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Supplementary Figure 1. DIGE analysis. Cluster analysis. ELISA assays. Prediction analysis (LDA). 1. 3. 2. Predictor discovery in training set. Predictor test in testing set. DIGE raw gel images Matched samples SJIA ( 10 F , 10 Q) POLY (5 F, 5 Q). 2d hierarchical clustering

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Classifier training

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Classifier training

Supplementary Figure 1

DIGE analysis

Cluster analysis

ELISA assays

Prediction analysis (LDA)

1

3

2

Predictor discovery

in training set

Predictor test

in testing set

DIGE

raw gel images

Matched samples

SJIA (10 F, 10 Q)

POLY (5 F, 5 Q)

2d hierarchical

clustering

heatmap plotting

12 ELISA Assay

development

4

5

7

Test to anticipate SJIA F in Q

randomization

Training set

SJIA (12 F, 12 Q)

Testing set

SJIA (10 F, 10 Q)

ELISA assay

FI (27 )

KD (10)

SJIA F(12) FI (15)

9

FDR analysis

ELISA assay

Q->F (5)

Q->Q (10)

Feature selection

Spot finding

spot alignment

feature extraction

15 protein

2d clustering

LDA

Fisher exact test

Normalization

manual review

Classifier

training

Blind

testing

Classifier

training

7 ELISA assay

Clustering

Box-and-Whisker Analysis

Fisher exact test

Fisher exact test

Manual review

Discriminate

SJIA F

SJIA Q

POLY F

POLY Q

Discriminate

SJIA F

KD

FI

Classify

SJIA F vsQ

Classify

SJIA F vsQ

Classify

SJIA F vs FI

MSMS

Protein ID


Classifier training

Supplementary Figure 2

A

B

Patient 1 and Patient 2 whole plasma

3

2

4

1

5

Removed proteins:

1 anti-trypsin

2 albumin

3 serrotransferrin

4 Ig heavy chain

5 Haptoglobin

6 Ig light chain

6

MW/1000

Patient 1 and Patient 2 after protein depletion

Hemoglobin

pH


Classifier training

SJIA

F

Q

C3

AGP1

ACT

SAP

SAA

S100A8

S100A9

HP

CRP

C9

C4

APO-IV

APO-L1

AMBP

KLKB1

VDB

CFH

ATIII

A2M

ATIII

APO-E

APO-D

FGG

FGB

TTR

GSN

APOA1

Figure 1


Classifier training

POLY

F

Q

SJIA

SJIA

SJIA

A

B

F

Q

F

KD

F

FI

0.30

0.25

TTR

CFH

0.20

APO A1

A2M

GSN

False discovery rate (FDR)

0.15

C4

AGP1

ACT

0.10

APO IV

SAP

HP

0.05

CRP

S100A8

S100A9

0.00

SAA

20

1

2

5

10

Number of features called significant

P value: 1.1 E -4

P value: 0.5

P value: 0.19

P value: 1.4 E -4

Figure 2


Classifier training

Goodness of class separation

ÔÇô D probability

SJIA Training

SJIA Test

Feature#

4

5

6

7

8

9

12

4

5

6

7

8

9

12

Figure 3


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