Table 2.
Correlations between the estimated TF-binding affinities based on inferred PBEM from in vitro data and the measured TF tag counts from in vivo ChIP-seq experiment
| ChIP-Seq | Called peaks | Rank | Paired PBMs agreement | R (top 500) | R (top 1000) | R (top 2000) | R (all peaks) |
|---|---|---|---|---|---|---|---|
| TF_31 (Zfx) | 10338 | 8 | Good | 0.38978 | 0.35943 | 0.33566 | 0.25502 |
| TF_44 (Gata4) | 16979 | 22 | Good | 0.29675 | 0.28458 | 0.2645 | 0.15614 |
| TF_23 (Tbx20) | 4012 | 33 | Good | 0.077781 | 0.062428 | 0.043291 | 0.043338 |
| TF_25 (Tbx5) | 56352 | 41 | Bad | 0.062865 | 0.090766 | 0.073079 | 0.053016 |
| TF_40 (Esrrb) | 21647 | 59 | Bad | 0.16334 | 0.12283 | 0.10351 | 0.064026 |
In the table, the first column describes ID of mouse TFs in DREAM5 challenges and the TF names to the ChIP-seq experiments; Called peaks are the number of called peaks in the ChIP-seq data; Rank represents rank order of TFs that were sorted in decreasing order of the final performance score across all tested algorithms in Figure 2 of original publication [1]; paired PBMs agreement indicates the agreement between training and testing PBMs; R is square root of R-square statistic from a linear regression model, where the relationship between the predicted TF-binding affinities and the observed ChIP-seq tag counts is investigated.