Table 7.
Guide RNA features based on Deep Learning models
| Categories/models | Efficient features | Inefficient features |
|---|---|---|
| Overall nucleotide usage | ||
| DeepCRISPR | A, U in the middle | C in the middle |
| CNN-SVR | A, U in the middle | G count |
| C-RNNCrispr | NN in positions 17–19 | |
| Position-specific nucleotides | ||
| DeepCRISPR | G in position 20 | A in position 20 |
| C in positions 17–20 | U in positions 17–20 | |
| G in position 16 | ||
| CNN-SVR | A in position 20 | G in position 20 |
| C in positions 17–20 | U in positions 17–20 | |
| C-RNNCrispr | A in position 20 | A in positions 3–6 |
| C in positions 17–19 | ||
| U in position 20 | ||
| Motifs | ||
| DeepCRISPR | C in PAM (CGG) | T in PAM (TGG) |
| G in PAM (GGG) | A in PAM (AGG) | |
| CNN-SVR | T in PAM (TGG) | C in PAM (CGG) |
| A in PAM (AGG) | G in PAM (GGG) | |
| Epigenetic | ||
| DeepCRISPR, CNN-SVR, | Open chromatin (esp. position 17) | Methylated DNA [RRBS] |
| C-RNNCrispr | [CTCF, DNase] |
CTCF: CCCTC-binding factor, RRBS: reduced representation bisulfite sequencing, N: any nucleotide.
Conflicting results are marked in bold.