Integrated Trait–Gene Analysis Methods

Methods and reported support

TWAS · FUSION

Tests genetically predicted expression, splicing, or APA usage against a trait. Available enet, lasso, and top1 models are evaluated; displayed results pass the configured Bonferroni rule.

SMR and HEIDI

Tests evidence compatible with a shared genetic effect, while HEIDI provides a separate heterogeneity assessment. Pleiotropy and linkage remain possible explanations.

Colocalization

Reports posterior probabilities PP.H0–PP.H4. PlantQTLdb displays shared-signal support at PP.H4 ≥ 0.5.

EWAS · MOMENT

Tests measured molecular feature–trait association under the configured genetic background model. Displayed results use P ≤ 1 × 10⁻³ and pass result-level quality rules.

Interpretation limits

These methods answer related but non-identical questions. Their results should be compared within the same dataset, trait, and molecular layer and interpreted together with locus structure and biological knowledge.