Traceable Claims in Bioinformatics

 Quick Analysis Plan Copied

 Long Analysis Plan

Confound module design: LOXL2b/stiffness vs gata4+ expansion

The core confound to visualize is stiffness: lesion-site stiffness rises sharply in gata4 wcm6/wcm6 mutants (388.4 ± 62.7 vs 256.9 ± 33.2 Pa WT) while distal tissue stiffness is unchanged (196.2 ± 70.7 vs 206.9 ± 24.9 Pa), localizing the mechanical phenotype to the lesion rather than a global tissue property (WT n=11, mutant n=12) AFM lesion vs distal stiffness data.

Second, plot the temporal cross-linking signal against gata4+ cell-state readouts: LOXL2b TMR-O activity rises +70% (1 wpi) and +100% (2 wpi) in mutants, while 44.3% of Gata4+ cells are EdU+ and 76% co-express Sox2 at 1 wpi — useful for testing whether ECM cross-linking tracks mutant status independently of the Gata4+ proliferative expansion TMR-O cross-linking and Gata4+ cell metrics.

Analysis plan. (1) Encode genotype, region (lesion/distal), and wpi as tidy columns; test stiffness with genotype × region two-way ANOVA (statsmodels) to confirm region-specific interaction. (2) Correlate per-animal TMR-O intensity with bridge diameter (glial −52.1%, axonal −51.4% at 2 wpi) to check whether cross-linking explains bridging deficits beyond genotype. (3) Include BAPN rescue groups (WT n=11, mutant n=7, mutant+BAPN n=9) as a causal confound control: if BAPN normalizes bridging without restoring gata4+ expansion, stiffness is downstream, not a driver of proliferation. (4) snRNA-seq (4,626 nuclei, Seurat) ECM-receptor GSEA enrichment in mutant glia provides transcriptomic corroboration BAPN rescue and snRNA-seq ECM enrichment.

Blindspots. The wcm6 allele is global, so glial-cell-type attribution is confounded; no direct ChIP for Gata4 at loxl2b; BAPN is not LOXL2b-exclusive; per-animal stiffness–crosslinking pairing is needed to move from group means to correlation. Bridging recovers by 4 wpi despite sustained mechanical changes, so 2 wpi snapshots may overstate permanence.