Table 1 Published prediction methods for enhancer and eRAN
From: Predicting active enhancers with DNA methylation and histone modification
Method name | Target | Features | Algorithm model | Years |
|---|---|---|---|---|
ChromHMM | Chromatin state | Histone modifications + TF binding | HMM | 2012 |
ChroModule | Chromatin state | Histone modifications + open chromatin | HMM | 2013 |
Segway | Regulatory pattern | Histone modifications + TF binding + open chromatin | DBN | 2013 |
ChromeGenSVM | Enhancer | Histone modifications | SVM | 2012 |
RFECS | Chromatin state | Histone modifications | RF | 2013 |
Enhancer-CRNN | Enhancer | Histone modifications | RNN | 2019 |
kmer-SVM | Regulatory pattern | DNA sequence | SVM | 2013 |
iEnhancer-2L | Enhancer/strength | DNA sequence | SVM | 2016 |
SeqEnhDL | Enhancer | DNA sequence | MLP, CNN, and RNN | 2021 |
iEnhancer-RD | Enhancer/strength | DNA sequence | DNN | 2021 |
LSTMAtt | Enhancer/strength | DNA sequence | Bi-LSTM | 2022 |
Logistic Regression Model (Without name) | eRNA | Histone modifications | Logistic regression | 2013 |
DeepITEH | Tissue-specific eRNAs | DNA sequence + histone modifications | Bert + Bi-LSTM + DNN | 2023 |