Classifier training FDR analysis Predictor discovery in training set 4 Training set SJIA (12 F, 12...
5
Classifier training FDR analysis Predictor discovery in training set 4 Training set SJIA (12 F, 12 Q) 1 DIGE raw gel images Matched samples SJIA (10 F, 10 Q) POLY (5 F, 5 Q) Spot finding spot alignment feature extraction Classifier training Classify SJIA F vs Q DIGE analysis Prediction analysis (LDA) Predictor test in testing set 5 Testing set SJIA (10 F, 10 Q) 2 Cluster analysis 2d hierarchical clustering heatmap plotting Normalization manual review Manual review MSMS Protein ID 3 15 protein 2d clustering 12 ELISA Assay development Feature selection 7 Discriminate SJIA F KD FI Supplementary Figure 1 Clustering Box-and-Whisker Analysis Discriminate SJIA F SJIA Q POLY F POLY Q ELISA assays 7 ELISA assay ELISA assay FI (27 ) KD (10) 9 ELISA assay Q->F (5) Q->Q (10) Test to anticipate SJIA F in Q LDA Fisher exact test randomizatio n Blind testing Classify SJIA F vs Q Fisher exact test SJIA F(12) FI (15) Classify SJIA F vs FI Fisher exact test
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Transcript of Classifier training FDR analysis Predictor discovery in training set 4 Training set SJIA (12 F, 12...
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
21
3
45
6
A B
Hemoglobin
21
3
45
6
Figure 1
F Q
SJIA
APOA1
GSN
APO-D APO-EATIII
A2M
ATIIICFH
TTR
VDBKLKB1AMBP
APO-L1 APO-IVC4
C9
CRP
HP
S100A9S100A8
SAA
SAPAGP1 C3
ACT
FGGFGB
SAAS100A9S100A8
CRPHP
SAPAPO IV
ACTAGP1
C4GSNA2M
APO A1CFHTTR
Figure 2
0.00
1 2 5 10 20
Number of features called significant
Fal
se d
isco
very
rat
e (F
DR
)
0.05
0.10
0.15
0.20
0.25
0.30F QSJIA
F QPOLY
KDSJIAF FI
SJIAF
P value: 1.1 E -4 P value: 0.5 P value: 0.19 P value: 1.4 E -4
A B
Go
od
nes
s o
f cl
ass
sep
arat
ion
– D
pro
bab
ilit
y
SJIA Training SJIA Test
127654Feature# 8 9 127654 8 9
Figure 3
