Table 2 Assessment for the disease activity of TAK patients using the topology structure of the gene co-expression network, the serum biomarkers, and the gene expression level respectively

Patient

Age (year)

Sex

Total score

CD3, p65

CD3, LAG3

CD3, PD-1

Corticosteroid (mg/d))

Other immunosuppressant drugs

y = 0.420x + 0.0755

y = 0.00367x + 0.000253

y = 0.116x− 0.0166

r = 0.926

r = 0.7823

r = 0.7494986

P = 4.4137E−05

P = 0.0044

P = 0.0080

#1

32

F

24

MTX

4

1

0

1

#2

51

F

10

MMF, MTX, INH

1

0

0

0

#3

39

F

0

MMF, MTX

4

0

0

0

#4

34

F

5

HCQ, AZA

4

0

1

0

#5

49

F

7.5

CTX, MTX

7

1

0

1

#6

28

F

7.5

HCQ

5

0

0

0

#7

26

F

45

MMF, CTX

1

0

0

0

#8

59

F

35

MTX

3

0

0

0

#9

37

F

10

MMF, MTX

7

0

1

1

#10

36

F

40

MTX

12

1

1

1

#11

32

F

10

CTX, MTX

9

1

0

1

#12

50

F

15

LEF

9

1

0

1

#13

40

F

15

MMF, MTX

11

1

1

1

#14

25

F

10

MMF, MTX

10

1

1

0

#15

38

F

10

HCQ, AZA

9

0

1

0

#16

34

F

45

MMF, MTX

11

1

1

1

#17

39

F

44

CTX

11

1

1

1

#18

40

F

10

MMF, MTX

6

1

1

1

#19

49

F

10

MTX

12

1

1

1

#20

50

M

0

MMF

9

1

1

0

Threshold

/

/

/

8

0.211

0.211

0.430

Sensitivity

/

/

/

90.9%

90.9%

81.8%

72.7%

Specificity

/

/

/

100.0%

77.8%

77.8%

66.7%

Positive predictive value

/

/

/

100.0%

83.3%

81.8%

72.7%

Negative predictive value

/

/

/

90.0%

87.5%

77.8%

66.7%

Patient

Total score

ESR (mm/h)

hs-CRP (mg/L)

IL-6 (pg/mL)

TNF-α (pg/mL)

Total score

TCR

(ref. range, 0~20)

(ref. range, 0~8.00)

(ref. range, < 5.9)

(ref. range, < 8.1)

mRNA level

#1

1

5

1

4.4

8.8

0

0.143

#2

1

21

2.86

3

7.5

0

0.331

#3

0

11

2.92

2

6.4

0

0.380

#4

0

12

0.84

2

4

2

0.945

#5

0

9

0.17

2

6

0

0.280

#6

0

7

0.91

2

6.1

1

0.305

#7

1

17

0.31

2

11

0

0.346

#8

0

12

0.44

2

4

1

0.195

#9

0

13

0.21

2.4

5.6

0

0.240

#10

0

16

0.77

2

7.8

4

0.685

#11

1

33

5.4

5.8

6.1

2

0.348

#12

1

19

14.7

5.7

8

2

0.423

#13

2

38

7.8

9.3

7.6

3

0.407

#14

2

16

23.7

7.5

4

3

0.893

#15

–

12

3.64

–

–

4

0.735

#16

0

6

0.34

2

5.2

3

0.969

#17

–

23

–

2.1

5.9

3

0.976

#18

1

1

5.85

3.5

24.5

1

0.442

#19

1

5

0.55

2.8

9.5

4

0.555

#20

1

16

8.51

2

5.6

2

0.256

Threshold

0.5

20

8.00

5.9

8.1

1.5

0.393

Sensitivity

77.8%

27.3%

30.0%

20.0%

20.0%

90.9%

/

Specificity

66.7%

88.9%

100.0%

100.0%

77.8%

88.9%

/

Positive predictive value

70.0%

75.0%

100.0%

100.0%

50.0%

90.9%

/

Negative predictive value

75.0%

50.0%

56.3%

52.9%

46.7%

88.9%

/

Patient

CD3, PD-L1

CTLA4, GATA3

PD-L1, GATA3

PD-L1, LAG3

PD-L1, p65

LAG3, p65

GATA3, CD40L

PD-1, p65

PD-1, PD-L1

y = 0.0549x + 0.000255

y = 14.429x + 0.0101

y = 11.58x + 0.0649

y = 0.0674x + 0.000206

y = 6.26x + 0.140

y = 74.5x + 0.183

y = 0.424x + 0.0790

y = 2.20x + 0.254

y = 0.294x + 0.023

r = 0.899

r = 0.902

r = 0.809

r = 0.879

r = 0.843

r = 0.769

r = 0.858

r = 0.750

r = 0.746

P = 0.00017

P = 0.00014

P = 0.0026

P = 0.00037

P = 0.0011

P = 0.0057

P = 0.00072

P = 0.0078

P = 0.0084

#1

0

0

0

1

0

0

0

0

1

#2

0

0

0

0

0

0

0

1

0

#3

1

1

1

0

1

0

0

0

0

#4

1

0

1

0

0

0

0

0

1

#5

0

0

1

1

1

0

0

1

1

#6

0

1

1

1

0

0

1

0

1

#7

0

0

0

0

1

0

0

0

0

#8

1

0

0

0

0

1

0

1

0

#9

0

0

1

1

1

1

0

0

1

#10

1

1

1

1

1

1

1

1

1

#11

1

1

1

0

1

1

1

0

1

#12

1

1

1

0

1

0

1

1

1

#13

1

0

1

1

1

1

1

1

1

#14

1

1

1

1

1

1

1

0

1

#15

1

1

1

1

1

0

1

1

1

#16

1

1

1

1

1

1

1

0

1

#17

1

0

1

1

1

1

1

1

1

#18

0

0

1

0

0

0

1

0

1

#19

1

1

1

1

1

1

1

1

1

#20

1

0

1

1

1

1

0

1

1

Threshold

0.279

0.173

0.701

0.226

0.281

0.242

0.318

0.281

0.363

Sensitivity

90.9%

63.6%

100.0%

72.7%

90.9%

72.7%

90.9%

63.6%

100.0%

Specificity

66.7%

77.8%

44.4%

55.6%

55.6%

77.8%

88.9%

66.7%

44.4%

Positive predictive value

76.9%

77.8%

68.8%

66.7%

71.4%

80.0%

90.9%

70.0%

68.8%

Negative predictive value

85.7%

63.6%

100.0%

62.5%

88.3%

70.0%

88.9%

60.0%

100.0%

Patient

Score

mRNA level

Score

mRNA level

Score

mRNA level

Score

#1

0

0.010

0

0.018

0

0.0007

0

#2

0

0.017

0

0.047

0

0.0006

0

#3

0

0.032

0

0.060

0

0.0022

0

#4

1

0.036

1

0.056

0

0.0013

0

#5

0

0.032

0

0.063

0

0.0020

0

#6

0

0.020

0

0.095

1

0.0010

0

#7

0

0.016

0

0.038

0

0.0017

0

#8

0

0.021

0

0.089

1

0.0019

0

#9

0

0.027

0

0.066

0

0.0023

0

#10

1

0.062

1

0.073

1

0.0030

1

#11

0

0.036

1

0.052

0

0.0028

1

#12

1

0.031

0

0.089

1

0.0013

0

#13

1

0.033

1

0.042

0

0.0037

1

#14

1

0.074

1

0.042

0

0.0037

1

#15

1

0.035

1

0.075

1

0.0073

1

#16

1

0.051

1

0.040

0

0.0075

1

#17

1

0.088

1

0.097

1

0.0019

0

#18

1

0.029

0

0.028

0

0.0009

0

#19

1

0.035

1

0.077

1

0.0043

1

#20

0

0.034

1

0.065

0

0.0038

1

Threshold

/

0.033

/

0.069

/

0.0025

/

Sensitivity

81.8%

/

81.8%

/

45.50%

/

72.7%

Specificity

88.9%

/

88.9%

/

77.8%

/

100%

Positive predictive value

90.0%

/

90.0%

/

71.4%

/

100%

Negative predictive value

80.0%

/

80.0%

/

53.8%

/

75%