Table 3.
Number of potentially important TFs in enhancers involved in EPIs identified by SPEID, TargetFinder, or both
| Cell line | Predicted important in both | Only in SPEID | Only in TargetFinder |
|---|---|---|---|
| GM12878 | 22 | 9 | 53 |
| HeLa-S3 | 13 | 15 | 37 |
| HUVEC | 1 | 14 | 7 |
| IMR90 | 4 | 31 | 16 |
| K562 | 27 | 26 | 85 |
| NHEK | 0 | 16 | 5 |
We consider the top 50% most informative features from TargetFinder as important. The two methods have the largest overlap in GM12878 and K562 cell lines, likely because TargetFinder used many more TF ChIP-seq signals for these two cell lines.