0.891±0.012 0.372±0.046 1
USF2 0.410±0.040 0.999±0.000 0.427±0.028 0.982±0.007 0.437±0.032 1
YY1 0.397±0.049 0.996±0.001 0.408±0.058 0.945±0.043 0.417±0.104 2