Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
Figure 4
Four Sets of Position-Specific DNA-Recognition Preferences in Zinc Fingers
The estimated sets of DNA-recognition preferences for the DNA-binding residues at positions 6, 3, 2, and −1 of the Zinc Finger domain are displayed as sequence logos. At each position, the associated distribution of nucleotides is displayed for each amino acid. The total height of letters represents the information content (in bits) of the position, and the relative height of each letter represents its probability. Color intensity indicates the level of confidence for a given amino acid at a certain position (where paler colors indicate lower confidence due to low occurrences of the amino acid at the specific position in the training data) (see Tables S1 and S2 for full data). Some of the DNA binding preferences are general, regardless of the residue's position within the zinc finger (e.g., lysine's tendency to bind guanine), while others are position-dependent (e.g., the tendency of phenylalanine to bind cytosine only when in position 2).