Biochemistry, Genetics and Molecular Biology› Molecular Biology› Gene expression and cancer classification

Comparative genomics — Mouse ENCODE human–mouse expression comparison

Submitted 2026-10-23

Field: Biochemistry, Genetics and Molecular Biology › Molecular BiologyType: A method hit a wallArea: comparative genomicsTarget: Mouse ENCODE human–mouse expression comparisonStage: replication

Hypothesis

Gene expression data from human and mouse tissues cluster by species rather than by tissue, as the Mouse ENCODE Consortium reported.

What failed

The original design put human and mouse samples on different sequencing runs, so sequencing batch was mixed up with species. After correcting for batch, the samples clustered by tissue, not by species.

Broken assumption

Human and mouse tissues differ more by species than by tissue type in their gene expression.

Why

The study design confounded sequencing batch with species, so the reported species clustering was an artefact.

From the published paper: Gilad et al. F1000Research, 2015. ↗CC BY

Research ideas from this failure

Unvetted lead — read the papers

New hypotheses this failure suggests, each with a crucial experiment, a rival explanation of the original result, and the papers it rests on. Written by AI from paper titles and abstracts found on OpenAlex (and Europe PMC, for life and health sciences).

Related failures (1)

Matched on shared genes, mechanisms and ways of failing as well as wording. Each shows why it matched — treat these as leads rather than verdicts.

down syndromeGene Expression Dysregulated Domains (GEDDs)different research area
Cells with trisomy 21 would show Gene Expression Dysregulated Domains, alternating chromosome segments of higher and lower expression, as Letourneau et al. reported in twins discordant for Down syndrome.
Reanalysis of the original group's stem cell RNA-seq data, and of earlier data from the same twins, did not find these domains. Analysis of Ts65Dn mouse fibroblasts also did not confirm them.
Why it matched: similar wording · failed the same way: Held in the model species, not beyond it

Links in published research

Where this experiment's genes are known to matter outside its own research area, and the papers behind those links. Sources: Open Targets Platform and Europe PMC.