Relevance of feng-dna-fm-20261013-protocol-gtex-wb-expression-long-768 to "Select regulatory variants and genes for functional follow-up"

Stable ID: use-case-mapping-feng-dna-fm-20261013-gtex-wb-expression-long-768

field

links:assessed_by:feng-dna-fm-20261013-protocol-gtex-wb-expression-long-768

value

feng-dna-fm-20261013-protocol-gtex-wb-expression-long-768

relevance

proxy

endpoint

Average per-gene Pearson correlation and MSE between predicted and observed whole-blood expression across GTEx subjects, from frozen embeddings of each subject's phased TSS-centred sequence plus a per-gene random forest

rationale

Proxy: tests whether a model's sequence representation captures inter-individual cis-sequence effects on expression, which bears on allele-effect prediction for a locus. It does not score individual variants, link elements to genes or measure perturbation outcomes, which the use case needs.

constraints

Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results.; Compare rows only within this protocol.

limitations

Labels are covariate-corrected whole-blood expression of GTEx subjects, not allele-specific or endogenous perturbation effects, and not in the user's cell type.; Each model's representation is frozen; a random forest is fitted per gene on expression labels, so this measures how much expression variation the embedding plus a supervised head explains, not a label-free variant-effect score.; Individual-level GTEx data are protected (GTEx Protected Data Access application); the benchmark cannot be rerun from public data.; Transcribed from the paper; Feng et al. did not develop the models (independent_paper). No reproduction by Rewire and no human scientific review.; The authors call overall performance modest and say the findings should be considered preliminary indicators (Results, Gene expression prediction, last paragraph).; Subjects are split 75:25 within each gene; no loci, genes or studies are held out, which the use case's validation requirements ask for.; 768 randomly selected genes only; not comparable with the all-gene rows.; Enformer is a supervised expression model used as a comparator.; Caduceus-Ph used the central 131 kb; HyenaDNA-450K and Enformer used the 196 kb window (Methods).

citation locators

source id: evidence-expansion-dna-foundation-models-2025-5d8ca9bc; locator: Table 4; Methods, 'Gene expression prediction datasets' and 'Gene expression prediction benchmark'; Data availability

source locator

evidence-expansion-dna-foundation-models-2025-5d8ca9bc: Table 4

headline metric

pearson-correlation

comparison group

feng-gtex-expression

comparison title

Feng et al. GTEx whole-blood expression prediction

stratum label

768-gene subset, long input

stratum order

2

reason

Add a relevance judgement for the Feng et al. gene-expression protocol (rewire-benchmark-data#19).

reviewed evaluations

feng-dna-fm-20261013-eval-gtex-caduceus-ph-long-sequence-input; feng-dna-fm-20261013-eval-gtex-enformer; feng-dna-fm-20261013-eval-gtex-hyenadna-450k

review

method: ai-assisted-source-review; scope-review; method note: Checked the endpoint against the use case's inputs, output and setting in data/entities/use-cases.jsonl; checked each limitation against Methods, Results, Data availability and Table 4; checked every evaluation on the protocol.; reviewer: claude; reviewer note: Independent Claude (Opus 5.5) review agent, separate from the extraction agent feng-19 that built this batch. Automated review only; no human review claimed. Transcription, not reproduction.; reviewed at: 2026-10-13T14:40:00Z; artifact sha256: 5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12663285/fullTextXML; note: Judgement written by the extraction agent. Independent review: proxy is justified because cross-individual expression prediction bears only on allele-effect prediction, which the use case treats as a separate comparison; it does not score variants or link elements to genes.

pins

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• subject: Select regulatory variants and genes for functional follow-up