Table 2.
Number of TF clusters (out of 503) predicted by both SPEID and PEP, only SPEID, and only PEP, to be in the top 10% feature importance in enhancers and promoters, in each cell line
| Cell line | Top 5% in both | Only in SPEID | Only in PEP |
|---|---|---|---|
| GM12878 | 22 | 28 | 26 |
| HeLa-S3 | 16 | 34 | 22 |
| HUVEC | 20 | 29 | 27 |
| IMR90 | 23 | 27 | 26 |
| K562 | 18 | 32 | 30 |
| NHEK | 14 | 36 | 17 |
| Chance | 5 | 45 | 45 |
Rows do not always sum to 50 due to exclusion of ties at the 10% cutoff, especially in PEP, whose feature importance scores are given in increments of 5%. For comparison, we have also provided chance values (e.g., if SPEID’s feature importance scores were randomly shuffled).