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Table of contents:
- Overview
- Performance Plots
- Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison
- Performance of Mastr(20) - scored lower in this pairwise comparison
- Compile and download dataset for PETfold_pre2.0(20) & Mastr(20) [.zip] - may take several seconds...
Overview
| Metric | PETfold_pre2.0(20) | Mastr(20) | |
|---|---|---|---|
| MCC | 0.570 | > | 0.000 |
| Average MCC ± 95% Confidence Intervals | 0.572 ± 0.022 | > | 0.000 ± 0.000 |
| Sensitivity | 0.534 | > | 0.000 |
| Positive Predictive Value | 0.609 | > | 0.000 |
| Total TP | 7139 | > | 0 |
| Total TN | 44597003 | < | 44608726 |
| Total FP | 6051 | > | 0 |
| Total FP CONTRA | 679 | > | 0 |
| Total FP INCONS | 3905 | > | 0 |
| Total FP COMP | 1467 | > | 0 |
| Total FN | 6221 | < | 13360 |
| P-value | 5.23657817852e-08 | ||
Performance plots
-
Comparison of performance of PETfold_pre2.0(20) and Mastr(20). Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for PETfold_pre2.0(20) and Mastr(20)).
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Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for PETfold_pre2.0(20) and Mastr(20)).
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Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) and Mastr(20). The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for PETfold_pre2.0(20) and Mastr(20)).
Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison
1. Total counts & total scores for PETfold_pre2.0(20)
| Total Base Pair Counts | |
|---|---|
| Total TP | 7139 |
| Total TN | 44597003 |
| Total FP | 6051 |
| Total FP CONTRA | 679 |
| Total FP INCONS | 3905 |
| Total FP COMP | 1467 |
| Total FN | 6221 |
| Total Scores | |
|---|---|
| MCC | 0.570 |
| Average MCC ± 95% Confidence Intervals | 0.572 ± 0.022 |
| Sensitivity | 0.534 |
| Positive Predictive Value | 0.609 |
| Nr of predictions | 27 |
2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| CRW_00298 | 0.58 | 0.54 | 0.63 | 267 | 1620473 | 212 | 31 | 129 | 52 | 227 | |
| CRW_00301 | 0.49 | 0.46 | 0.53 | 240 | 1762048 | 265 | 37 | 178 | 50 | 279 | |
| CRW_00306 | 0.60 | 0.57 | 0.63 | 263 | 1445430 | 208 | 26 | 131 | 51 | 199 | |
| CRW_00310 | 0.55 | 0.51 | 0.59 | 264 | 1805500 | 238 | 32 | 154 | 52 | 257 | |
| CRW_00326 | 0.64 | 0.60 | 0.68 | 299 | 1627669 | 193 | 22 | 120 | 51 | 203 | |
| CRW_00330 | 0.55 | 0.51 | 0.60 | 262 | 1988577 | 231 | 26 | 150 | 55 | 255 | |
| CRW_00332 | 0.51 | 0.48 | 0.56 | 227 | 1769613 | 237 | 20 | 161 | 56 | 250 | |
| CRW_00333 | 0.48 | 0.43 | 0.53 | 220 | 1892069 | 260 | 36 | 160 | 64 | 294 | |
| CRW_00345 | 0.56 | 0.53 | 0.60 | 262 | 1586434 | 224 | 28 | 147 | 49 | 236 | |
| CRW_00346 | 0.59 | 0.55 | 0.63 | 278 | 1584648 | 213 | 32 | 132 | 49 | 223 | |
| CRW_00348 | 0.58 | 0.54 | 0.61 | 272 | 1615059 | 225 | 29 | 143 | 53 | 231 | |
| CRW_00358 | 0.56 | 0.53 | 0.60 | 269 | 1674914 | 228 | 29 | 153 | 46 | 238 | |
| CRW_00366 | 0.60 | 0.56 | 0.64 | 269 | 1579331 | 210 | 25 | 128 | 57 | 213 | |
| CRW_00370 | 0.60 | 0.57 | 0.64 | 288 | 1640315 | 211 | 20 | 143 | 48 | 218 | |
| CRW_00371 | 0.58 | 0.55 | 0.60 | 275 | 1611455 | 232 | 17 | 163 | 52 | 221 | |
| CRW_00372 | 0.59 | 0.55 | 0.62 | 275 | 1625865 | 212 | 23 | 143 | 46 | 223 | |
| CRW_00379 | 0.58 | 0.52 | 0.65 | 277 | 2126526 | 213 | 25 | 125 | 63 | 257 | |
| CRW_00403 | 0.53 | 0.52 | 0.54 | 240 | 1606084 | 283 | 31 | 173 | 79 | 224 | |
| CRW_00411 | 0.58 | 0.54 | 0.61 | 269 | 1615064 | 222 | 21 | 149 | 52 | 227 | |
| CRW_00598 | 0.54 | 0.51 | 0.58 | 250 | 1665793 | 234 | 28 | 154 | 52 | 241 | |
| CRW_00758 | 0.57 | 0.54 | 0.61 | 263 | 1640333 | 241 | 27 | 143 | 71 | 220 | |
| CRW_00759 | 0.56 | 0.53 | 0.59 | 254 | 1636715 | 232 | 18 | 158 | 56 | 227 | |
| CRW_00760 | 0.53 | 0.49 | 0.57 | 239 | 1638533 | 247 | 16 | 167 | 64 | 247 | |
| CRW_00772 | 0.78 | 0.76 | 0.80 | 306 | 945618 | 127 | 7 | 69 | 51 | 98 | |
| CRW_01153 | 0.59 | 0.56 | 0.63 | 283 | 1606076 | 220 | 25 | 144 | 51 | 220 | |
| CRW_01171 | 0.52 | 0.48 | 0.56 | 245 | 1593566 | 240 | 31 | 163 | 46 | 261 | |
| CRW_01300 | 0.60 | 0.55 | 0.67 | 283 | 1693295 | 193 | 17 | 125 | 51 | 232 |
Performance of Mastr(20) - scored lower in this pairwise comparison
1. Total counts & total scores for Mastr(20)
| Total Base Pair Counts | |
|---|---|
| Total TP | 0 |
| Total TN | 44608726 |
| Total FP | 0 |
| Total FP CONTRA | 0 |
| Total FP INCONS | 0 |
| Total FP COMP | 0 |
| Total FN | 13360 |
| Total Scores | |
|---|---|
| MCC | 0.000 |
| Average MCC ± 95% Confidence Intervals | 0.000 ± 0.000 |
| Sensitivity | 0.000 |
| Positive Predictive Value | 0.000 |
| Nr of predictions | 27 |
2. Individual counts for Mastr(20) [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| CRW_00298 | 0.00 | 0.00 | 0.00 | 0 | 1620900 | 0 | 0 | 0 | 0 | 494 | |
| CRW_00301 | 0.00 | 0.00 | 0.00 | 0 | 1762503 | 0 | 0 | 0 | 0 | 519 | |
| CRW_00306 | 0.00 | 0.00 | 0.00 | 0 | 1445850 | 0 | 0 | 0 | 0 | 462 | |
| CRW_00310 | 0.00 | 0.00 | 0.00 | 0 | 1805950 | 0 | 0 | 0 | 0 | 521 | |
| CRW_00326 | 0.00 | 0.00 | 0.00 | 0 | 1628110 | 0 | 0 | 0 | 0 | 502 | |
| CRW_00330 | 0.00 | 0.00 | 0.00 | 0 | 1989015 | 0 | 0 | 0 | 0 | 517 | |
| CRW_00332 | 0.00 | 0.00 | 0.00 | 0 | 1770021 | 0 | 0 | 0 | 0 | 477 | |
| CRW_00333 | 0.00 | 0.00 | 0.00 | 0 | 1892485 | 0 | 0 | 0 | 0 | 514 | |
| CRW_00345 | 0.00 | 0.00 | 0.00 | 0 | 1586871 | 0 | 0 | 0 | 0 | 498 | |
| CRW_00346 | 0.00 | 0.00 | 0.00 | 0 | 1585090 | 0 | 0 | 0 | 0 | 501 | |
| CRW_00348 | 0.00 | 0.00 | 0.00 | 0 | 1615503 | 0 | 0 | 0 | 0 | 503 | |
| CRW_00358 | 0.00 | 0.00 | 0.00 | 0 | 1675365 | 0 | 0 | 0 | 0 | 507 | |
| CRW_00366 | 0.00 | 0.00 | 0.00 | 0 | 1579753 | 0 | 0 | 0 | 0 | 482 | |
| CRW_00370 | 0.00 | 0.00 | 0.00 | 0 | 1640766 | 0 | 0 | 0 | 0 | 506 | |
| CRW_00371 | 0.00 | 0.00 | 0.00 | 0 | 1611910 | 0 | 0 | 0 | 0 | 496 | |
| CRW_00372 | 0.00 | 0.00 | 0.00 | 0 | 1626306 | 0 | 0 | 0 | 0 | 498 | |
| CRW_00379 | 0.00 | 0.00 | 0.00 | 0 | 2126953 | 0 | 0 | 0 | 0 | 534 | |
| CRW_00403 | 0.00 | 0.00 | 0.00 | 0 | 1606528 | 0 | 0 | 0 | 0 | 464 | |
| CRW_00411 | 0.00 | 0.00 | 0.00 | 0 | 1615503 | 0 | 0 | 0 | 0 | 496 | |
| CRW_00598 | 0.00 | 0.00 | 0.00 | 0 | 1666225 | 0 | 0 | 0 | 0 | 491 | |
| CRW_00758 | 0.00 | 0.00 | 0.00 | 0 | 1640766 | 0 | 0 | 0 | 0 | 483 | |
| CRW_00759 | 0.00 | 0.00 | 0.00 | 0 | 1637145 | 0 | 0 | 0 | 0 | 481 | |
| CRW_00760 | 0.00 | 0.00 | 0.00 | 0 | 1638955 | 0 | 0 | 0 | 0 | 486 | |
| CRW_00772 | 0.00 | 0.00 | 0.00 | 0 | 946000 | 0 | 0 | 0 | 0 | 404 | |
| CRW_01153 | 0.00 | 0.00 | 0.00 | 0 | 1606528 | 0 | 0 | 0 | 0 | 503 | |
| CRW_01171 | 0.00 | 0.00 | 0.00 | 0 | 1594005 | 0 | 0 | 0 | 0 | 506 | |
| CRW_01300 | 0.00 | 0.00 | 0.00 | 0 | 1693720 | 0 | 0 | 0 | 0 | 515 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.