Metabolic Pathway Analysis

Related to Figure 3.

This section scores and compares five metabolic pathways — OXPHOS, glycolysis, TCA cycle, fatty acid oxidation (FAO), and the pentose phosphate pathway (PPP) — across the Ren1c+/- knockout and captopril-treated SMMHC-CreERT2 models. The analysis builds on the Seurat objects produced in sections 3 and 4.

Steps

  1. Metabolic gene sets and functions — define OXPHOS, glycolysis, TCA, FAO, and PPP gene lists; load Hallmark gene sets from MSigDB; define calcMetabolicScores and calcStatistics
  2. Score metabolic pathways — apply UCell scoring across both models, run Wilcoxon rank-sum tests, compute Cohen's d effect sizes, and export results
  3. FAO sub-signature decomposition — split FAO genes into transport/CPT1, mitochondrial β-oxidation, and peroxisomal sub-groups; score each with UCell; compute per-sub-group effect sizes and gene-level dot plots