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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 - PowerPoint PPT Presentation
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Classifier training
FDR analysis
Predictor discoveryin training set
4
Training setSJIA (12 F, 12 Q)
1
DIGEraw gel images
Matched samplesSJIA (10 F, 10 Q)POLY (5 F, 5 Q)
Spot findingspot alignment
feature extraction
Classifier training
ClassifySJIA F vs Q
DIGE analysis Prediction analysis (LDA)
Predictor testin testing set
5
Testing setSJIA (10 F, 10 Q)
2
Cluster analysis
2d hierarchicalclustering
heatmap plotting
Normalizationmanual review
Manual review
MSMS Protein ID
3
15 protein2d clustering
12 ELISA Assay development
Feature selection
7
DiscriminateSJIA F
KDFI
Supplementary Figure 1
ClusteringBox-and-Whisker Analysis
DiscriminateSJIA FSJIA QPOLY FPOLY Q
ELISA assays
7 ELISA assay
ELISA assayFI (27 )KD (10)
9
ELISA assayQ->F (5)Q->Q (10)
Test to anticipate SJIA F in Q
LDAFisher exact test
randomization
Blind testing
ClassifySJIA F vs Q
Fisher exact test
SJIA F(12) FI (15)
ClassifySJIA F vs FI
Fisher exact test
number spot label Protein biomarker
1 1 (a,b) APO-AI2 2 GSN3 3 TTR4 4 FGB5 5 FGG6 6 APO-D7 7 APO-E8 8 (a,b) ATIII9 9 (a,b) A2M10 10 (a,b) CFH11 11 VDB12 12 KLKB113 13 (a,b) AMBP14 14 APO-AIV15 15 APO-L16 16 (a,b,c) C417 17 (a,b) C918 18 CRP19 19 (a,b,c) HP20 20 S100A921 21 S100A822 22 (a,b) SAA23 23 SAP24 24 ACT25 25 AGP126 26 C3
Supplementary Figure 2
pH
MW
/100
0
1 anti-trypsin
2 albumin
3 serrotransferrin
4 Ig heavy chain
5 Haptoglobin
6 Ig light chain
Removed proteins:
Patient 1 and Patient 2 whole plasma
Patient 1 and Patient 2 after protein depletion
213
45
6
A B
Hemoglobin
213
45
6
S100A8/S100A9
Rela
tive
DIGE
MEA
SURE
MEN
TS
F KD FISJIA
APOA1 SAPCRP HP S100A9 SAAS100A8A2M
Q
Supplementary Figure 3
F KD FISJIA
APOA1 SAPCRP HP SAAA2M
Q
Rela
tive
ELIS
A M
EASU
REM
ENTS
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