IEP: expression read as function

Reviewing the Inferred from Expression Pattern evidence code

AI Gene Review · projects/IEP · 2026

Bottom line

  • IEP infers a role in a process from a change in the gene's own expression. We surveyed all 25,401 IEP rows in GOA and reviewed 550 in the repo.
  • The typical IEP row is true but peripheral: 22.5% accepted, 55.6% kept as non-core, 16.7% flagged.
  • 1,110 of 1,147 CC rows breaking GORULE:0000006 come from one ECO class and could be fixed by one mapping change.

The question for every IEP row

IEP has the lowest ACCEPT rate after IPI

Seven failure patterns

Pattern Example
Inducible bystander ("response to X" cloud) rat Gstt1, Gsta4, Qdpr
Developmental time-course → tissue term rat Ckmt2 heart development
One screen, one term, N genes PMID:21492153 → 8 genes
Hub inversion: regulator annotated as responder ARATH PIF3
Regulon membership ≠ function ECOLI arnF, yeast THI22
Marker-gene circularity DICDI cotB, mhcA
Wrong granularity, both directions ARATH CRY1/CRY2, SOC1

A batch tested by its own tiers

PMID:25858512: 372 miRNAs detected, 12 changed in LTP, 3 validated. MGI annotated 130 to long-term synaptic potentiation.

Tier miRNA Action
Validated Mir26a-1, Mir384 ACCEPT
Changed, untested Mir30e MARK_AS_OVER_ANNOTATED
Detected only Mir100, Mir127 REMOVE

The tier predicts the verdict. The batch also omits let-7a, one of the three validated miRNAs.

Aspect violations are an ECO-mapping artifact

Caveat: who judged

  • Dispositions come from this repo's AI reviews, primed to look for over-annotation.
  • So rates measure one reviewer population; the cross-code ordering is more trustworthy than any single rate.
  • The worked examples carry the argument. The developmental-vs-stimulus flag gap (22.6% vs 16.8%) is not significant (Fisher p = 0.21).

Status and next steps

  • Done: two-view survey, global atlas, failure-pattern catalogue, ECO diagnosis, miRNA cohort.
  • Open: a developmental-branch cohort; the E. coli PMID:11967071 batch (152 genes → DNA damage response); 22 PENDING rat Casp3 rows; independent disposition data; HEP.

Read more: projects/IEP.md · projects/IEP/iep-corpus-survey.md · projects/IEP/iep-global-atlas.md