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Protein Profiling and Prediction Analysis for Systemic Juvenile Idiopathic Arthritis

This study investigates predictive protein clustering in SJIA with ELISA assays. Predictor discovery in training set and testing, DIGE gel images matched samples (SJIA, POLY), hierarchical clustering. ELISA assay development and testing for SJIA anticipation. Feature selection, protein clustering, classifier training, blind testing, SJIA discrimination and classification. Normalization, Fisher exact test, manual review, discriminate SJIA subclasses, classification with MSMS protein ID. Supplementary figures detail the experimental setup, protein depletions, and measurement comparisons.

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Protein Profiling and Prediction Analysis for Systemic Juvenile Idiopathic Arthritis

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  1. 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 vs Q Classify SJIA F vs Q Classify SJIA F vs FI MSMS Protein ID

  2. 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 3 2 4 1 5 Hemoglobin 6 pH

  3. SJIA SJIA F Q KD FI F Q KD FI Relative DIGE MEASUREMENTS Relative ELISA MEASUREMENTS A2M APOA1 CRP HP S100A9 S100A8 SAA SAP A2M APOA1 CRP HP S100A8 /S100A9 SAA SAP Supplementary Figure 3

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