Table 1 Summary of property encodings for transcription factors (TFs)
Property | Description | Encoding |
|---|---|---|
TF_Class | Encoded 2–3 top levels of five digit code based on TFClass classification; i.e. superclass followed by class (see text) | A 47-dimensional vector where ith position (superclass) and jth position (class) are 1, other positions are 0 |
PD | TF has a frequent Pfam domain (yes/no) | 1/0 |
DBD | TF has a DNA-binding domain (DBD) (yes/no) | 1/0 |
N_DBD | Number of DBDs (see text) | 11/10/00 |
PPI | TF has a protein-protein interaction (PPI) (yes/no) | 1/0 |
N_PPI | Number of PPIs (see text) | 11/10/00 |
N_PhS | Number of Phosphorylation sites (see text) | 11/10/00 |
PTM | TF has a post-translational modification (PTM) (yes/no) | 1/0 |
Ind_PTM | TF has a specific PTM (yes/no) | An ordered 6-dimensional vector where position i corresponding to PTM i is 1/0 |
N_ZFD | Number of the zinc finger domains (see text) | 11/10/00 |