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Table 2 Genes selected by elastic-net regularized multinomial logistic regression for the association between the genes and the dominant genotypes of M.tb strains

From: Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line

  Gene Symbol Elastic net Fold Regulation (L3-CAS1 vs. Con.) Adjusted P-value (L3-CAS1 vs. Con.) Fold Regulation (L4.5 vs. Con.) Adjusted p value (L4.5 vs. Con.) Fold Regulation (L4.5 vs. L3-CAS1) Adjusted p value (L4.5 vs. L3-CAS1)
1 CFLAR 100%  − 1.544 0.082 1.376 0.117 2.125 0.044
2 TIFA 93.9%  − 1.392 0.199  − 1.206 0.399 1.154 0.256
3 HRAS 91.8% 3.279 0.0001 6.681 0.0001 2.038 0.001
4 IRAK1 82.36% 1.395 0.082 1.136 0.503  − 1.228 0.256
5 CD14 77.93% 4.724 0.0001  − 1.217 0.171  − 5.749 0.0001
6 BTK 67.28%  − 4.258 0.055  − 440.602 0.001  − 103.476 0.0001
7 MAPK8IP3 59.63%  − 13.117 0.0002  − 12.323 0.0003 1.064 0.114
8 IFNG 55.51%  − 24.028 0.0001  − 9.426 0.0002 2.549 0.001
9 JUN 41.91% 3.146 0.0001 12.582 0.0002 3.999 0.001
10 IL1A 39.77% 2.204 0.0001 3.160 0.0001 1.434 0.081
11 CD80 33.64%  − 3.630 0.0001  − 5.856 0.0002  − 1.613 0.044
12 PSIP1 31.03%  − 3.972 0.045  − 2.075 0.126 1.914 0.011
13 PTGS2 29.73% 40.880 0.0001 84.449 0.0001 2.066 0.001
14 BCL3 26.79%  − 12.098 0.035  − 1.617 0.188 7.482 0.0001
15 HSPA1A 26.63% 10.581 0.0001 4.009 0.0002  − 2.639 0.001
16 RHOA 26.27%  − 1.245 0.055 1.526 0.003 1.900 0.011
17 CCL2 26.23% 2.023 0.045 5.993 0.0002 2.962 0.001
18 CXCL8 24.92% 6.364 0.0001 20.966 0.0001 3.294 0.0001
19 HSPD1 23.79% 7.345 0.0001 9.759 0.0002 1.329 0.114
20 TLR2 22.52%  − 8.980 0.0001 1.651 0.0017 14.826 0.0001
21 EGFR 21.83%  − 3.547 0.035 1.286 0.433 4.561 0.0001
Misclassification error rate   14.8%
lambda   0.00849
Alpha   0.50
  1. Lambda is the tuning parameter and it is for controlling the overall strength of the penalty. Alpha is a controlled parameter between LASSO (L1) and ridge (L2) penalties. Alpha = 0.5 corresponds to elastic-net regularization. Importance value for each selected gene was reported, p values adjusted by Benjamini-Hochberg-FDR correction at α = 0.05