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Table 4 Developed clinico-genomic model through the full biomarker-by-treatment interaction Cox model subject to the adaptive lasso penalty

From: Robust estimation of the expected survival probabilities from high-dimensional Cox models with biomarker-by-treatment interactions in randomized clinical trials

Prognostic component
Clinical variables (p = 4) Treatment (−0.889u), ER status (−0.091u), Tumor size (0.175u), Nodal status (0.418u)
Genomic variables (p = 98) ACTB (0.020), ADCYAP1 (0.009), ANGPTL4 (0.034), ARL8A (0.020), BBC3 (−0.088), BDH2 (−0.067), CAPS (0.064), CASC3 (−0.058), CCDC74A (0.080), CDC6 (−0.069),
CDH3 (0.027), CFLP1 (−0.143), CSNK1A1 (−0.079), CSNK1D (−0.063), CXXC5 (−0.141), DHPS (0.148), DNAJC4 (−0.154), DPY19L4 (0.015), ELAVL4 (−0.107), ELN (0.015), ENO1 (0.012), ERBB4 (−0.047), FABP5 (0.063), FAM84B (−0.084), FBXW11 (0.069),
FKSG30 (−0.049), FLJ22659 (0.006), FLJ22795 (0.009), FLJ35390 (0.096), FRAG1 (0.075),
FRMD4A (0.106), GHR (−0.067), GPRIN1 (0.009), GSN (0.039), HIST1H2AA (−0.085), HIST2H2BE (0.009), IDUA (0.038), IGJ (−0.110), IGKV2.24 (0.029), ILF2 (0.014),
KCNE4 (−0.075), KIAA1920 (−0.025), KIF2C (0.093), KRT81 (−0.106), L3MBTL2 (−0.057), LCE3E (−0.101), LOC400590 (−0.021), MAD2L2 (−0.098), MAP3K13 (0.115),
MBOAT2 (0.101), MED13L (−0.090), METTL3 (−0.138), MSI2 (−0.039), MTCH2 (0.018), MVP (0.068), NAT1 (−0.019), NAT10 (−0.085), NDC80 (0.082), NECAB3 (0.075),
NXPH3 (0.001), OGFR (−0.040), PCK2 (−0.061), PGM5 (0.139), PHGDH (0.107),
PITPNC1 (0.089), PRPF40A (0.041), PTTG1 (0.091), RBM14 (0.090), RELB (−0.016), RHBDD1 (−0.070), RND3 (0.022), RPL34 (<0,001), RPS2 (−0.050), SFRP1 (−0.121),
SLC25A28 (−0.057), SLC25A31 (0.154), SLC25A5 (−0.047), SLC30A10 (0.018),
SLC6A19 (−0.056), SMCP (0.055), SOX4 (0.112), SPDEF (0.079), SPP1 (0.090), ST6GALNAC4 (−0.058), STEAP3 (−0.005), STK11IP (−0.009), SULT1A2 (−0.085),
TBXAS1 (<0,001), TCEB2 (0.058), TFRC (−0.132), TMSB10 (−0.096), TRABD (−0.037), TUBB2C (0.103), UBE2W (0.116), UGDH (0.039), XYLT1 (0.082), ZNF592 (0.072), ZNF609 (−0.081)
Treatment-effect modifying component
Genomic variables (p = 24) ATAD3A (−0.100), C16orf14 (0.165), C1orf93 (−0.115), CCL21 (−0.046), CD9 (−0.191), CIAPIN1 (−0.063), CLIC1 (0.148), DKFZP434A0131 (0.167), FAM148A (−0.085),
FNDC4 (0.010), FURIN (0.030), KRTAP2.4 (0.256), MED13L (0.046), MIA (−0.064), MMD (−0.104), ORMDL3 (−0.023), RPLP0 (0.006), SIAH2 (0.123), SLC39A14 (0.007), SSBP2 (−0.099), THOP1 (−0.279), THRAP1 (−0.049), TMEM45B (−0.169), UNC119 (0.017)
Prediction measures
 C-statistic (C) 0.80 (1CV), 0.67 (2CV)
 ΔC-statistic (ΔC) 0.23 (1CV), 0.02 (2CV)
  1. uunpenalized regression coefficient, 1CV and 2CV: single and double cross-validation