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Table 1 Significant SNPs, genes, and pathways identified by homoplasy counting

From: Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis

  

Discovery dataset (n = 108)

Validation dataset (n = 214)

SNP-level

 

Strains with SNP (N)

 

Strains with SNP (N)

 

Gene (Rv-number)

Nucleotide change

TBM (n = 54)

PTB (n = 54)

P-value

TBM (n = 52)

PTB (n = 162)

P-value^

Unnamed (Rv0218)

261,869CT

25

10

0.002

21

24

0.001

PPE54 (Rv3343c)

3736,628TG

22

35

0.008

27

87

0.472

PEPGRS19 (Rv1067c)

1,190,093AC

2

11

0.01

5

18

0.487

PEPGRS44 (Rv2591)

2922,848AT

0

6

0.01

2

7

0.625

PPE3 (Rv0280)

340,372TC

2

10

0.025

4

13

0.589

PEPGRS9 (Rv0746)

836,272AG

7

1

0.029

3

9

0.603

PEPGRS26 (Rv1441c)

16,18,978TC

0

5

0.032

2

3

0.369

Unnamed (Rv0064)

713,36GC

24

34

0.034

29

98

0.355

PEPGRS18 (Rv0980c)

1095,644CT

0

4

0.044

2

2

0.238

Gene-level

 

SNPs in gene (N)

 

SNPs in gene (N)

 

Gene (Rv number)

TBM

PTB

P-value

TBM

PTB

P-value

PEPGRS19 (Rv1067c)

2

13

0.004

5

22

0.318

Unnamed (Rv0218)

27

11

0.007

21

32

0.001

PEPGRS26 (Rv1441c)

0

5

0.031

2

4

0.491

glmS (Rv3436c)

0

5

0.031

0

0

n.a.

Unnamed (Rv3740c)

0

4

0.05

3

0

0.011

Pathway-level

 

Genes with mutation (N)

 

Genes with mutation (N)

 

Pathway name

TBM

PTB

P-value

TBM

PTB

P-value

Ethylbenzene degradation

68

54

0.032

65

224

0.071

  1. NOTE. P-values are based on permutation analysis; bold p-values indicate validated, Bonferroni-corrected significant enrichment
  2. ^ P-value thresholds in the validation set were Bonferroni-corrected for multiple testing by dividing them by the number of top hits in the discovery set: SNP-level: p < 0.05/9; gene-level: p < 0.05/5; pathway-level: p < 0.05/1
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BMC Genomics

ISSN: 1471-2164

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