validate_gene_trait
Put a hypothesis of the form "gene G is involved in trait T" through POPPER-style sequential falsification on two public tables, each test fixed in advance and run in a fixed order. (1) GTEx v8 expression: either G's co-expression across the 54 tissues with the trait's own gene(s), such as IL2 for IL-2 production, or G's expression in named tissues against its own elsewhere. (2) The GWAS Catalog: how many studies place an association inside G for traits in the named GWAS Catalog categories. Each p is G's rank among the 19,107 protein-coding genes GTEx measures, so it is exact under the null that G is just another gene, with no model of how expression or GWAS hits are distributed. Each p becomes an e-value (κ calibrator), the running product is the evidence, and testing stops at the first product above 1/α, which is POPPER's own sequential stop. Benchmarked on POPPER's TargetVal (Schmidt et al. 2022 CRISPR screens): it holds Type-I below α and has far less power than an agent writing its own tests, because two tables answer fewer questions; the result says which tests were run and what each could and could not show.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gene | Yes | the hypothesis gene, as its current HGNC symbol (protein-coding). | |
| alpha | No | the level the sequential test stops and decides at: supported when the product of e-values exceeds 1/α. | |
| kappa | No | κ of the p-to-e calibrator e = κ·p^(κ−1). Advanced. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| tissues | No | tissue test: GTEx tissue names where involvement implies higher expression, such as Whole Blood or Spleen. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| categories | Yes | GWAS Catalog parent categories an involved gene's associations should fall in, such as Immune system disorder. | |
| trait_genes | No | co-expression: the trait's own gene(s) as HGNC symbols, such as IL2 for IL-2 production. | |
| expression_test | No | which GTEx test: co-expression with the trait's own gene(s), or expression in named tissues against the gene's own elsewhere. One only, because both read GTEx and one table is one piece of evidence. Values: coexpression (Co-expression with the trait's gene), tissue (Expression in named tissues). | coexpression |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| e | Yes | the stopped product of e-values: the evidence against "G is just another gene" | |
| tests | Yes | every falsification test in its registered order: what it reads, its statistic, G's value, its rank among the genes and its p, and whether it was run before the stop | |
| result | Yes | the full result | |
| nullRate | Yes | these settings' own Type-I rate: how many of the universe's genes, each taken as the hypothesis, the same test would support | |
| supported | Yes | whether the stopped product of e-values exceeds 1/α |