PANTHER and PhD-SNPg: Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) reverses the order
- Low severity
- Not yet reviewed
- Ordering reversal
- Different tasks across studies
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PANTHER above PhD-SNPg in 6 of 6 comparisons; other studies rank PhD-SNPg above PANTHER in 6 of 6.
An automatic lead, not a finding of error. The results below are shown as published, everywhere on the site, until a reviewer decides otherwise.
Which studies agree
Clinical likelihood ratios and balanced… ranks PhD-SNPg above PANTHER in all 6 of its comparisons. Livesey and Marsh 2025 ranks PANTHER above PhD-SNPg in all 6 of its comparisons.
- Rank PhD-SNPg higher (1): Clinical likelihood ratios and balanced…
- Rank PANTHER higher (1): Livesey and Marsh 2025 (disagrees)
- Mixed (0): none
Each paper sits where at least two thirds of its comparisons point; Mixed means neither model reaches two thirds. The larger, outlined dot is the paper that disagrees.
| Paper | Role | Ranks PhD-SNPg higher | Ranks PANTHER higher | Ties |
|---|---|---|---|---|
| Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) and 1 more record · DOI | Disagrees | 0 | 6 | 0 |
| Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes and 1 more record · DOI | Agrees | 6 | 0 | 0 |
Comparisons in Livesey and Marsh 2025 (6)
| Protocol | Dataset | Metric | PhD-SNPg | PANTHER | Higher |
|---|---|---|---|---|---|
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS sets | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, 36 human DMS sets), percent | 18.9 | 44.4 | PANTHER |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS sets | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), |Spearman| with DMS on shared variants, 36 human DMS sets), percent | 0.667 | 1.86 | PANTHER |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, direct assays only | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, direct DMS assays only), percent | 20.1 | 44.1 | PANTHER |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, indirect assays only | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, indirect DMS assays only), percent | 18.1 | 44.6 | PANTHER |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions only | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, SNV-accessible substitutions only), percent | 18.9 | 45.7 | PANTHER |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions with gaps filled | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS, SNV-accessible substitutions, missing predictions filled with the VEP's most benign score), percent | 20.4 | 37.7 | PANTHER |
Comparisons in Clinical likelihood ratios and balanced… (6)
What disagrees
- Other studies
- rank PhD-SNPg above PANTHER in 6 of 6 comparisons
- This study
- ranks PANTHER above PhD-SNPg in 6 of 6 comparisons
- Compared
- PANTHER, PhD-SNPg
- Study that disagrees
- Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML), Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8)
- Other studies
- Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes, Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx)
- Rule
- Ordering reversal; different tasks across studies
- Model identity
- Matched across studies partly through links not yet reviewed
The compared numbers
Each value links to its result record and source. Compare values within one protocol; the rule compares rankings, not raw values across protocols.
Follow-up
Current state: Not yet reviewed.
No one has reviewed this finding yet.
How to help resolve this
If you know why these studies disagree, for example a different population, metric or preprocessing step, or you have a corrected value, tell us through the contribution form. A reviewer checks every submission against its source before anything changes, and the step is added to the follow-up above.
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