RNA and Protein Tissue Shortlists in a Fixed Atlas

**Background:** Correlations between RNA and protein abundance do not directly specify whether a researcher would select the same tissues from each modality. **Objective:** Compare exploratory top-three tissue sets from restricted mitochondrial relative-pathway RNA scores with protein-abundance comparator sets in the fixed 29-tissue Wang atlas, and identify specified score and membership choices that change that finite comparison. **Methods:** Public processed gene-level measurements were linked to official MitoCarta3.0 terminal memberships. Pathways required at least five uniquely mapped genes with positive, complete measurements in both modalities across all 29 labels. Arithmetic gene means and mean target/reference ratios yielded dimensionless scores. All-gene and nuclear-only panels were evaluated with published abundances and within-gene median scaling. Exact sets, overlap, capture fractions and Jaccard agreement were calculated with an explicit boundary-tie rule; six perturbation families were evaluated separately. An independently coded scalar replay checked all 23,012 scenarios. Pathways and scenarios were not biological replicates; no population tests or sampling intervals were calculated. **Results:** In the published-abundance/all-gene baseline, 8, 29, 16 and 2 of 55 pathways shared zero, one, two and three selected tissues, respectively. Exact recovery occurred for 3 of 55 nuclear-only pathways and 2 of 55 pathways in each median-scaled configuration. In the all-gene published-abundance configuration, replacing the reference aggregation with a geometric reference changed RNA sets for 33 of 55 pathways and protein sets for 38 of 55; excluding individually overlapping references changed each modality for 4 of 55. These are finite, family-specific changes, not uncertainty intervals. **Conclusion:** RNA and protein generally yield different exploratory tissue shortlists under this restricted score. When protein-based relative abundance is the intended atlas-selection target, pathway-specific agreement should be inspected before substituting an RNA shortlist. Protein abundance is a measured comparator, not pathway activity; biological causes, donor-population transfer and prospective tissue-model utility remain untested.