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Table 7 LASSO Regression

From: Extensive transcriptomic study emphasizes importance of vesicular transport in C9orf72 expansion carriers

Variable Order LASSO Single-Gene
Gene Chr Coef1 Coef2 SE P-value
Age at Onset 1 VEGFA chr6 0.14 7.36 1.61 9.17E-05
Age at Death 1 AUTS2 chr7 0.68 23.86 4.64 1.41E-05
2 TAF8 chr6 7.00 28.34 6.58 1.55E-04
3 NAGS chr17 0.16 10.87 2.58 2.02E-04
4 RP1-130H16.18 chr22 2.88 15.96 3.82 2.23E-04
5 DOCK10 chr2 -1.31 -13.55 3.26 2.38E-04
6 CLEC4E chr12 0.56 4.53 1.09 2.43E-04
7 APOBR chr16 0.88 6.59 1.60 2.71E-04
8 LYST chr1 -5.12 -29.58 7.43 3.86E-04
9 SLC39A11 chr17 0.25 13.82 3.48 3.96E-04
10 RP11-3G21.1 chr8 0.29 6.95 1.78 4.67E-04
11 TIMM13 chr19 -0.38 -22.98 6.48 0.001
12 VCX chrX 3.39 12.55 3.56 0.001
13 SELPLG chr12 0.05 6.55 2.08 0.004
Expansion Size 1 CDKL1 chr14 3.06 21.39 4.52 5.28E-05
2 FAM87A chr8 -0.50 -9.21 2.24 2.94E-04
3 RP11-481 J2.3 chr16 0.64 7.52 2.14 0.001
4 EFCAB14 chr1 -2.38 -34.03 9.98 0.002
Sense RNA Foci 1 CATIP-AS1 chr2 -0.002 -0.10 0.02 6.34E-05
Antisense RNA Foci 1 CCDC127 chr5 0.003 0.16 0.04 0.001
Poly(GP) 1 EEF2K chr16 -10.11 - 495.81 133.94 9.69E-04
Methylation 1 AC006946.16 chr22 -0.03 -8.14 2.05 4.32E-04
2 RP11-555 M1.3 chr3 0.07 4.18 1.33 0.004
3 A1BG chr19 -0.009 -8.69 2.78 0.004
Disease Subgroup 1 TMPPE chr3 0.02 3.03 1.10 0.006
2 EDEM2 chr20 0.93 8.44 3.13 0.007
3 CD37 chr19 -0.39 -6.42 2.41 0.008
4 MZT2B chr2 -1.15 -22.86 8.75 0.009
5 PLK5 chr19 -0.02 -2.52 1.00 0.01
6 NOTUM chr17 -0.32 -4.87 2.30 0.03
Variable Order Gene Chr Coef1 HR CI P-value
Survival after Onset 1 SGSM3 chr22 -0.02 0.10 0.04–0.28 1.31E-05
2 EFNA2 chr19 -0.03 0.19 0.07–0.51 0.001
  1. Genes selected using Least Absolute Shrinkage and Selection Operator (LASSO) regression are shown for variables of interest. The chromosome (Chr) and LASSO coefficient (Coef1) are included. Additionally, the results of the single-gene analysis are displayed for genes identified through LASSO regression, including the coefficient (Coef2), standard error (SE), hazard ratio (HR), 95% confidence interval (CI), and/or p-value. Genes denoted by a bold font are displayed in Fig. 6. Of note, this table has been generated after adjustment for cell-type-specific markers