predictor discovery in training set 6 training set sjia (24 f, 14 q) poly (15 f, 10 q) 1 dige raw...
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Predictor discoveryin training set
6
Training setSJIA (24 F, 14 Q)POLY (15 F, 10 Q)
1
DIGEraw gel images
SJIA (13 F, 13 Q)POLY (5 F, 5 Q)
Spot findingspot alignment
feature extraction
889 discrete spot features
Classifier training
Ten-foldcross-validation
ClassifySJIA F vs QPOLY F vs Q
DIGE analysis
Prediction analysis of microarray (PAM)
Class predictionin testing set
7
Testing setSJIA (24 F, 14 Q)POLY (15 F, 11 Q)
Predictors of 4 ~ 12 features
PAMclass prediction algorithm
Construct estimates ofpredicted class probabilities
Analysis of goodness of class separation
2
Cluster analysis
7 feature biomarker panel
2d hierarchicalclustering
heatmap plotting
Normalizationmanual review
Manual review
MSMS ID97 spots
P < 10-5
3
Mann Whitney
10 proteincandidates
4
Literature review+ literature candidates- check antibodyavailability
5
12 ELISA assays
Figure 1
8
Prospective StudyN.D.
DiscriminateSJIA F
KDFI
F Q F Q
SJIA POLY
Figure 2
F Q
SJIA
Figure 3
A2MCFHR1ATIIIATIIIGSNA2MGSNTTRAPOA1APOA1APOA1APOA1APOA1APOA1SAPAPOIVHPCRPHPHPHPHPHPHPMRP8MRP8MRP14SAASAASAA
SAPAPOAIVHPCRPHPA2MCFHR1GSNGSNA2MATIIIATIIITTRAPOA1APOA1APOIVAPOA1APOA1APOA1MRP14HPHPHPHPHPMRP8MRP8SAASAASAA
F Q F Q
SJIA POLYFigure 4
POLY QPOLY F POLY QPOLY F
TRAINING TESTING
Figure 5A
SJIA QSJIA F SJIA QSJIA F
TRAINING TESTING
Figure 5B
Figure 6AG
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POLY Training POLY Testing
128754Feature# 128754
Figure 6BG
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SJIA Training SJIA Testing
127654Feature# 8 9 127654 8 9
SJIA QSJIA F SJIA QSJIA F
TRAINING TESTING
Figure 7
Training setn = 38
24 14
Clinicaldiagnosis F Q
n =
PAM
18 5
6 9
Classified as F
Classified as Q
PercentAgreementwith clinicaldiagnosis
75% 64%+ -
71%
Overall
P < 0.05
Testing setn = 38
24 14
Clinicaldiagnosis F Q
n =
PAM
21 4
3 10
Classified as F
Classified as Q
PercentAgreementwith clinicaldiagnosis
88% 71%+ -
82%
Overall
P < 0.001
A B
Figure 8
C
Biomarker panelof 7 members
1. HP
2. APO AI
3. A2M
4. SAP
5. CRP
6. MRP8/MRP14
7. SAA
SJIA SJIA
1213 12
SJIAF KD FI
SAP
SAA
MRP8
MRP14
HP
CRP
APOA1
A2M
Data setn = 27
13
Clinicaldiagnosis
SJIAF
NOT-SJIAF
n =
Unsupervised clustering
10
3
1
23
Clustered as SJIA FClustered
as NOT-SJIA F
PercentAgreementwith clinicaldiagnosis
77% 96%+ -
85%
Overall
P < 10-5
24
Figure 9
Spot Cluster ID Protein ID T test P value Mann Whitney Test P value
6 A2M 1.05 X 10-4 2.31 X 10-6
7 CFHR1 2.31 X 10-4 1.92 X 10-7
3 ATIII 1.73 X 10-6 5.77 X 10-6
2 ATIII 1.17 X 10-6 1.35 X 10-6
1 GSN 7.68 X 10-6 2.31 X 10-6
19 A2M 1.79 X 10-6 5.77 X 10-6
4 GSN 4.23 X 10-6 1.92 X 10-7
21 TTR 2.16 X 10-6 2.31 X 10-6
26 APOA1 1.84 X 10-6 2.31 X 10-6
16 APOA1 3.27 X 10-7 2.31 X 10-6
25 APOA1 4.28 X 10-6 3.85 X 10-7
22 APOA1 1.32 X 10-6 3.85 X 10-7
11 APOA1 1.10 X 10-6 7.69 X 10-7
17 APOA1 3.50 X 10-7 7.69 X 10-7
24 SAP 4.16 X 10-6 3.65 X 10-6
5 APOAIV 1.30 X 10-8 3.65 X 10-6
12 HP 3.93 X 10-9 3.65 X 10-6
14 CRP 8.99 X 10-7 7.69 X 10-7
27 HP 4.03 X 10-7 1.35 X 10-6
20 HP 8.23 X 10-8 8.65 X 10-6
29 HP 1.22 X 10-9 1.35 X 10-6
13 HP 5.38 X 10-11 3.85 X 10-7
28 HP 9.54 X 10-8 1.35 X 10-6
15 HP 8.86 X 10-10 3.85 X 10-7
9 MRP8 2.32 X 10-10 3.85 X 10-7
8 MRP8 1.97 X 10-9 3.85 X 10-7
18 MRP14 2.15 X 10-10 3.85 X 10-7
30 SAA 1.26 X 10-8 3.65 X 10-6
23 SAA 3.03 X 10-9 3.65 X 10-6
10 SAA 1.22 X 10-9 1.35 X 10-6
Supplement Table 1