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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,

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Presentation on theme: "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,"— Presentation transcript:

1 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 randomization Blind testing Classify SJIA F vs Q Fisher exact test SJIA F(12) FI (15) Classify SJIA F vs FI Fisher exact test

2 numberspot label Protein biomarker 11 (a,b)APO-AI 22GSN 33TTR 44FGB 55FGG 66APO-D 77APO-E 88 (a,b)ATIII 99 (a,b)A2M 1010 (a,b)CFH 11 VDB 12 KLKB1 1313 (a,b)AMBP 14 APO-AIV 15 APO-L 1616 (a,b,c)C4 1717 (a,b)C9 18 CRP 1919 (a,b,c)HP 20 S100A9 21 S100A8 2222 (a,b)SAA 23 SAP 24 ACT 25 AGP1 26 C3 Supplementary Figure 2 pH MW/1000 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 2 1 3 4 5 6 AB Hemoglobin 2 1 3 4 5 6

3 Figure 1 FQ SJIA APOA1 GSN APO-D APO-E ATIII A2M ATIII CFH TTR VDB KLKB1 AMBP APO-L1 APO-IV C4 C9 CRP HP S100A9 S100A8 SAA SAP AGP1 C3 ACT FGG FGB

4 SAA S100A9 S100A8 CRP HP SAP APO IV ACT AGP1 C4 GSN A2M APO A1 CFH TTR Figure 2 0.00 12510 20 Number of features called significant False discovery rate (FDR) 0.05 0.10 0.15 0.20 0.25 0.30 FQ SJIA FQ POLY KD SJIA FFI SJIA F P value: 1.1 E -4P value: 0.5P value: 0.19P value: 1.4 E -4 AB

5 Goodness of class separation –  probability SJIA TrainingSJIA Test 127654 Feature# 8912765489 Figure 3

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