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Table 1 Summary of property encodings for transcription factors (TFs)

From: Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function

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