Supplementary Data: PAR(2) — Circadian gene expression hierarchy via AR(2) eigenvalue modulus (GSE54650, 12 mouse tissues)

Supplementary_Table_S1_Dataset_Summaries.csv Dataset summaries — 12 mouse tissues, AR(2) eigenvalue hierarchy statistics Supplementary_Table_S1b_Per_Gene_Eigenvalues.csv Per-gene AR(2) eigenvalue moduli — clock and target genes, all 13 datasets Supplementary_Table_S2_ODE_Validation.csv ODE model validation — AR(2) eigenvalue recovery from five canonical circadian ODE models Supplementary_Table_S3_Literature_Validation.csv Literature validation — 59 curated circadian genes benchmarked against AR(2) rankings Supplementary_Table_S4_Falsification_Test.csv Falsification test — BMAL1 vs. arrhythmic and amplitude-matched controls Supplementary_Table_S5_NonCircadian_Validation.csv Non-circadian validation — immune response and cancer state-transition datasets Supplementary_Table_S6_Monte_Carlo.csv Monte Carlo simulation — eigenvalue hierarchy stability under sampling noise Supplementary_Table_S7_Method_Comparison.csv Method comparison — AR(2) vs. Cosinor vs. JTK_CYCLE, 20,955 liver genes Supplementary_Table_S8_Fit_Diagnostics.csv AR(2) fit diagnostics — exclusion rates, R², RMSE, Ljung-Box, residual normality, 12 tissues Supplementary_Table_S9_AR1_vs_AR2_Benchmarks.csv