Table 3.
Comparison of R-loop prediction algorithms. The ability of R-looper and R-loop DB algorithms to predict R-loop clusters was analyzed for a range of footprinted loci. Values correspond to the observed over expected ratios for direct intersect or nearest distance. Expected values were generated by shuffling predictions along the amplicon 125 times. Distances or intersects were calculated either to the start (100 bp), end (100 bp) of each footprint or with the whole footprint (middle position for distance). A value of zero indicates that no match was observed or that no prediction was made. ‘na’ indicates that this region was not computed to possible R-loops.
| R-looper |
Distance |
Intersect |
R-loop DB |
Distance |
Intersect |
Location | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Whole | Start | End | Whole | Start | End | Gene | Whole | Start | End | Whole | Start | End | |
| BTF3 | 4.7 | 4.7 | 3.7 | 12.5 | 35.9 | 15 | BTF3 | 4.7 | 4.7 | 4.1 | 5.0 | 3.0 | 4.9 | PROMOTER |
| CNBP | 1.5 | 1.7 | 1.7 | 0.0 | 0.0 | 0.0 | CNBP | 4.3 | 4.5 | 4.3 | 3.7 | 2.9 | 3.8 | PROMOTER |
| EEF2 | 2.6 | 1.7 | 3.1 | 0.1 | 0.0 | 1.0 | EEF2 | 4.7 | 4.7 | 4.3 | 8.1 | 7.4 | 7.5 | PROMOTER |
| GADD45A | 3.7 | 2.4 | 2.6 | 4 | 4.8 | 8.7 | GADD45A | 4.4 | 4.1 | 2.5 | 4.4 | 3.4 | 3.2 | PROMOTER |
| MTERFD3 | 4.2 | 2.7 | 4 | 2.4 | 0 | 2.1 | MTERFD3 | 4.8 | 4.6 | 2.1 | 4.8 | 18.9 | 0.8 | PROMOTER |
| PIN4 | 3.7 | 2.6 | 2.5 | 6.5 | 21.1 | 8.7 | PIN4 | 2.9 | 2.4 | 2.7 | 4.4 | 7.3 | 2.9 | PROMOTER |
| RPL4 | 3.2 | 3.9 | 2 | 0 | 0 | 0 | RPL4 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | PROMOTER |
| Average | 3.4 | 2.8 | 2.8 | 3.6 | 8.8 | 5.1 | Average | 3.7 | 3.6 | 2.9 | 4.3 | 6.1 | 3.3 | PROMOTER |
| CALM3 | 4.1 | 3.9 | 3.4 | 8.4 | 9 | 12.9 | CALM3 | 4.1 | 4.3 | 4.7 | 4.6 | 5.4 | 5.7 | GENEBODY |
| FUS | 4.4 | 3.9 | 4.5 | 8.8 | 19.1 | 29.2 | FUS | 3.3 | 3.2 | 3.8 | 5.0 | 2.4 | 6.3 | GENEBODY |
| KAT5 | 2.8 | 3.1 | 2.3 | 5.8 | 13.3 | 6.8 | KAT5 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GENEBODY |
| MRFAP1L1 | 4.4 | 3.9 | 3.6 | 10 | 2.7 | 4.2 | MRFAP1L1 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GENEBODY |
| POGK | 4.2 | 4.2 | 3 | 3.5 | 28.9 | 2 | POGK | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GENEBODY |
| RPL13A | 4.6 | 4.2 | 4.3 | 14.2 | 20.5 | 36.3 | RPL13A | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GENEBODY |
| RPS24 | 3.9 | 2.2 | 4.1 | 9.6 | 1 | 19.8 | RPS24 | 3.8 | 2.1 | 4.0 | 7.8 | 0.0 | 18.7 | GENEBODY |
| Average | 4.1 | 3.6 | 3.6 | 8.6 | 13.5 | 15.9 | Average | 1.6 | 1.4 | 1.8 | 2.5 | 1.1 | 4.4 | GENEBODY |
| CEP95 | 4.7 | 3.8 | 3.3 | 8.8 | 18.5 | 3.9 | CEP95 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TERMINAL |
| MORF4L2 | 2.8 | 3 | 4 | 4.7 | 24.9 | 0 | MORF4L2 | 4.9 | 4.9 | 4.4 | 6.1 | 11.5 | 2.9 | TERMINAL |
| MYLIP | 4 | 3.7 | 4 | 6.9 | 3.6 | 12.1 | MYLIP | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TERMINAL |
| SNRPN70 | 4 | 3.2 | 4.2 | 6.2 | 8.2 | 24 | SNRPN70 | 3.6 | 2.1 | 4.0 | 4.2 | 12.4 | 1.7 | TERMINAL |
| TRIM33 | 4.5 | 3.3 | 4.3 | 7.5 | 7.1 | 8.1 | TRIM33 | na | na | na | na | na | na | TERMINAL |
| Average | 4.0 | 3.4 | 4.0 | 6.8 | 12.5 | 9.6 | Average | 2.1 | 1.8 | 2.1 | 2.6 | 6.0 | 1.2 | TERMINAL |
All values represent observed/expected ratios.
Observed values were computed by measuring the distances or %intersects between predictions (R-looper and RloopDB) and actual SMRF-seq footprints.
SMRF-seq, single-molecule R-loop footprinting coupled with PacBio sequencing.
Expected values were computed similarly after shuffling predictions 125 times.
Distances or intersects were calculated either to the start (100 bp), end (100 bp) of each footprint or with the whole footprint (middle position for distance).