Table 1.
Prediction results of TFs with good PBM quality by using BayesPI2 energy-independent model and energy-dependent model including dinucleotide interactions
| TF family | Rank | CorrCoef (Ind) | Length (Ind) | Number (Ind) | CorrCoef (Dep) | Length (Dep) | Number (Dep) | |
|---|---|---|---|---|---|---|---|---|
| TF_7 | bHLH | 1 | 0.78 | 13 | 1 | 0.786 | 10 | 1 |
| TF_26 | bHLH | 2 | 0.66 | 10 | 1 | 0.67 | 13 | 1 |
| TF_56 | C2H2 Z F(4) | 3 | 0.76 | 12 | 1 | 0.788 | 13 | 1 |
| TF_55 | AT hook | 4 | 0.8 | 8 | 1 | 0.8 | 9 | 1 |
| TF_17 | NR | 5 | 0.76 | 9 | 1 | 0.757 | 8 | 1 |
| TF_11 | NR | 6 | 0.826 | 10 | 1 | 0.833 | 10 | 1 |
| TF_16 | Myb/SANT | 7 | 0.808 | 10 | 1 | 0.817 | 9 | 1 |
| TF_31 | C2H2 ZF (13) | 8 | 0.585 | 12 | 1 | 0.59 | 11 | 1 |
| TF_15 | Pou + Homeo | 9 | 0.62 | 11 | 1 | 0.655 | 11 | 1 |
| TF_45 | Myb/SANT | 11 | 0.8 | 12 | 1 | 0.78 | 11 | 1 |
| TF_42* | Forkhead | 12 | 0.75 | 12 | 1 | 0.805 | 13 | 1 |
| TF_64 | C2H2 ZF (3) | 13 | 0.75 | 8 | 1 | 0.75 | 10 | 1 |
| TF_52 | NR | 14 | 0.807 | 12 | 1 | 0.79 | 10 | 1 |
| TF_3* | Forkhead | 16 | 0.67 | 10 | 1 | 0.724 | 11 | 1 |
| TF_27* | bZIP | 17 | 0.526 | 9 | 1 | 0.635 | 11 | 1 |
| TF_18 | Sox | 18 | 0.638 | 8 | 1 | 0.677 | 8 | 1 |
| TF_22* | T-box | 19 | 0.675 | 9 | 1 | 0.746 | 12 | 1 |
| TF_47 | Homeo | 21 | 0.726 | 12 | 1 | 0.767 | 11 | 1 |
| TF_44 | GATA | 22 | 0.633 | 12 | 1 | 0.68 | 10 | 1 |
| TF_28 | C2H2 ZF (8) | 23 | 0.58 | 11 | 1 | 0.6 | 11 | 1 |
| TF_13* | Pou + Homeo | 24 | 0.584 | 9 | 1 | 0.675 | 13 | 1 |
| TF_5 | C2H2 ZF (3) | 25 | 0.59 | 10 | 1 | 0.618 | 11 | 1 |
| TF_43 | Forkhead | 27 | 0.577 | 10 | 1 | 0.614 | 12 | 1 |
| TF_19 | Sox | 29 | 0.559 | 8 | 1 | 0.59 | 11 | 1 |
| TF_39 | C2H2 ZF (3) | 30 | 0.63 | 11 | 1 | 0.668 | 13 | 1 |
| TF_51* | Pou + Homeo | 31 | 0.615 | 12 | 1 | 0.67 | 13 | 1 |
| TF_23 | T-box | 33 | 0.64 | 12 | 1 | 0.66 | 13 | 1 |
| TF_12* | NR | 35 | 0.55 | 13 | 1 | 0.606 | 13 | 1 |
| TF_49 | NR | 34 | 0.675 | 10 | 1 | 0.676 | 11 | 1 |
| TF_53* | RFX | 39 | 0.696 | 12 | 1 | 0.77 | 13 | 1 |
| TF_14 | Myb/SANT | 40 | 0.6 | 8 | 1 | 0.62 | 9 | 1 |
| TF_48 | NR | 43 | 0.755 | 12 | 1 | 0.78 | 12 | 1 |
| TF_38 | DM | 45 | 0.67 | 9 | 1 | 0.689 | 8 | 1 |
| TF_32 | C2H2 ZF (6) | 55 | 0.587 | 9 | 1 | 0.62 | 8 | 1 |
In the table, the 34 TFs were classified by applying fuzzy neuronal gas algorithm on the paired PBM quality-control parameters (i.e. the length of the major and minor axes of the PCA ellipses), where a good agreement between training and testing PBMs indicates good PBM data quality; Rank means TFs are sorted in decreasing order of their final performance score across all tested algorithms in Figure 2 of original publication [1]; CorrCoef , Length, and Number are Pearson correlation between predicted intensities and testing probe intensities, the length of motif, the first or second motif, respectively; (Ind) and (Dep) represent BayesPI2 energy-independent model and energy-dependent model including dinucleotide interaction, respectively; TFs marked by star and bold text indicate that the increase in Pearson correlation coefficient is greater than 0.05 by using BayesPI2 energy-dependent model including dinucleotide interaction energies.