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

BMC Bioinformatics

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

	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	–	–	–	–	–	–

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

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