Relevance of Recovery of known expression-outlier genes and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, OUTRIDER) to "Select a patient-RNA splicing-variant validation workflow"
- Use case
- Select a patient-RNA splicing-variant validation workflow
- Assessed by
- Recovery of known expression-outlier genes and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, OUTRIDER)
- Relevance
- Proxy evidence
- Endpoint
- TP, FN, TN and FP counts with accuracy, precision, recall, F1 and MCC for OUTRIDER with and without 100 GTEx controls
Proxy: expression-outlier recovery of known loss-of-function genes in the same patient RNA-seq, which supports but does not identify splice-altering variants.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
36 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations2 values
| Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations2 values
| Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group silverstein2026-neuromuscular Context-only references | Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group silverstein2026-neuromuscular Context-only references | Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title RNA-seq tools on known diagnoses and true-negative samples, neuromuscular patient RNA-seq (Silverstein et al. 2026) Context-only references | Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title RNA-seq tools on known diagnoses and true-negative samples, neuromuscular patient RNA-seq (Silverstein et al. 2026) Context-only references | Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints3 values
| Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints3 values
| Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint TP, FN, TN and FP counts with accuracy, precision, recall, F1 and MCC for OUTRIDER with and without 100 GTEx controls Context-only references | Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint TP, FN, TN and FP counts with accuracy, precision, recall, F1 and MCC for OUTRIDER with and without 100 GTEx controls Context-only references | Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: needs review
2 source records and release history
- Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) · Original source · medRxiv preprint version 1, posted 2026-01-28; JATS source XML
- Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Original source · medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML)
Technical metadata and extraction receipts
Stable ID: use-case-mapping-rna-splicing-20261011-silverstein2026-expression
- field
- links:assessed_by:rna-splicing-20261011-silverstein2026-protocol-expression
- value
- rna-splicing-20261011-silverstein2026-protocol-expression
- relevance
- proxy
- endpoint
- TP, FN, TN and FP counts with accuracy, precision, recall, F1 and MCC for OUTRIDER with and without 100 GTEx controls
- rationale
- Proxy: expression-outlier recovery of known loss-of-function genes in the same patient RNA-seq, which supports but does not identify splice-altering variants.
- constraints
- Inspect every linked evaluation's source locator and population before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; truth sets, inputs and metrics differ between sources.; Compare tools only where their populations match; Table S9 denominators differ by tool.
- limitations
- OUTRIDER + GTEx was run on muscle only (14 positives); OUTRIDER on muscle and fibroblast (15 positives).; The authors did not develop rMATS-turbo, MINTIE, FRASER, LeafcutterMD, OUTRIDER or the DROP MAE module. ANEVA-h is the authors' own method: two of its authors (K. R. Ganapathy and S. Silverstein) are the first and third authors of reference 36, the ANEVA-h preprint, so the ANEVA-H row is recorded as author_reported.; Positives are counted per known event or gene, negatives per true-negative sample: a negative sample with any reported outlier counts as one false positive. Accuracy, precision and MCC therefore mix event-level and sample-level units (Methods 'True Positive and Negative Detection').; Variants with clinically interpretable mechanisms were selected; the authors state this favours clearly defined events and likely underestimates tool sensitivity, and that binary outlier scoring of negatives may overestimate false-positive rates and lowers MCC (Discussion, limitations paragraph).; Retrospective study of a single centre's neuromuscular cohort; no confidence intervals are printed.; Preprint (medRxiv v1), not peer reviewed.; Table S7 true-negative rows do not reproduce Table S9 rows 7 and 8: read as in Tables S3, S4 and S8 ('YES' = no outlier), Table S7 gives OUTRIDER 8 of 9 negative samples without outliers (Table S9: 4) and OUTRIDER + GTEx 1 of 6 (Table S9: 1 of 5). The prose rates (56% and 83%) match Table S9 for OUTRIDER and Table S7 for OUTRIDER + GTEx.
- citation locators
- source id: rna-splicing-20261011-silverstein2026-source-tables-s1-s10; locator: Table S9 rows 7 and 8; source id: rna-splicing-20261011-silverstein2026-source-article; locator: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7
- source locator
- rna-splicing-20261011-silverstein2026-source-tables-s1-s10: Table S9 rows 7 and 8; rna-splicing-20261011-silverstein2026-source-article: Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7
- headline metric
- recall
- comparison group
- silverstein2026-neuromuscular
- comparison title
- RNA-seq tools on known diagnoses and true-negative samples, neuromuscular patient RNA-seq (Silverstein et al. 2026)
- stratum label
- Expression-outlier caller
- stratum order
- 2
- reason
- Not shown: Table S7 true-negative rows conflict with Table S9 rows 7 and 8 for OUTRIDER and OUTRIDER + GTEx. Kept at needs_review by the independent review (docs/reviews/use-cases/splicing-cnv-use-cases-2026-10-12.md).