Table 2. The TRANSFAC categorization of transcription factors (TFs)
|
TF categorization from TRANSFAC 6.0 |
|
|
|
Superclass |
Class |
Training matrices, n |
Test alignments, n |
|
1: Basic domains |
1.1 : Leucine zipper factors (bZIP) |
34 |
82 |
48 |
1.2 : Helix-loop-helix factors (bHLH) |
13 |
|||
1.3 : Helix-loop-helix/leucine zipper factors |
22 |
|||
1.4 : NF-1 |
6 |
|||
1.5 : RF-X |
1 |
|||
1.6 : bHSH |
6 |
|||
2: Zinc-coordinating DNA-binding domains |
2.1 : Cys4 zinc finger or nuclear receptor type |
14 |
52 |
36 |
2.2 : Diverse Cys4 zinc fingers |
13 |
|||
2.3 : Cys2His2 zinc domain |
21 |
|||
2.4 : Cys5 cycteine-zinc cluster |
3 |
|||
2.5 : Zinc fingers of alternating composition |
1 |
|||
3: Helix-turn-helix |
3.1 : Homeo domain |
41 |
76 |
64 |
3.2 : Paired box |
6 |
|||
3.3 : Fork head / winged helix |
4 |
|||
3.4 : Heat shock factors |
7 |
|||
3.5 : Tryptophan clusters |
17 |
|||
3.6 : TEA domain |
1 |
|||
4: beta-scaffold factors |
4.1 : RHR (Rel homology region) |
15 |
60 |
13 |
4.2 : STAT |
13 |
|||
4.3 : p53 |
2 |
|||
4.4 : MADs box |
9 |
|||
4.5 : b -Barrel a -helix TFs |
1 |
|||
4.6 : TATA-biding proteins |
3 |
|||
4.7 : HMG |
5 |
|||
4.8 : Heteromeric CCAAT factors |
9 |
|||
4.9 : Grainyhead |
2 |
|||
4.10: Cold-shock domain factors |
0 |
|||
4.11: Runt |
1 |
|||
0: Others TFs |
... |
... |
1 |
|
For the training set, the counts are made on TFs that have >10 biologically identified binding sites; for the test set, TFs with at least 6 sites are counted.