---
license: cc-by-nc-4.0
language:
- en
tags:
- biology
- genomics
- dna
- variant-effect-prediction
- dnabert
- deepvregulome
- transcription-factors
- histone-modifications
- ENCODE
- chip-seq
- regulatory-variants
- cancer-genomics
- glioblastoma
- noncoding-variants
- fine-tuned
- sequence-classification
datasets:
- ENCODE
library_name: transformers
pipeline_tag: text-classification
model-index:
- name: AEBP2
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.57
- name: F1
type: f1
value: 88.27
- name: ROC-AUC
type: roc_auc
value: 92.65
- name: PR-AUC
type: pr_auc
value: 93.95
- name: AGO1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 94.81
- name: F1
type: f1
value: 92.98
- name: ROC-AUC
type: roc_auc
value: 97.19
- name: PR-AUC
type: pr_auc
value: 96.16
- name: AGO2
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 91.55
- name: F1
type: f1
value: 89.26
- name: ROC-AUC
type: roc_auc
value: 95.16
- name: PR-AUC
type: pr_auc
value: 94.66
- name: AHR
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 91.82
- name: F1
type: f1
value: 91.39
- name: ROC-AUC
type: roc_auc
value: 97.21
- name: PR-AUC
type: pr_auc
value: 96.43
- name: ARHGAP35
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 86.18
- name: F1
type: f1
value: 85.43
- name: ROC-AUC
type: roc_auc
value: 93.57
- name: PR-AUC
type: pr_auc
value: 93.39
- name: ARID1B
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 89.32
- name: F1
type: f1
value: 88.77
- name: ROC-AUC
type: roc_auc
value: 95.17
- name: PR-AUC
type: pr_auc
value: 94.59
- name: ARID2
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 89.24
- name: F1
type: f1
value: 88.78
- name: ROC-AUC
type: roc_auc
value: 93.47
- name: PR-AUC
type: pr_auc
value: 91.82
- name: ARID4B
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 89.94
- name: F1
type: f1
value: 88.99
- name: ROC-AUC
type: roc_auc
value: 94.05
- name: PR-AUC
type: pr_auc
value: 92.27
- name: ASH1L
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 85.96
- name: F1
type: f1
value: 84.17
- name: ROC-AUC
type: roc_auc
value: 92.97
- name: PR-AUC
type: pr_auc
value: 93.93
- name: ATF2
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 90.69
- name: F1
type: f1
value: 90.57
- name: ROC-AUC
type: roc_auc
value: 94.77
- name: PR-AUC
type: pr_auc
value: 94.25
- name: ATF3
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 87.61
- name: F1
type: f1
value: 87.36
- name: ROC-AUC
type: roc_auc
value: 92.96
- name: PR-AUC
type: pr_auc
value: 92.73
- name: ATF4
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 93.0
- name: F1
type: f1
value: 92.84
- name: ROC-AUC
type: roc_auc
value: 97.72
- name: PR-AUC
type: pr_auc
value: 97.64
- name: ATF7
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 86.72
- name: F1
type: f1
value: 86.65
- name: ROC-AUC
type: roc_auc
value: 92.77
- name: PR-AUC
type: pr_auc
value: 93.41
- name: ATM
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 86.67
- name: F1
type: f1
value: 85.99
- name: ROC-AUC
type: roc_auc
value: 93.74
- name: PR-AUC
type: pr_auc
value: 94.31
- name: BACH1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 85.62
- name: F1
type: f1
value: 83.64
- name: ROC-AUC
type: roc_auc
value: 90.78
- name: PR-AUC
type: pr_auc
value: 88.15
- name: BATF
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 93.58
- name: F1
type: f1
value: 93.82
- name: ROC-AUC
type: roc_auc
value: 98.16
- name: PR-AUC
type: pr_auc
value: 97.93
- name: BCL11A
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 85.41
- name: F1
type: f1
value: 84.36
- name: ROC-AUC
type: roc_auc
value: 92.15
- name: PR-AUC
type: pr_auc
value: 91.13
- name: BCL11B
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 86.93
- name: F1
type: f1
value: 86.01
- name: ROC-AUC
type: roc_auc
value: 92.01
- name: PR-AUC
type: pr_auc
value: 89.38
- name: BCL3
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 85.55
- name: F1
type: f1
value: 83.8
- name: ROC-AUC
type: roc_auc
value: 93.27
- name: PR-AUC
type: pr_auc
value: 92.67
- name: BCL6
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 90.97
- name: F1
type: f1
value: 90.9
- name: ROC-AUC
type: roc_auc
value: 96.3
- name: PR-AUC
type: pr_auc
value: 95.48
- name: BCOR
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 89.08
- name: F1
type: f1
value: 88.74
- name: ROC-AUC
type: roc_auc
value: 95.34
- name: PR-AUC
type: pr_auc
value: 94.44
- name: BHLHE40
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.01
- name: F1
type: f1
value: 88.0
- name: ROC-AUC
type: roc_auc
value: 92.37
- name: PR-AUC
type: pr_auc
value: 91.72
- name: BRCA1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.43
- name: F1
type: f1
value: 84.43
- name: ROC-AUC
type: roc_auc
value: 91.88
- name: PR-AUC
type: pr_auc
value: 90.63
- name: C11orf30
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 95.13
- name: F1
type: f1
value: 94.98
- name: ROC-AUC
type: roc_auc
value: 98.63
- name: PR-AUC
type: pr_auc
value: 98.61
- name: CBFA2T2
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 93.06
- name: F1
type: f1
value: 93.09
- name: ROC-AUC
type: roc_auc
value: 97.31
- name: PR-AUC
type: pr_auc
value: 97.25
- name: CBFA2T3
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 92.59
- name: F1
type: f1
value: 92.67
- name: ROC-AUC
type: roc_auc
value: 96.97
- name: PR-AUC
type: pr_auc
value: 96.03
- name: CBFB
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.89
- name: F1
type: f1
value: 87.72
- name: ROC-AUC
type: roc_auc
value: 93.81
- name: PR-AUC
type: pr_auc
value: 91.26
- name: CBX1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.75
- name: F1
type: f1
value: 87.21
- name: ROC-AUC
type: roc_auc
value: 94.69
- name: PR-AUC
type: pr_auc
value: 92.62
- name: CC2D1A
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 87.14
- name: F1
type: f1
value: 86.24
- name: ROC-AUC
type: roc_auc
value: 92.24
- name: PR-AUC
type: pr_auc
value: 91.48
- name: CDC5L
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 86.47
- name: F1
type: f1
value: 85.08
- name: ROC-AUC
type: roc_auc
value: 93.59
- name: PR-AUC
type: pr_auc
value: 93.67
- name: CEBPA
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 92.39
- name: F1
type: f1
value: 98.89
- name: ROC-AUC
type: roc_auc
value: 99.7
- name: PR-AUC
type: pr_auc
value: 99.6
- name: CEBPB
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 91.69
- name: F1
type: f1
value: 98.47
- name: ROC-AUC
type: roc_auc
value: 99.54
- name: PR-AUC
type: pr_auc
value: 99.42
- name: CEBPG
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 90.11
- name: F1
type: f1
value: 90.14
- name: ROC-AUC
type: roc_auc
value: 96.25
- name: PR-AUC
type: pr_auc
value: 96.42
- name: CEBPZ
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 90.82
- name: F1
type: f1
value: 86.79
- name: ROC-AUC
type: roc_auc
value: 89.86
- name: PR-AUC
type: pr_auc
value: 85.64
- name: CHD2
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 87.52
- name: F1
type: f1
value: 86.08
- name: ROC-AUC
type: roc_auc
value: 93.75
- name: PR-AUC
type: pr_auc
value: 91.52
- name: CREB1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.96
- name: F1
type: f1
value: 89.04
- name: ROC-AUC
type: roc_auc
value: 95.48
- name: PR-AUC
type: pr_auc
value: 96.05
- name: CREB3L1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.6
- name: F1
type: f1
value: 86.11
- name: ROC-AUC
type: roc_auc
value: 93.55
- name: PR-AUC
type: pr_auc
value: 91.45
- name: CREM
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 86.61
- name: F1
type: f1
value: 86.56
- name: ROC-AUC
type: roc_auc
value: 92.96
- name: PR-AUC
type: pr_auc
value: 93.26
- name: CTBP2
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 92.98
- name: F1
type: f1
value: 92.36
- name: ROC-AUC
type: roc_auc
value: 96.78
- name: PR-AUC
type: pr_auc
value: 94.11
- name: CTCFL
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 98.39
- name: F1
type: f1
value: 98.4
- name: ROC-AUC
type: roc_auc
value: 99.71
- name: PR-AUC
type: pr_auc
value: 99.7
- name: DACH1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 87.72
- name: F1
type: f1
value: 87.31
- name: ROC-AUC
type: roc_auc
value: 92.88
- name: PR-AUC
type: pr_auc
value: 92.63
- name: DEAF1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 90.85
- name: F1
type: f1
value: 90.18
- name: ROC-AUC
type: roc_auc
value: 94.68
- name: PR-AUC
type: pr_auc
value: 95.53
- name: DEK
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 89.7
- name: F1
type: f1
value: 88.82
- name: ROC-AUC
type: roc_auc
value: 95.38
- name: PR-AUC
type: pr_auc
value: 93.29
- name: DIDO1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 86.58
- name: F1
type: f1
value: 85.66
- name: ROC-AUC
type: roc_auc
value: 92.29
- name: PR-AUC
type: pr_auc
value: 92.48
- name: DMAP1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.15
- name: F1
type: f1
value: 86.04
- name: ROC-AUC
type: roc_auc
value: 92.88
- name: PR-AUC
type: pr_auc
value: 89.99
- name: DRAP1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.55
- name: F1
type: f1
value: 87.7
- name: ROC-AUC
type: roc_auc
value: 93.04
- name: PR-AUC
type: pr_auc
value: 91.43
- name: E2F1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 92.88
- name: F1
type: f1
value: 86.4
- name: ROC-AUC
type: roc_auc
value: 95.25
- name: PR-AUC
type: pr_auc
value: 91.61
- name: E2F4
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 92.64
- name: F1
type: f1
value: 90.76
- name: ROC-AUC
type: roc_auc
value: 97.32
- name: PR-AUC
type: pr_auc
value: 97.07
- name: E2F6
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 95.14
- name: F1
type: f1
value: 93.71
- name: ROC-AUC
type: roc_auc
value: 98.25
- name: PR-AUC
type: pr_auc
value: 96.91
- name: E2F7
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 86.4
- name: F1
type: f1
value: 85.34
- name: ROC-AUC
type: roc_auc
value: 91.15
- name: PR-AUC
type: pr_auc
value: 91.4
- name: E4F1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 87.05
- name: F1
type: f1
value: 83.51
- name: ROC-AUC
type: roc_auc
value: 91.86
- name: PR-AUC
type: pr_auc
value: 88.4
- name: EBF1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 90.59
- name: F1
type: f1
value: 90.64
- name: ROC-AUC
type: roc_auc
value: 95.31
- name: PR-AUC
type: pr_auc
value: 94.3
- name: EED
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 88.9
- name: F1
type: f1
value: 88.18
- name: ROC-AUC
type: roc_auc
value: 94.22
- name: PR-AUC
type: pr_auc
value: 92.87
- name: EGR1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 89.43
- name: F1
type: f1
value: 89.26
- name: ROC-AUC
type: roc_auc
value: 93.84
- name: PR-AUC
type: pr_auc
value: 93.58
- name: EGR2
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 95.68
- name: F1
type: f1
value: 99.22
- name: ROC-AUC
type: roc_auc
value: 99.75
- name: PR-AUC
type: pr_auc
value: 99.6
- name: ELF1
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 86.71
- name: F1
type: f1
value: 86.32
- name: ROC-AUC
type: roc_auc
value: 93.8
- name: PR-AUC
type: pr_auc
value: 94.5
- name: ELF3
results:
- task:
type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
- name: Accuracy
type: accuracy
value: 89.85
- name: F1
type: f1
value: 89.43
- name: ROC-AUC
type: roc_auc
value: 95.06
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type: text-classification
name: Transcription Factor Binding Prediction
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type: ENCODE
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value: 88.57
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value: 88.43
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
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type: ENCODE
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value: 88.53
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 86.79
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value: 86.64
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 86.59
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type: f1
value: 85.8
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 89.21
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type: f1
value: 88.59
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 86.94
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value: 86.19
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
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type: accuracy
value: 85.84
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type: f1
value: 80.68
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 88.9
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value: 87.49
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 90.97
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value: 87.65
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value: 96.01
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 91.18
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value: 91.14
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 89.71
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value: 89.41
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 87.93
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value: 88.02
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type: text-classification
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type: ENCODE
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type: accuracy
value: 85.43
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value: 85.33
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 92.45
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type: f1
value: 91.3
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 90.77
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type: f1
value: 90.48
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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value: 87.54
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value: 85.89
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 88.94
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type: f1
value: 88.07
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 96.07
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value: 95.99
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 87.93
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type: f1
value: 86.42
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type: text-classification
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dataset:
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type: ENCODE
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value: 89.53
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value: 82.52
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 90.43
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value: 88.75
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 89.17
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value: 88.82
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results:
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type: text-classification
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type: ENCODE
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value: 90.65
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value: 89.32
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results:
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type: text-classification
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type: ENCODE
metrics:
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value: 88.52
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value: 87.13
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 87.15
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value: 86.93
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results:
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type: text-classification
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dataset:
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type: ENCODE
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type: accuracy
value: 85.91
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type: f1
value: 85.24
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results:
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type: text-classification
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type: ENCODE
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value: 89.93
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value: 89.05
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type: text-classification
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dataset:
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type: ENCODE
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type: accuracy
value: 88.72
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value: 86.04
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type: text-classification
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dataset:
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type: ENCODE
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value: 86.44
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type: f1
value: 85.35
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 86.05
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value: 84.14
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type: text-classification
name: Transcription Factor Binding Prediction
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type: ENCODE
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value: 88.28
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value: 87.47
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type: text-classification
name: Transcription Factor Binding Prediction
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type: ENCODE
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value: 87.78
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type: f1
value: 86.2
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type: text-classification
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dataset:
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type: ENCODE
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type: accuracy
value: 90.99
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value: 87.95
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 86.81
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value: 84.82
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value: 86.41
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type: ENCODE
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value: 86.42
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value: 84.12
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dataset:
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type: ENCODE
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type: accuracy
value: 86.86
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value: 86.86
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 93.91
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value: 93.91
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type: text-classification
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type: ENCODE
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value: 94.74
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value: 94.7
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results:
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name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 92.55
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value: 92.65
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name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 87.44
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name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 88.25
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type: ENCODE
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value: 84.57
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name: Transcription Factor Binding Prediction
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type: ENCODE
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value: 85.96
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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results:
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name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 85.24
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value: 84.32
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 89.15
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value: 89.07
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 89.51
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value: 88.5
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 89.25
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value: 89.19
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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value: 90.71
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value: 90.78
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 87.84
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value: 86.5
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 88.16
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type: f1
value: 87.72
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 86.83
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type: f1
value: 85.69
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value: 92.53
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
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type: accuracy
value: 94.14
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type: f1
value: 93.57
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value: 98.35
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
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type: accuracy
value: 88.8
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type: f1
value: 88.4
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 89.33
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type: f1
value: 88.85
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value: 93.58
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- name: MNT
results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
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type: accuracy
value: 85.79
- name: F1
type: f1
value: 85.08
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value: 92.76
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- name: MTA1
results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
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value: 85.15
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type: text-classification
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value: 84.43
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type: text-classification
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type: text-classification
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type: text-classification
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type: text-classification
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type: text-classification
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value: 86.73
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value: 87.09
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dataset:
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results:
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type: text-classification
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dataset:
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type: ENCODE
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value: 90.62
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value: 95.17
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 85.9
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value: 86.39
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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value: 89.19
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value: 88.58
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 87.55
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value: 87.06
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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value: 87.65
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value: 87.25
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: text-classification
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dataset:
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type: text-classification
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type: text-classification
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value: 84.45
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type: text-classification
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type: ENCODE
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type: text-classification
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type: ENCODE
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value: 90.5
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type: text-classification
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dataset:
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type: ENCODE
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value: 86.25
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value: 85.74
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type: text-classification
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dataset:
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type: ENCODE
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value: 89.59
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type: f1
value: 85.4
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results:
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type: text-classification
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dataset:
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type: ENCODE
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value: 96.57
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type: text-classification
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dataset:
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type: ENCODE
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value: 92.56
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value: 92.48
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results:
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type: text-classification
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type: ENCODE
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value: 97.0
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type: text-classification
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type: ENCODE
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value: 92.73
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value: 91.61
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type: text-classification
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type: ENCODE
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type: accuracy
value: 88.92
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value: 87.6
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results:
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type: text-classification
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dataset:
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type: ENCODE
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value: 85.25
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value: 84.38
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type: text-classification
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type: ENCODE
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value: 86.71
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value: 84.55
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type: text-classification
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dataset:
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type: ENCODE
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value: 87.81
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results:
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type: text-classification
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dataset:
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type: ENCODE
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value: 90.37
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value: 89.28
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results:
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type: text-classification
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type: ENCODE
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value: 85.25
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 91.79
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value: 90.4
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 88.14
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value: 87.7
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type: text-classification
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dataset:
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type: ENCODE
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type: accuracy
value: 87.76
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type: f1
value: 81.96
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results:
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type: text-classification
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type: ENCODE
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value: 88.25
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value: 90.07
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value: 89.17
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value: 89.44
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type: ENCODE
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value: 86.9
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results:
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value: 89.46
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value: 89.63
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results:
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dataset:
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type: ENCODE
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value: 92.08
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value: 90.13
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value: 90.65
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value: 87.69
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value: 85.07
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dataset:
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value: 90.12
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value: 89.27
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value: 79.12
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value: 86.71
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value: 86.92
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value: 87.18
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value: 85.24
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value: 84.86
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type: ENCODE
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results:
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dataset:
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type: ENCODE
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value: 91.44
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value: 90.22
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name: Transcription Factor Binding Prediction
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type: ENCODE
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value: 91.37
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value: 91.12
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results:
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name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 88.58
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value: 87.43
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 95.79
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value: 95.78
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 89.15
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value: 87.65
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 90.59
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type: f1
value: 89.11
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 90.12
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value: 87.92
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 94.49
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value: 93.59
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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value: 89.34
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value: 87.07
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type: text-classification
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type: ENCODE
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
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type: ENCODE
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value: 90.73
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value: 89.46
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 90.79
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value: 90.81
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 85.56
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type: text-classification
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type: ENCODE
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value: 89.36
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results:
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type: text-classification
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dataset:
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type: ENCODE
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type: accuracy
value: 96.74
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results:
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type: text-classification
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dataset:
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type: ENCODE
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value: 85.79
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value: 81.76
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 91.69
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value: 90.15
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 88.15
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value: 87.4
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type: text-classification
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dataset:
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type: ENCODE
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value: 88.37
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value: 86.69
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results:
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type: text-classification
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dataset:
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type: ENCODE
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value: 86.23
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value: 85.39
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 89.46
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value: 86.81
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 90.27
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value: 90.29
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 89.35
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value: 89.2
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results:
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type: text-classification
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dataset:
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type: ENCODE
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type: accuracy
value: 89.66
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value: 89.49
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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type: accuracy
value: 93.0
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value: 92.84
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: accuracy
value: 85.52
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value: 80.8
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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value: 86.8
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value: 85.45
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results:
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type: text-classification
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dataset:
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type: ENCODE
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value: 94.7
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value: 94.48
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results:
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dataset:
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value: 90.57
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value: 89.79
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results:
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type: text-classification
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type: accuracy
value: 86.86
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value: 86.05
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results:
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type: text-classification
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value: 82.45
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dataset:
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value: 87.77
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value: 97.99
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dataset:
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type: ENCODE
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value: 87.42
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value: 84.62
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results:
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name: Transcription Factor Binding Prediction
dataset:
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value: 85.17
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value: 84.45
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value: 89.92
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value: 91.72
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value: 91.73
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value: 89.06
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results:
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type: ENCODE
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value: 94.95
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value: 94.93
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value: 91.39
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value: 89.66
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dataset:
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value: 90.01
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value: 88.14
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value: 89.51
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value: 89.25
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dataset:
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value: 86.69
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type: accuracy
value: 91.61
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value: 90.04
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dataset:
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type: ENCODE
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value: 83.11
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name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
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value: 86.93
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dataset:
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type: ENCODE
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value: 86.59
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results:
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dataset:
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type: ENCODE
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value: 89.91
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type: ENCODE
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value: 90.29
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results:
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dataset:
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type: ENCODE
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value: 90.33
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results:
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dataset:
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type: ENCODE
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results:
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dataset:
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type: ENCODE
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value: 87.09
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value: 86.97
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results:
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dataset:
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results:
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dataset:
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type: ENCODE
metrics:
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results:
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type: text-classification
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dataset:
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type: ENCODE
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value: 91.69
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results:
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name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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value: 86.94
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value: 85.85
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 89.73
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value: 88.24
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value: 94.0
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 91.8
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type: f1
value: 91.33
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
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type: ENCODE
metrics:
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type: accuracy
value: 87.82
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type: f1
value: 85.07
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value: 94.37
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
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type: accuracy
value: 94.73
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type: f1
value: 99.21
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value: 99.82
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results:
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type: text-classification
name: Transcription Factor Binding Prediction
dataset:
name: ENCODE ChIP-seq
type: ENCODE
metrics:
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type: accuracy
value: 85.26
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type: f1
value: 83.98
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value: 91.92
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results:
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type: text-classification
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value: 88.84
---
# DeepVRegulome
**464 fine-tuned DNABERT models for regulatory variant effect prediction**
DeepVRegulome is an end-to-end framework for predicting the functional impact
of small somatic variants in non-coding regulatory regions using fine-tuned
[DNABERT](https://github.com/jerryji1993/DNABERT) models. It covers **458
transcription factors**, **4 histone modifications**, and **2 splice sites**
(acceptor + donor) from ENCODE ChIP-seq and GENCODE data, validated against
Yan et al. (2021) SNP-SELEX experimental variant-effect measurements.
| Resource | Link |
|----------|------|
| Paper | [arXiv:2511.09026](https://arxiv.org/abs/2511.09026) |
| Code | [GitHub: DavuluriLab/DeepVRegulome](https://github.com/DavuluriLab/DeepVRegulome) |
| PyPI | `pip install deepvregulome` |
| Web App | [deepvregulome.streamlit.app](https://deepvregulome.streamlit.app) |
| Live Demo | [HuggingFace Space](https://huggingface.co/spaces/duttaprat/DeepVRegulome) |
## Key Features
- **464 fine-tuned models** (458 TF-binding + 4 histone mark + 2 splice-site) trained on ENCODE ChIP-seq peaks and GENCODE exon-intron junctions
- **Splice-site disruption scoring** for acceptor (3') and donor (5') junction variants
- **Variant effect scoring** via log-odds ratio between reference and alternate alleles
- **Attention-based motif analysis** for interpretable predictions
- **Experimentally validated** against SNP-SELEX (Yan et al., 2021, Nature Genetics): mean per-TF AUROC = 0.611 across 61 evaluable TFs
- **Benchmarked** against DeepSEA, Enformer, Borzoi, and AlphaGenome
## Installation
```bash
pip install deepvregulome
```
## Quick Start (with `deepvregulome` package)
```python
import deepvregulome as dvr
# Initialize
pipeline = dvr.DVR()
# List all 462 available models
models = pipeline.list_models()
print(f"{len(models)} models available")
# Score a variant
results = pipeline.score_variant(
chrom="chr1", pos=1000000, ref="A", alt="G",
models=["CTCF", "SP1", "MYC"]
)
print(results)
```
## Quick Start (direct `transformers` usage)
```python
from transformers import AutoModelForSequenceClassification, AutoTokenizer
import torch
# Load any model using subfolder
model_name = "CTCFL" # or "SP1", "MYC", "H3K27ac", etc.
tokenizer = AutoTokenizer.from_pretrained(
"duttaprat/DeepVRegulome", subfolder=f"models/{model_name}"
)
model = AutoModelForSequenceClassification.from_pretrained(
"duttaprat/DeepVRegulome", subfolder=f"models/{model_name}"
)
model.eval()
# Convert DNA to 6-mer representation
def to_kmer(seq, k=6):
return " ".join([seq[i:i+k] for i in range(len(seq) - k + 1)])
# Predict binding probability
sequence = "ATCGATCG..." # 301bp DNA sequence
inputs = tokenizer(to_kmer(sequence), return_tensors="pt",
max_length=512, truncation=True, padding=True)
with torch.no_grad():
prob = torch.softmax(model(**inputs).logits, dim=-1)[0][1].item()
print(f"{model_name} binding probability: {prob:.4f}")
```
## Variant Effect Scoring
```python
import math
def score_variant(model, tokenizer, ref_seq, alt_seq):
probs = {}
for name, seq in [("REF", ref_seq), ("ALT", alt_seq)]:
inputs = tokenizer(to_kmer(seq), return_tensors="pt",
max_length=512, truncation=True, padding=True)
with torch.no_grad():
probs[name] = torch.softmax(model(**inputs).logits, dim=-1)[0][1].item()
eps = 1e-7
lo_ref = math.log((probs["REF"] + eps) / (1 - probs["REF"] + eps))
lo_alt = math.log((probs["ALT"] + eps) / (1 - probs["ALT"] + eps))
return {
"prob_ref": probs["REF"],
"prob_alt": probs["ALT"],
"log_odds_change": lo_alt - lo_ref,
"disrupted": abs(lo_alt - lo_ref) > 2.0,
}
```
## Available Models (462)
Each model is stored in a `models//` subfolder. Load with:
```python
AutoModel.from_pretrained("duttaprat/DeepVRegulome", subfolder="models/")
```
### Transcription Factor Models (458)
| Model | Accuracy | F1 | ROC-AUC | PR-AUC | ChIP-seq Peaks |
|-------|----------|-----|---------|--------|----------------|
| `CTCFL` | 98.39 | 98.4 | 99.71 | 99.7 | 12,743 |
| `ZNF426` | 97.09 | 96.64 | 98.08 | 98.65 | 7,915 |
| `SAFB` | 97.02 | 96.81 | 98.38 | 98.57 | 5,361 |
| `RBM34` | 97.0 | 96.53 | 98.18 | 98.44 | 928 |
| `TAF15` | 96.74 | 96.41 | 99.02 | 98.58 | 17,900 |
| `PCBP1` | 96.7 | 95.94 | 99.19 | 98.66 | 16,229 |
| `SRSF3` | 96.6 | 96.52 | 98.2 | 95.53 | 1,610 |
| `RBM14` | 96.57 | 95.73 | 98.8 | 98.4 | 2,463 |
| `KDM4A` | 96.07 | 95.99 | 99.08 | 98.72 | 25,968 |
| `NFYA` | 95.91 | 95.19 | 96.88 | 93.73 | 4,313 |
| `SPI1` | 95.79 | 95.78 | 98.75 | 98.38 | 104,150 |
| `HLF` | 95.71 | 95.83 | 98.88 | 98.74 | 66,792 |
| `EGR2` | 95.68 | 99.22 | 99.75 | 99.6 | 57,610 |
| `HNRNPLL` | 95.43 | 93.73 | 98.77 | 97.88 | 25,270 |
| `HNRNPK` | 95.41 | 94.27 | 97.05 | 96.06 | 24,014 |
| `FIP1L1` | 95.35 | 94.16 | 98.25 | 98.13 | 10,123 |
| `ZNF654` | 95.31 | 95.28 | 97.93 | 98.17 | 33,357 |
| `ZNF146` | 95.23 | 94.66 | 97.57 | 97.69 | 38,167 |
| `E2F6` | 95.14 | 93.71 | 98.25 | 96.91 | 30,723 |
| `C11orf30` | 95.13 | 94.98 | 98.63 | 98.61 | 58,686 |
| `FUS` | 95.03 | 93.76 | 94.87 | 93.76 | 7,495 |
| `USF1` | 94.95 | 94.93 | 98.05 | 97.78 | 60,863 |
| `ZNF770` | 94.91 | 95.01 | 98.04 | 97.28 | 57,572 |
| `AGO1` | 94.81 | 92.98 | 97.19 | 96.16 | 16,201 |
| `MAFG` | 94.74 | 94.7 | 97.91 | 97.78 | 44,030 |
| `ZFHX2` | 94.73 | 99.21 | 99.82 | 99.74 | 61,052 |
| `THAP1` | 94.7 | 94.48 | 98.22 | 97.82 | 5,210 |
| `HES2` | 94.55 | 84.34 | 97.15 | 84.39 | 6,520 |
| `SRSF1` | 94.49 | 93.59 | 98.34 | 97.9 | 9,933 |
| `NFE2` | 94.22 | 99.19 | 99.76 | 99.72 | 53,717 |
| `MITF` | 94.14 | 93.57 | 98.35 | 98.12 | 36,171 |
| `MAFF` | 93.91 | 93.91 | 97.86 | 97.17 | 65,684 |
| `PCBP2` | 93.89 | 93.23 | 96.53 | 96.61 | 5,328 |
| `ZIC2` | 93.77 | 93.9 | 97.82 | 96.94 | 56,766 |
| `GLIS2` | 93.74 | 93.14 | 98.22 | 97.8 | 33,566 |
| `ZNF121` | 93.64 | 98.86 | 99.34 | 99.26 | 35,805 |
| `SP2` | 93.6 | 93.13 | 96.81 | 95.36 | 27,956 |
| `SCRT2` | 93.59 | 98.97 | 99.56 | 99.17 | 59,462 |
| `BATF` | 93.58 | 93.82 | 98.16 | 97.93 | 36,658 |
| `HNRNPL` | 93.57 | 92.29 | 97.59 | 96.88 | 24,447 |
| `NFE2L2` | 93.53 | 91.27 | 97.24 | 96.09 | 26,392 |
| `ZNF585B` | 93.43 | 93.4 | 97.78 | 98.0 | 7,381 |
| `NFYB` | 93.31 | 91.7 | 96.3 | 95.22 | 14,696 |
| `ZSCAN4` | 93.25 | 92.72 | 97.64 | 97.75 | 23,997 |
| `ZNF316` | 93.22 | 93.43 | 97.42 | 97.55 | 97,518 |
| `ZNF140` | 93.19 | 92.79 | 96.45 | 96.93 | 7,623 |
| `ZNF777` | 93.12 | 92.58 | 97.24 | 97.07 | 7,181 |
| `CBFA2T2` | 93.06 | 93.09 | 97.31 | 97.25 | 32,239 |
| `ATF4` | 93.0 | 92.84 | 97.72 | 97.64 | 39,441 |
| `TFAP4` | 93.0 | 92.84 | 96.79 | 94.97 | 27,035 |
| `CTBP2` | 92.98 | 92.36 | 96.78 | 94.11 | 7,351 |
| `E2F1` | 92.88 | 86.4 | 95.25 | 91.61 | 18,927 |
| `MXD3` | 92.88 | 92.08 | 98.24 | 97.87 | 14,677 |
| `ZNF202` | 92.87 | 92.87 | 96.29 | 96.5 | 6,476 |
| `ZNF266` | 92.84 | 92.56 | 96.93 | 96.93 | 5,097 |
| `ZNF263` | 92.83 | 91.44 | 97.39 | 96.16 | 35,011 |
| `ZNF433` | 92.77 | 92.49 | 96.97 | 97.7 | 3,530 |
| `RBM39` | 92.73 | 91.61 | 97.44 | 96.77 | 29,478 |
| `ZNF680` | 92.69 | 92.24 | 97.36 | 97.68 | 10,483 |
| `ZNF341` | 92.66 | 92.24 | 97.24 | 96.26 | 33,413 |
| `E2F4` | 92.64 | 90.76 | 97.32 | 97.07 | 11,270 |
| `CBFA2T3` | 92.59 | 92.67 | 96.97 | 96.03 | 51,994 |
| `ZNF555` | 92.57 | 92.23 | 94.78 | 96.56 | 6,664 |
| `RBM25` | 92.56 | 92.48 | 96.96 | 97.05 | 47,193 |
| `MAFK` | 92.55 | 92.65 | 97.36 | 97.6 | 121,216 |
| `ZNF623` | 92.53 | 92.19 | 96.77 | 97.51 | 14,353 |
| `KAT2A` | 92.45 | 91.3 | 92.39 | 92.84 | 171 |
| `SIN3B` | 92.45 | 90.29 | 97.21 | 96.89 | 11,700 |
| `CEBPA` | 92.39 | 98.89 | 99.7 | 99.6 | 57,842 |
| `U2AF2` | 92.37 | 91.72 | 96.2 | 94.8 | 2,777 |
| `ZBTB10` | 92.27 | 91.31 | 96.02 | 94.41 | 15,441 |
| `PBX3` | 92.25 | 92.23 | 96.51 | 95.35 | 12,981 |
| `SAP30` | 92.08 | 90.13 | 96.21 | 92.3 | 15,727 |
| `PHF8` | 92.03 | 88.66 | 96.25 | 95.67 | 30,275 |
| `PAX5` | 92.02 | 90.77 | 96.81 | 94.42 | 36,090 |
| `ZNF785` | 92.01 | 91.35 | 97.35 | 97.16 | 6,605 |
| `ZNF76` | 92.0 | 90.95 | 93.83 | 89.14 | 11,676 |
| `HNF4G` | 91.93 | 90.87 | 96.43 | 95.82 | 35,204 |
| `AHR` | 91.82 | 91.39 | 97.21 | 96.43 | 10,611 |
| `ZC3H11A` | 91.8 | 91.33 | 96.31 | 97.12 | 9,905 |
| `RFX1` | 91.79 | 90.4 | 96.44 | 96.43 | 38,873 |
| `SMAD4` | 91.75 | 91.7 | 96.19 | 94.92 | 43,342 |
| `UBTF` | 91.73 | 89.06 | 94.72 | 91.45 | 19,173 |
| `ZNF704` | 91.71 | 90.84 | 94.66 | 94.52 | 1,834 |
| `CEBPB` | 91.69 | 98.47 | 99.54 | 99.42 | 148,540 |
| `TAL1` | 91.69 | 90.15 | 96.07 | 95.03 | 36,574 |
| `ZBTB7A` | 91.69 | 90.22 | 97.14 | 95.99 | 37,497 |
| `NFIL3` | 91.67 | 91.52 | 96.42 | 96.0 | 38,852 |
| `XRCC5` | 91.61 | 90.04 | 95.9 | 93.22 | 32,847 |
| `U2AF1` | 91.6 | 89.92 | 96.08 | 96.0 | 8,379 |
| `ZNF34` | 91.58 | 91.34 | 95.28 | 96.71 | 9,650 |
| `FOXP2` | 91.57 | 90.78 | 96.14 | 93.84 | 24,150 |
| `AGO2` | 91.55 | 89.26 | 95.16 | 94.66 | 33,079 |
| `RUNX3` | 91.53 | 98.64 | 99.5 | 99.27 | 69,903 |
| `ZBED5` | 91.49 | 91.43 | 97.14 | 96.94 | 5,100 |
| `RARA` | 91.46 | 91.59 | 95.97 | 94.89 | 42,489 |
| `FOS` | 91.45 | 98.69 | 99.62 | 99.63 | 169,317 |
| `SP3` | 91.44 | 90.22 | 95.27 | 94.77 | 23,619 |
| `NANOG` | 91.43 | 90.45 | 95.72 | 94.36 | 15,681 |
| `USF2` | 91.39 | 89.66 | 96.88 | 96.27 | 37,240 |
| `HNF4A` | 91.37 | 91.63 | 96.12 | 95.11 | 89,892 |
| `SP5` | 91.37 | 91.12 | 95.54 | 94.28 | 23,155 |
| `ZNF354C` | 91.37 | 90.59 | 95.08 | 96.39 | 1,640 |
| `ZNF444` | 91.35 | 90.8 | 95.64 | 94.38 | 25,366 |
| `GMEB2` | 91.33 | 90.21 | 95.76 | 95.89 | 4,800 |
| `ZNF677` | 91.33 | 91.35 | 94.68 | 94.52 | 5,777 |
| `ETV5` | 91.18 | 90.89 | 96.55 | 95.11 | 29,604 |
| `IRF4` | 91.18 | 91.14 | 96.12 | 95.26 | 21,810 |
| `PRPF4` | 91.14 | 89.78 | 96.21 | 95.93 | 8,605 |
| `FOXA3` | 91.12 | 91.46 | 96.8 | 96.6 | 45,297 |
| `ZNF292` | 91.11 | 90.59 | 94.63 | 96.11 | 1,900 |
| `GLIS1` | 91.07 | 90.1 | 96.04 | 95.32 | 58,506 |
| `FOXA2` | 91.05 | 91.28 | 96.39 | 96.06 | 99,343 |
| `KLF9` | 90.99 | 87.95 | 95.59 | 94.68 | 32,290 |
| `SOX5` | 90.98 | 90.85 | 95.23 | 93.77 | 37,979 |
| `BCL6` | 90.97 | 90.9 | 96.3 | 95.48 | 38,142 |
| `IRF3` | 90.97 | 87.65 | 96.01 | 95.01 | 5,726 |
| `ZNF223` | 90.97 | 90.6 | 95.52 | 95.63 | 5,176 |
| `HCFC1` | 90.96 | 85.32 | 94.4 | 91.32 | 19,700 |
| `DEAF1` | 90.85 | 90.18 | 94.68 | 95.53 | 3,170 |
| `HNRNPH1` | 90.85 | 89.75 | 96.02 | 95.65 | 2,446 |
| `CEBPZ` | 90.82 | 86.79 | 89.86 | 85.64 | 1,971 |
| `PTBP1` | 90.8 | 89.88 | 94.48 | 89.35 | 8,063 |
| `STAT3` | 90.79 | 90.81 | 96.82 | 96.85 | 65,231 |
| `KAT2B` | 90.77 | 90.48 | 96.6 | 96.8 | 3,106 |
| `SOX13` | 90.76 | 90.83 | 96.32 | 95.69 | 48,796 |
| `ZNF423` | 90.75 | 90.32 | 94.63 | 93.05 | 11,299 |
| `STAT2` | 90.73 | 89.46 | 95.84 | 93.72 | 4,303 |
| `MEIS2` | 90.71 | 90.78 | 96.27 | 96.07 | 52,199 |
| `ATF2` | 90.69 | 90.57 | 94.77 | 94.25 | 110,897 |
| `NFIA` | 90.67 | 90.58 | 95.6 | 95.07 | 27,816 |
| `PATZ1` | 90.67 | 89.53 | 96.62 | 95.93 | 35,416 |
| `ZNF398` | 90.66 | 89.94 | 94.96 | 92.96 | 26,224 |
| `KLF1` | 90.65 | 89.32 | 94.52 | 92.79 | 40,024 |
| `NFIB` | 90.65 | 87.93 | 96.05 | 95.1 | 27,982 |
| `SCRT1` | 90.65 | 90.42 | 94.93 | 94.54 | 25,487 |
| `PLRG1` | 90.64 | 90.06 | 96.68 | 96.85 | 2,256 |
| `PRDM1` | 90.62 | 95.17 | 98.83 | 98.73 | 50,489 |
| `ZNF133` | 90.61 | 90.22 | 95.36 | 94.71 | 8,423 |
| `EBF1` | 90.59 | 90.64 | 95.31 | 94.3 | 56,947 |
| `SREBF2` | 90.59 | 89.11 | 96.2 | 95.55 | 4,933 |
| `THAP11` | 90.57 | 89.79 | 94.85 | 93.4 | 31,698 |
| `POU5F1` | 90.56 | 89.71 | 96.35 | 95.35 | 7,870 |
| `ZNF48` | 90.56 | 89.58 | 94.31 | 91.0 | 28,840 |
| `RB1` | 90.5 | 87.95 | 94.0 | 91.78 | 31,314 |
| `HNF1A` | 90.44 | 90.13 | 93.47 | 91.12 | 12,818 |
| `ZBTB6` | 90.44 | 90.06 | 95.43 | 95.01 | 13,955 |
| `KDM5B` | 90.43 | 88.75 | 96.53 | 95.91 | 18,356 |
| `GLI4` | 90.37 | 90.04 | 96.45 | 96.57 | 6,130 |
| `RERE` | 90.37 | 89.28 | 95.15 | 93.11 | 11,849 |
| `ZNF521` | 90.37 | 90.04 | 96.17 | 96.82 | 1,585 |
| `FOXP1` | 90.33 | 89.44 | 95.14 | 93.99 | 31,380 |
| `ZBTB26` | 90.33 | 87.38 | 93.76 | 90.92 | 32,837 |
| `ZNF596` | 90.31 | 89.88 | 95.56 | 95.65 | 14,087 |
| `ZBTB21` | 90.29 | 89.52 | 96.14 | 95.86 | 18,547 |
| `HMGXB4` | 90.27 | 89.5 | 93.94 | 91.67 | 25,984 |
| `TEAD1` | 90.27 | 90.29 | 95.53 | 94.84 | 33,326 |
| `SFPQ` | 90.18 | 90.09 | 91.7 | 90.66 | 335 |
| `ZNF660` | 90.18 | 89.77 | 94.75 | 94.22 | 29,821 |
| `ZNF658` | 90.14 | 88.6 | 93.92 | 94.54 | 1,325 |
| `SKI` | 90.12 | 89.27 | 95.47 | 93.65 | 30,460 |
| `SRF` | 90.12 | 87.92 | 96.0 | 94.95 | 27,692 |
| `CEBPG` | 90.11 | 90.14 | 96.25 | 96.42 | 87,912 |
| `ZHX1` | 90.1 | 88.61 | 94.55 | 92.57 | 5,512 |
| `RUNX1` | 90.07 | 89.3 | 94.29 | 91.85 | 7,554 |
| `RXRB` | 90.07 | 89.83 | 94.62 | 92.92 | 38,236 |
| `ZBTB48` | 90.05 | 89.29 | 96.26 | 95.22 | 24,899 |
| `ZNF747` | 90.02 | 88.84 | 95.87 | 95.94 | 1,427 |
| `VEZF1` | 90.01 | 88.14 | 94.32 | 93.48 | 35,726 |
| `GATA1` | 89.96 | 87.31 | 93.39 | 91.08 | 33,326 |
| `ZNF670` | 89.95 | 88.3 | 95.12 | 95.63 | 1,288 |
| `ARID4B` | 89.94 | 88.99 | 94.05 | 92.27 | 42,648 |
| `ZNF449` | 89.94 | 89.32 | 94.61 | 94.5 | 18,374 |
| `KLF17` | 89.93 | 89.05 | 96.18 | 95.48 | 25,375 |
| `ZBTB20` | 89.91 | 88.23 | 95.2 | 92.94 | 31,889 |
| `ELF3` | 89.85 | 89.43 | 95.06 | 93.86 | 35,966 |
| `ZMIZ1` | 89.85 | 90.09 | 95.22 | 95.28 | 1,077 |
| `ZNF16` | 89.85 | 89.14 | 95.41 | 95.27 | 2,784 |
| `ZNF143` | 89.84 | 98.49 | 99.48 | 99.5 | 66,295 |
| `ZSCAN5A` | 89.84 | 89.2 | 93.59 | 90.92 | 8,202 |
| `ZNF513` | 89.78 | 88.85 | 94.49 | 95.41 | 11,211 |
| `PPARG` | 89.77 | 89.47 | 94.59 | 93.53 | 23,903 |
| `ZBTB8A` | 89.73 | 88.24 | 94.0 | 92.72 | 32,420 |
| `IRF5` | 89.71 | 89.41 | 93.56 | 94.62 | 2,755 |
| `ZMYM3` | 89.71 | 89.32 | 95.52 | 95.45 | 43,157 |
| `DEK` | 89.7 | 88.82 | 95.38 | 93.29 | 8,490 |
| `GABPB1` | 89.7 | 89.12 | 94.29 | 92.92 | 47,437 |
| `ZNF629` | 89.69 | 88.91 | 94.14 | 92.43 | 37,813 |
| `ETV1` | 89.68 | 89.39 | 95.3 | 95.09 | 20,672 |
| `ZNF394` | 89.67 | 88.63 | 94.54 | 94.01 | 28,297 |
| `TEAD4` | 89.66 | 89.49 | 95.4 | 94.56 | 34,189 |
| `PHF20` | 89.63 | 88.59 | 94.4 | 91.57 | 13,930 |
| `NFYC` | 89.59 | 89.07 | 95.3 | 95.46 | 15,080 |
| `RBBP5` | 89.59 | 85.4 | 96.01 | 94.46 | 30,322 |
| `ELK1` | 89.58 | 84.66 | 91.33 | 89.55 | 12,298 |
| `HMBOX1` | 89.55 | 88.79 | 95.65 | 94.82 | 24,883 |
| `KDM5A` | 89.53 | 82.52 | 92.86 | 90.18 | 13,023 |
| `MEF2B` | 89.51 | 88.5 | 94.65 | 93.45 | 34,822 |
| `WHSC1` | 89.51 | 89.25 | 94.42 | 89.89 | 1,801 |
| `ZNF692` | 89.51 | 88.62 | 94.15 | 92.63 | 30,183 |
| `SAP130` | 89.46 | 89.63 | 93.52 | 92.26 | 58,021 |
| `TCF7L2` | 89.46 | 86.81 | 94.06 | 91.99 | 28,567 |
| `SETDB1` | 89.45 | 87.69 | 96.29 | 95.41 | 4,903 |
| `ZKSCAN1` | 89.45 | 87.61 | 94.37 | 92.44 | 20,226 |
| `EGR1` | 89.43 | 89.26 | 93.84 | 93.58 | 67,451 |
| `GATA4` | 89.43 | 88.99 | 94.52 | 91.79 | 12,156 |
| `SUZ12` | 89.36 | 82.88 | 94.21 | 91.33 | 24,316 |
| `HDAC6` | 89.35 | 87.38 | 95.07 | 94.75 | 5,762 |
| `TEAD3` | 89.35 | 89.2 | 95.32 | 93.94 | 42,854 |
| `SRSF9` | 89.34 | 87.07 | 96.1 | 95.7 | 846 |
| `MLX` | 89.33 | 88.85 | 93.58 | 91.33 | 14,640 |
| `ARID1B` | 89.32 | 88.77 | 95.17 | 94.59 | 45,992 |
| `ZSCAN30` | 89.31 | 88.65 | 94.12 | 92.49 | 24,704 |
| `ZFP36` | 89.3 | 86.44 | 94.32 | 92.7 | 32,993 |
| `ZFP64` | 89.3 | 88.8 | 94.25 | 93.12 | 9,433 |
| `ZNF518A` | 89.3 | 88.1 | 94.68 | 95.04 | 16,690 |
| `ZNF512` | 89.29 | 87.52 | 95.55 | 95.6 | 17,500 |
| `MEF2C` | 89.25 | 89.19 | 94.66 | 93.88 | 11,421 |
| `ARID2` | 89.24 | 88.78 | 93.47 | 91.82 | 11,585 |
| `IKZF5` | 89.21 | 88.59 | 94.7 | 92.99 | 25,386 |
| `PRDM2` | 89.19 | 88.58 | 93.29 | 91.23 | 3,824 |
| `KDM6A` | 89.17 | 88.82 | 95.31 | 94.56 | 12,193 |
| `RXRA` | 89.17 | 89.44 | 94.78 | 93.82 | 85,611 |
| `MEF2A` | 89.15 | 89.07 | 95.08 | 95.07 | 22,725 |
| `NRF1` | 89.15 | 87.63 | 93.52 | 92.27 | 41,391 |
| `SREBF1` | 89.15 | 87.65 | 95.62 | 95.11 | 13,518 |
| `BCOR` | 89.08 | 88.74 | 95.34 | 94.44 | 41,985 |
| `FOSL1` | 89.06 | 88.05 | 94.11 | 93.96 | 43,596 |
| `ZFP69B` | 89.05 | 88.39 | 94.54 | 93.79 | 21,782 |
| `ZNF837` | 89.0 | 88.53 | 94.06 | 94.52 | 2,332 |
| `CREB1` | 88.96 | 89.04 | 95.48 | 96.05 | 89,914 |
| `KDM3A` | 88.94 | 88.07 | 92.68 | 88.4 | 15,970 |
| `POU2F2` | 88.92 | 88.77 | 93.25 | 89.71 | 19,963 |
| `RBPJ` | 88.92 | 87.6 | 94.85 | 93.61 | 24,864 |
| `EED` | 88.9 | 88.18 | 94.22 | 92.87 | 33,175 |
| `IRF2` | 88.9 | 87.49 | 93.77 | 92.14 | 31,753 |
| `CBFB` | 88.89 | 87.72 | 93.81 | 91.26 | 18,476 |
| `ZNF362` | 88.88 | 87.44 | 94.25 | 92.46 | 20,426 |
| `HMG20A` | 88.87 | 88.31 | 94.68 | 93.45 | 24,288 |
| `NR2F6` | 88.87 | 88.87 | 93.72 | 92.0 | 59,262 |
| `MIXL1` | 88.8 | 88.4 | 94.17 | 93.38 | 25,659 |
| `ZNF768` | 88.79 | 88.37 | 92.77 | 94.22 | 7,605 |
| `ZNF791` | 88.77 | 87.99 | 94.79 | 95.45 | 3,900 |
| `GTF2B` | 88.76 | 86.89 | 94.01 | 94.5 | 1,890 |
| `ZNF652` | 88.76 | 88.46 | 95.01 | 94.59 | 15,412 |
| `CBX1` | 88.75 | 87.21 | 94.69 | 92.62 | 12,838 |
| `KLF4` | 88.72 | 86.04 | 92.03 | 91.82 | 6,883 |
| `HHEX` | 88.7 | 88.36 | 95.48 | 94.32 | 7,808 |
| `ZFP91` | 88.7 | 87.92 | 93.44 | 93.1 | 12,862 |
| `ETS1` | 88.69 | 84.7 | 94.07 | 90.02 | 30,554 |
| `FOSL2` | 88.66 | 88.52 | 92.87 | 91.8 | 54,934 |
| `GMEB1` | 88.61 | 86.89 | 94.78 | 94.21 | 22,958 |
| `MYRF` | 88.61 | 88.08 | 92.66 | 88.81 | 6,038 |
| `CREB3L1` | 88.6 | 86.11 | 93.55 | 91.45 | 16,274 |
| `MBD2` | 88.6 | 85.96 | 94.29 | 92.38 | 20,596 |
| `SP7` | 88.58 | 87.43 | 93.73 | 92.33 | 43,425 |
| `ZNF384` | 88.58 | 88.42 | 94.86 | 94.74 | 49,451 |
| `ZNF664` | 88.58 | 88.58 | 94.23 | 93.8 | 26,774 |
| `AEBP2` | 88.57 | 88.27 | 92.65 | 93.95 | 2,439 |
| `HOMEZ` | 88.57 | 88.43 | 94.49 | 93.05 | 25,047 |
| `DRAP1` | 88.55 | 87.7 | 93.04 | 91.43 | 23,241 |
| `ZNF514` | 88.55 | 88.75 | 93.62 | 94.15 | 1,637 |
| `HSF1` | 88.53 | 86.77 | 93.77 | 93.41 | 3,588 |
| `FOXA1` | 88.52 | 88.77 | 94.82 | 94.45 | 144,475 |
| `KLF10` | 88.52 | 87.13 | 93.65 | 91.19 | 18,933 |
| `ZNF18` | 88.49 | 87.85 | 93.25 | 92.44 | 18,879 |
| `GATAD1` | 88.45 | 87.54 | 92.76 | 90.62 | 22,354 |
| `BRCA1` | 88.43 | 84.43 | 91.88 | 90.63 | 4,271 |
| `GATA3` | 88.41 | 88.76 | 93.95 | 93.68 | 89,323 |
| `TBX3` | 88.37 | 86.69 | 92.33 | 87.32 | 16,097 |
| `HIC1` | 88.34 | 87.87 | 95.07 | 94.7 | 24,393 |
| `ELF4` | 88.29 | 85.91 | 91.81 | 90.4 | 19,552 |
| `KLF7` | 88.28 | 87.47 | 95.07 | 95.1 | 11,741 |
| `HBP1` | 88.25 | 87.02 | 94.35 | 92.31 | 13,101 |
| `MAZ` | 88.25 | 88.01 | 93.3 | 92.34 | 57,653 |
| `RLF` | 88.25 | 87.22 | 91.97 | 89.17 | 9,482 |
| `YY2` | 88.25 | 87.53 | 94.5 | 93.99 | 9,753 |
| `ZNF561` | 88.25 | 87.47 | 92.52 | 89.34 | 21,469 |
| `PBX2` | 88.24 | 86.87 | 92.57 | 90.17 | 38,883 |
| `ESRRA` | 88.17 | 86.95 | 93.13 | 89.98 | 41,619 |
| `GATA2` | 88.17 | 88.14 | 93.72 | 92.79 | 71,662 |
| `ZNF189` | 88.17 | 87.09 | 93.99 | 92.74 | 35,323 |
| `MIER2` | 88.16 | 87.72 | 93.74 | 92.28 | 15,598 |
| `DMAP1` | 88.15 | 86.04 | 92.88 | 89.99 | 21,794 |
| `TBX21` | 88.15 | 87.4 | 94.73 | 94.2 | 38,025 |
| `RFX3` | 88.14 | 87.7 | 92.23 | 93.25 | 6,180 |
| `FEZF1` | 88.12 | 87.4 | 94.8 | 93.99 | 31,350 |
| `ZNF248` | 88.12 | 87.31 | 92.8 | 92.85 | 2,499 |
| `ZNF600` | 88.11 | 87.42 | 93.97 | 90.88 | 45,001 |
| `NR2F2` | 88.09 | 88.0 | 95.03 | 94.56 | 55,514 |
| `ZNF560` | 88.07 | 87.67 | 95.15 | 96.12 | 3,447 |
| `BHLHE40` | 88.01 | 88.0 | 92.37 | 91.72 | 90,623 |
| `NFKBIZ` | 88.0 | 86.89 | 93.2 | 90.86 | 12,731 |
| `SOX6` | 87.97 | 87.18 | 92.97 | 91.69 | 36,530 |
| `NCOA1` | 87.95 | 83.89 | 92.56 | 89.24 | 26,193 |
| `ZNF2` | 87.94 | 86.44 | 92.68 | 91.0 | 24,945 |
| `JUNB` | 87.93 | 88.02 | 92.72 | 91.19 | 51,972 |
| `KDM4B` | 87.93 | 86.42 | 93.56 | 94.18 | 7,803 |
| `ZNF10` | 87.88 | 87.16 | 93.83 | 93.93 | 17,922 |
| `MYB` | 87.86 | 86.65 | 94.72 | 93.1 | 3,337 |
| `MGA` | 87.84 | 86.5 | 91.45 | 85.5 | 28,338 |
| `ZBTB2` | 87.82 | 86.59 | 94.58 | 94.15 | 16,341 |
| `ZEB1` | 87.82 | 85.07 | 94.37 | 93.15 | 20,733 |
| `REPIN1` | 87.81 | 86.18 | 94.22 | 94.58 | 5,721 |
| `ZNF148` | 87.79 | 85.69 | 92.13 | 92.12 | 21,902 |
| `ERF` | 87.78 | 86.48 | 92.92 | 90.58 | 27,611 |
| `KLF8` | 87.78 | 86.2 | 91.63 | 88.66 | 27,450 |
| `MYC` | 87.77 | 87.53 | 93.73 | 92.94 | 94,483 |
| `TRIM22` | 87.77 | 97.99 | 99.03 | 99.13 | 55,932 |
| `RFX5` | 87.76 | 81.96 | 92.33 | 89.55 | 24,728 |
| `DACH1` | 87.72 | 87.31 | 92.88 | 92.63 | 18,904 |
| `ZNF239` | 87.71 | 86.87 | 92.62 | 91.05 | 4,689 |
| `ZNF366` | 87.69 | 97.9 | 99.1 | 98.73 | 44,505 |
| `PRDM6` | 87.65 | 87.25 | 94.46 | 92.98 | 42,954 |
| `ATF3` | 87.61 | 87.36 | 92.96 | 92.73 | 94,190 |
| `RAD51` | 87.58 | 84.45 | 93.59 | 92.92 | 36,133 |
| `PRDM4` | 87.55 | 87.06 | 93.45 | 92.04 | 20,853 |
| `KAT8` | 87.54 | 85.89 | 92.39 | 89.64 | 31,059 |
| `MBD1` | 87.54 | 84.57 | 92.74 | 88.6 | 18,264 |
| `PKNOX1` | 87.54 | 87.54 | 94.59 | 94.36 | 113,107 |
| `WT1` | 87.54 | 86.69 | 92.85 | 89.27 | 26,226 |
| `CHD2` | 87.52 | 86.08 | 93.75 | 91.52 | 41,627 |
| `ZXDB` | 87.51 | 86.1 | 91.92 | 88.84 | 30,796 |
| `HMG20B` | 87.5 | 86.97 | 93.22 | 90.82 | 12,656 |
| `SIX5` | 87.49 | 79.23 | 89.33 | 86.03 | 10,595 |
| `MAX` | 87.44 | 87.59 | 92.05 | 89.23 | 94,496 |
| `TRIM24` | 87.42 | 84.62 | 93.51 | 90.72 | 35,639 |
| `NONO` | 87.4 | 82.54 | 89.28 | 84.68 | 29,192 |
| `NFE2L1` | 87.36 | 83.51 | 90.34 | 91.43 | 10,261 |
| `ZNF391` | 87.36 | 86.05 | 92.69 | 90.97 | 12,610 |
| `ZSCAN16` | 87.36 | 87.06 | 92.03 | 89.65 | 6,915 |
| `GATAD2A` | 87.27 | 87.34 | 92.84 | 92.14 | 59,253 |
| `SMARCA4` | 87.23 | 87.23 | 92.59 | 91.47 | 94,655 |
| `SMC3` | 87.23 | 86.92 | 93.67 | 94.33 | 89,498 |
| `ZNF282` | 87.23 | 85.73 | 92.1 | 90.4 | 12,994 |
| `ZNF645` | 87.19 | 85.99 | 93.82 | 93.71 | 3,597 |
| `SIRT6` | 87.18 | 86.27 | 91.81 | 89.63 | 831 |
| `ZBTB11` | 87.17 | 83.11 | 93.24 | 92.37 | 34,307 |
| `ZNF205` | 87.17 | 85.68 | 93.89 | 92.45 | 17,444 |
| `KLF13` | 87.15 | 86.93 | 90.16 | 85.26 | 11,590 |
| `NKRF` | 87.15 | 82.95 | 93.67 | 92.25 | 27,626 |
| `OSR2` | 87.15 | 86.49 | 92.7 | 90.29 | 33,243 |
| `CC2D1A` | 87.14 | 86.24 | 92.24 | 91.48 | 24,056 |
| `NFIC` | 87.14 | 87.09 | 92.88 | 93.61 | 74,803 |
| `ZNF138` | 87.12 | 86.79 | 93.04 | 94.92 | 1,611 |
| `PHB2` | 87.11 | 86.36 | 93.7 | 93.49 | 8,362 |
| `ZHX2` | 87.11 | 84.59 | 92.57 | 90.95 | 14,751 |
| `ZBTB44` | 87.09 | 86.97 | 91.7 | 89.35 | 19,961 |
| `ZNF614` | 87.09 | 86.34 | 92.96 | 90.43 | 21,841 |
| `ZNF501` | 87.07 | 84.58 | 89.56 | 85.25 | 18,650 |
| `ZNF547` | 87.07 | 87.18 | 93.08 | 93.55 | 4,777 |
| `E4F1` | 87.05 | 83.51 | 91.86 | 88.4 | 27,783 |
| `ZNF530` | 87.0 | 86.21 | 92.54 | 93.54 | 2,193 |
| `MYNN` | 86.97 | 85.32 | 92.29 | 90.37 | 19,348 |
| `INSM2` | 86.94 | 86.19 | 92.8 | 91.74 | 16,385 |
| `ZBTB7B` | 86.94 | 85.85 | 93.93 | 93.22 | 9,156 |
| `BCL11B` | 86.93 | 86.01 | 92.01 | 89.38 | 11,525 |
| `ZBTB12` | 86.93 | 86.23 | 92.9 | 91.71 | 10,363 |
| `PML` | 86.92 | 85.32 | 93.87 | 93.51 | 18,068 |
| `SALL2` | 86.9 | 86.55 | 93.23 | 94.22 | 2,489 |
| `NR2F1` | 86.87 | 86.87 | 93.08 | 92.05 | 70,026 |
| `LCORL` | 86.86 | 86.86 | 93.26 | 93.83 | 10,617 |
| `THRB` | 86.86 | 86.05 | 92.7 | 91.63 | 14,895 |
| `ZGPAT` | 86.84 | 85.13 | 90.76 | 86.79 | 33,522 |
| `MIER3` | 86.83 | 85.69 | 92.53 | 91.2 | 19,565 |
| `KMT2B` | 86.81 | 84.82 | 92.77 | 91.54 | 17,871 |
| `TGIF2` | 86.8 | 85.45 | 92.88 | 90.99 | 18,162 |
| `IKZF2` | 86.79 | 86.64 | 92.67 | 91.71 | 52,015 |
| `ZBTB33` | 86.78 | 92.02 | 97.16 | 96.92 | 96,111 |
| `NEUROD1` | 86.73 | 85.61 | 92.99 | 91.71 | 19,165 |
| `ATF7` | 86.72 | 86.65 | 92.77 | 93.41 | 105,695 |
| `ELF1` | 86.71 | 86.32 | 93.8 | 94.5 | 70,684 |
| `RELB` | 86.71 | 84.55 | 93.6 | 91.95 | 36,669 |
| `SMARCE1` | 86.71 | 86.36 | 92.37 | 91.4 | 48,505 |
| `ZNF843` | 86.68 | 85.41 | 92.05 | 89.55 | 22,911 |
| `ATM` | 86.67 | 85.99 | 93.74 | 94.31 | 2,162 |
| `ZNF473` | 86.67 | 86.34 | 92.54 | 93.0 | 2,252 |
| `MXD4` | 86.63 | 84.43 | 91.34 | 88.33 | 18,180 |
| `CREM` | 86.61 | 86.56 | 92.96 | 93.26 | 72,466 |
| `ZNF707` | 86.61 | 86.66 | 93.38 | 93.31 | 3,329 |
| `ZNF157` | 86.6 | 86.52 | 89.54 | 86.21 | 3,778 |
| `IKZF3` | 86.59 | 85.8 | 91.99 | 88.04 | 29,535 |
| `DIDO1` | 86.58 | 85.66 | 92.29 | 92.48 | 7,186 |
| `ZSCAN26` | 86.56 | 85.08 | 93.43 | 94.67 | 2,537 |
| `MXI1` | 86.53 | 86.12 | 94.05 | 94.26 | 52,982 |
| `ZSCAN18` | 86.51 | 85.15 | 92.3 | 92.92 | 4,130 |
| `CDC5L` | 86.47 | 85.08 | 93.59 | 93.67 | 5,151 |
| `KLF5` | 86.44 | 85.35 | 92.7 | 90.15 | 11,680 |
| `ZNF512B` | 86.43 | 83.44 | 93.26 | 91.76 | 8,552 |
| `LARP7` | 86.42 | 84.12 | 93.32 | 92.81 | 27,160 |
| `ZNF280C` | 86.42 | 86.07 | 92.27 | 92.66 | 1,292 |
| `L3MBTL2` | 86.41 | 86.23 | 91.05 | 89.82 | 52,245 |
| `MCM2` | 86.41 | 85.41 | 93.45 | 94.29 | 4,549 |
| `E2F7` | 86.4 | 85.34 | 91.15 | 91.4 | 2,985 |
| `ZNF404` | 86.4 | 85.45 | 91.88 | 93.7 | 2,249 |
| `MTA1` | 86.34 | 84.24 | 93.57 | 92.13 | 22,370 |
| `GTF2F1` | 86.32 | 83.54 | 92.14 | 90.16 | 39,350 |
| `ZNF324` | 86.32 | 84.57 | 93.81 | 93.44 | 14,713 |
| `RAD21` | 86.3 | 97.92 | 99.11 | 98.99 | 188,052 |
| `NR2C1` | 86.27 | 81.88 | 90.51 | 85.79 | 31,898 |
| `RBAK` | 86.25 | 85.74 | 92.56 | 93.16 | 3,642 |
| `TCF7` | 86.23 | 85.39 | 92.08 | 90.33 | 30,462 |
| `ZNF776` | 86.23 | 85.19 | 92.22 | 92.04 | 2,838 |
| `ARHGAP35` | 86.18 | 85.43 | 93.57 | 93.39 | 4,817 |
| `STAT1` | 86.15 | 83.28 | 92.57 | 90.18 | 11,457 |
| `ZNF621` | 86.14 | 85.57 | 92.51 | 92.93 | 1,976 |
| `YBX3` | 86.12 | 84.54 | 90.9 | 90.72 | 2,599 |
| `ZNF610` | 86.07 | 84.35 | 91.36 | 89.32 | 13,333 |
| `GLI2` | 86.05 | 86.28 | 91.17 | 92.26 | 5,650 |
| `KLF6` | 86.05 | 84.14 | 91.14 | 87.94 | 15,409 |
| `OVOL3` | 86.05 | 85.14 | 90.46 | 88.66 | 9,089 |
| `ASH1L` | 85.96 | 84.17 | 92.97 | 93.93 | 7,269 |
| `KLF16` | 85.91 | 85.24 | 90.83 | 90.08 | 48,641 |
| `NR3C1` | 85.91 | 85.89 | 93.29 | 93.1 | 62,779 |
| `ZNF114` | 85.91 | 82.83 | 91.36 | 91.57 | 1,444 |
| `PRDM10` | 85.9 | 86.39 | 91.62 | 88.42 | 68,962 |
| `ZSCAN29` | 85.87 | 82.16 | 90.3 | 85.84 | 21,597 |
| `IRF1` | 85.84 | 80.68 | 89.75 | 87.82 | 32,357 |
| `ZSCAN9` | 85.83 | 84.87 | 91.14 | 89.95 | 17,526 |
| `ZFP3` | 85.82 | 84.76 | 93.06 | 93.73 | 4,550 |
| `MNT` | 85.79 | 85.08 | 92.76 | 93.16 | 83,589 |
| `TAF7` | 85.79 | 81.76 | 93.28 | 92.37 | 21,002 |
| `MZF1` | 85.78 | 85.16 | 91.67 | 89.93 | 17,643 |
| `ZFP37` | 85.78 | 83.76 | 89.27 | 86.32 | 16,553 |
| `PHF21A` | 85.74 | 85.18 | 88.24 | 82.19 | 8,878 |
| `TOE1` | 85.74 | 82.45 | 89.5 | 89.69 | 29,556 |
| `BACH1` | 85.62 | 83.64 | 90.78 | 88.15 | 41,151 |
| `ZNF7` | 85.61 | 84.92 | 92.67 | 92.68 | 8,038 |
| `ZNF211` | 85.59 | 84.6 | 91.95 | 92.44 | 1,919 |
| `ZSCAN23` | 85.58 | 84.31 | 92.3 | 91.5 | 8,505 |
| `FOXM1` | 85.57 | 83.72 | 90.82 | 89.44 | 20,757 |
| `SUPT5H` | 85.56 | 81.99 | 93.26 | 92.1 | 22,469 |
| `BCL3` | 85.55 | 83.8 | 93.27 | 92.67 | 43,282 |
| `TFDP1` | 85.52 | 80.8 | 89.14 | 84.38 | 30,292 |
| `TAF9B` | 85.46 | 83.58 | 87.02 | 79.88 | 13,069 |
| `ZNF792` | 85.46 | 83.82 | 92.95 | 91.81 | 24,699 |
| `JUND` | 85.43 | 85.33 | 93.1 | 93.42 | 166,033 |
| `SIN3A` | 85.43 | 85.07 | 93.29 | 93.11 | 65,597 |
| `BCL11A` | 85.41 | 84.36 | 92.15 | 91.13 | 33,663 |
| `NR2C2` | 85.39 | 80.24 | 89.73 | 86.9 | 29,811 |
| `POLR2G` | 85.39 | 84.83 | 92.98 | 93.64 | 59,528 |
| `ZNF311` | 85.34 | 84.08 | 92.44 | 93.57 | 2,206 |
| `ZNF571` | 85.34 | 84.53 | 92.7 | 93.55 | 1,488 |
| `EP400` | 85.29 | 82.21 | 89.96 | 88.24 | 25,324 |
| `ZFP1` | 85.26 | 83.98 | 91.92 | 90.8 | 12,129 |
| `RCOR2` | 85.25 | 84.38 | 90.5 | 88.89 | 19,532 |
| `REST` | 85.25 | 84.97 | 90.84 | 91.49 | 119,743 |
| `MCM3` | 85.24 | 84.32 | 93.0 | 93.26 | 2,561 |
| `SP1` | 85.24 | 84.86 | 91.19 | 91.14 | 120,925 |
| `PHF5A` | 85.23 | 82.4 | 90.52 | 88.55 | 9,570 |
| `ZNF169` | 85.23 | 84.36 | 91.23 | 90.6 | 2,873 |
| `TSHZ1` | 85.17 | 84.45 | 92.39 | 91.76 | 11,804 |
| `MTA2` | 85.15 | 84.91 | 90.5 | 89.57 | 59,001 |
| `GFI1B` | 85.11 | 84.57 | 91.26 | 90.52 | 10,694 |
| `ZNF558` | 85.1 | 84.16 | 91.1 | 91.2 | 13,849 |
| `ZNF19` | 85.06 | 84.17 | 91.34 | 93.34 | 1,998 |
| `SMAD5` | 85.03 | 79.12 | 92.23 | 90.37 | 22,402 |
| `SNRNP70` | 85.02 | 82.87 | 89.28 | 89.69 | 871 |
### Histone Modification Models (4)
| Model | Accuracy | F1 | ROC-AUC | PR-AUC | ChIP-seq Peaks |
|-------|----------|-----|---------|--------|----------------|
| `H4K12ac` | 89.57 | 89.53 | 96.1 | 95.46 | 42,837 |
| `H2AK9ac` | 88.91 | 89.24 | 94.58 | 92.7 | 129,243 |
| `H3K9me1` | 85.43 | 87.45 | 93.75 | 91.95 | 196,657 |
| `H3K23me2` | 85.39 | 85.45 | 93.76 | 93.34 | 77,099 |
## Model Architecture
All models are fine-tuned from the DNABERT pretrained checkpoint (`6-new-12w-0`),
which uses a 6-mer tokenization of DNA sequences. Each model is a
`BertForSequenceClassification` with 2 output classes (bound / unbound).
- **Base model:** DNABERT (Ji et al., 2021, Bioinformatics)
- **Input:** 6-mer tokenized DNA sequences (301bp)
- **Training data:** ENCODE ChIP-seq peaks (positive) vs. length/GC-matched genomic background (negative)
- **Negative sequences:** Generated via MMseqs2 clustering at 80% identity threshold to ensure sequence diversity
## Experimental Validation
DeepVRegulome was validated against the Yan et al. (2021) SNP-SELEX dataset
(GSE118725, Nature Genetics), which provides experimentally measured allelic
effects of genetic variants on transcription factor binding for 270 TFs.
- **61 TFs** overlap between DeepVRegulome's 458 TF models and SNP-SELEX
- **Mean per-TF AUROC:** 0.611
- **53/61 TFs** achieve BH-corrected significance at q < 0.05
- DeepVRegulome significantly outperforms DeepSEA (Wilcoxon p = 3.1 x 10^-5)
- Performance is statistically indistinguishable from Enformer (p = 0.353) and Borzoi (p = 0.329)
## Citation
If you use DeepVRegulome, please cite:
```bibtex
@article{dutta2025deepvregulome,
title={DeepVRegulome: Deep Learning Predicts Functional Impact of Short Genomic
Variants on the Human Regulome with Application to Cancer},
author={Dutta, Pratik and Obusan, Matthew and Sathian, Rekha and Davuluri, Ramana V.},
journal={arXiv preprint arXiv:2511.09026},
year={2025}
}
```
## License
CC-BY-NC-4.0