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Supplementary Table S3. Differentially Expressed Genes Between Responders and Non-Responders

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Spassova et al.: Supplementary materials and methods Supplementary Table S3. Differentially expressed genes between responders and non-responders # Gene Function Gene Ontology Classification 1 CCL5 Chemokine ligand 5, chemotactic GO:0010536 positive regulation of activation of Janus kinase for T-cells activity;GO:2000503 positive regulation of natural killer cell chemotaxis;GO:0010820 positive regulation of T cell chemotaxis 2 LAG3 Lymphocyte-activation gene 3, GO:0045085 negative regulation of interleukin-2 biosynthetic immune checkpoint receptor process;GO:0045954 positive regulation of natural killer cell mediated cytotoxicity;GO:0002717 positive regulation of natural killer cell mediated immunity 3 PRF1 Perforin-1, pore forming cytolytic GO:0051712 positive regulation of killing of cells of other protein found in the granules of organism;GO:0002357 defense response to tumor cytotoxic T-cells and NK-cells cell;GO:0051709 regulation of killing of cells of other organism 4 CXCL9 Chemokine ligand 9, T-cell GO:0051281 positive regulation of release of sequestered chemoattractant calcium ion into cytosol;GO:0051279 regulation of release of sequestered calcium ion into cytosol;GO:0010524 positive regulation of calcium ion transport into cytosol 5 IRF4 Interferon regulatory factor 4, TF GO:0072540 T-helper 17 cell lineage commitment;GO:0002295 T-helper cell lineage commitment;GO:0072539 T-helper 17 cell differentiation 6 IL2RB IL2 receptor subunit beta, mediates GO:0038110 interleukin-2-mediated signaling proliferation of T-cells pathway;GO:0035723 interleukin-15-mediated signaling pathway;GO:0071350 cellular response to interleukin-15 7 GZMK Granzyme K, serine protease in the GO:0006508 proteolysis;GO:0019538 protein metabolic cytoplasmic granules of cytotoxic process;GO:1901564 organonitrogen compound metabolic lymphocytes process 8 CD3D T-cell surface glycoprotein CD3 GO:0045059 positive thymic T cell selection;GO:0045061 delta chain thymic T cell selection;GO:0043368 positive T cell selection 9 CD247 T-cell surface glycoprotein CD3 GO:0038096 Fc-gamma receptor signaling pathway involved in zeta chain phagocytosis;GO:0050690 regulation of defense response to virus by virus;GO:2000010 positive regulation of protein localization to cell surface 10 GZMA Granzyme A, serine protease in the GO:0032078 negative regulation of endodeoxyribonuclease cytoplasmic granules of cytotoxic activity;GO:0032076 negative regulation of deoxyribonuclease lymphocytes activity;GO:0032071 regulation of endodeoxyribonuclease activity 11 SIGLEC1 Sialoadhesin, cell adhesion GO:0007160 cell-matrix adhesion;GO:0031589 cell-substrate molecule, binding neutrophils, adhesion;GO:0098609 cell-cell adhesion monocytes, NK-, B, T-cells 12 SOCS1 Suppressor of cytokine signaling 1, GO:0043377 negative regulation of CD8-positive, alpha-beta T negative regulator of cytokine cell differentiation;GO:0043376 regulation of CD8-positive, signaling alpha-beta T cell differentiation;GO:2001186 negative regulation of CD8-positive, alpha-beta T cell activation 13 ISG20 Interferon-stimulated gene 20 kDa GO:0045071 negative regulation of viral genome protein replication;GO:0000738 DNA catabolic process, exonucleolytic;GO:1903901 negative regulation of viral life cycle 14 PTPRC Protein tyrosine phosphatase, GO:0001915 negative regulation of T cell mediated receptor type C, essential regulator cytotoxicity;GO:2000473 positive regulation of hematopoietic of T- and B-cell antigen receptor stem cell migration;GO:0050857 positive regulation of antigen signaling receptor-mediated signaling pathway 15 CD38 cyclic ADP ribose hydrolase, GO:0014824 artery smooth muscle contraction;GO:0045907 functions in cell adhesion, signal positive regulation of vasoconstriction;GO:0014829 vascular transduction and calcium signaling smooth muscle contraction 16 IL10RA IL10 receptor alpha subunit, GO:0032496 response to lipopolysaccharide;GO:0002237 inhibits the synthesis of response to molecule of bacterial origin;GO:0050807 regulation proinflammatory cytokines of synapse organization Spassova et al.: Supplementary materials and methods 17 ISG15 Interferon-stimulated gene 15, GO:0045648 positive regulation of erythrocyte secreted by monocytes and differentiation;GO:0045071 negative regulation of viral genome lymphpcytes and functions as replication;GO:0032020 ISG15-protein conjugation cytokine 18 SLAMF7 Self-ligand receptor of the GO:0042267 natural killer cell mediated signaling lymphocytic activation cytotoxicity;GO:0002228 natural killer cell mediated molecule family immunity;GO:0030101 natural killer cell activation 19 CD8A Cell surface GO:0045065 cytotoxic T cell differentiation;GO:0030217 T cell glycoprotein/coreceptor, found on differentiation;GO:0002456 T cell mediated immunity most cytotoxic T-cells 20 IL16 Pro-interleukin-16, functions as GO:0050930 induction of positive chemotaxis;GO:0050927 chemoattractant, modulator of T- positive regulation of positive chemotaxis;GO:0050926 cell activation regulation of positive chemotaxis 21 HLA-DMB HLA class II histocompatibility GO:2001190 positive regulation of T cell activation via T cell antigen, DM beta chain receptor contact with antigen bound to MHC molecule on antigen presenting cell;GO:2001188 regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;GO:0002503 peptide antigen assembly with MHC class II protein complex 22 IFI16 Interferon-inducible myeloid GO:0097202 activation of cysteine-type endopeptidase differentiation transcriptional activity;GO:0045071 negative regulation of viral genome activator replication;GO:0030224 monocyte differentiation 23 CYFIP2 Cytoplasmic FMR1 interacting GO:0051388 positive regulation of neurotrophin TRK receptor protein 2, involved in T-cell signaling pathway;GO:0097202 activation of cysteine-type adhesion endopeptidase activity;GO:0051386 regulation of neurotrophin TRK receptor signaling pathway 24 CXCL11 Chemokine 11, chemotactic for GO:0051281 positive regulation of release of sequestered activated T-cells calcium ion into cytosol;GO:0051279 regulation of release of sequestered calcium ion into cytosol;GO:0010524 positive regulation of calcium ion transport into cytosol 25 JAK3 Tyrosine-protein kinase, associated GO:0045626 negative regulation of T-helper 1 cell with cytokine receptors differentiation;GO:0045625 regulation of T-helper 1 cell differentiation;GO:0045623 negative regulation of T-helper cell differentiation 26 CMKLR1 Chemokine like receptro 1, GO:0010759 positive regulation of macrophage attraction of dendritic cells and chemotaxis;GO:1905523 positive regulation of macrophage macrophages migration;GO:0010758 regulation of macrophage chemotaxis 27 CCL3 Chemokine ligand 3, attracts GO:0014808 release of sequestered calcium ion into cytosol by macrophages, monocytes and sarcoplasmic reticulum;GO:1903514 release of sequestered neutrophils calcium ion into cytosol by endoplasmic reticulum;GO:2000503 positive regulation of natural killer cell chemotaxis 28 CD74 HLA class II histocompatibility GO:0002906 negative regulation of mature B cell apoptotic antigen, gamma chain process;GO:0046598 positive regulation of viral entry into host cell;GO:0002905 regulation of mature B cell apoptotic process 29 PLAUR Urokinase receptor, involved in GO:2001268 negative regulation of cysteine-type endopeptidase tissue reorganization activity involved in apoptotic signaling pathway;GO:0042730 fibrinolysis;GO:2001267 regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway 30 FCER1A Fc fragment of IgE, high affinity I, GO:0001798 positive regulation of type IIa receptro for; alpha polypeptide - hypersensitivity;GO:0001805 positive regulation of type III plays a central role in allergic hypersensitivity;GO:0002894 positive regulation of type II disease hypersensitivity 31 IDO1 Indoleamine-pyrrole 2,3- GO:0019441 tryptophan catabolic process to dioxygenase - immune modulation kynurenine;GO:0034276 kynurenic acid biosynthetic by limiting T-cell function process;GO:0002666 positive regulation of T cell tolerance induction 32 CXCL10 Chemokine 10, attraction of GO:0051281 positive regulation of release of sequestered monocytes, dendritic cells, T-, calcium ion into cytosol;GO:1901740 negative regulation of NK-cells myoblast fusion;GO:0051279 regulation of release of sequestered calcium ion into cytosol Spassova et al.: Supplementary materials and methods 33 ITGAL Integrin alpha L, cellular adhesion GO:0002291 T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;GO:0043312 neutrophil degranulation;GO:0002286 T cell activation involved in immune response 34 CD53 Leukocyte surface antigen , growth GO:1901741 positive regulation of myoblast regulation in T- and NK-cells fusion;GO:1901739 regulation of myoblast fusion;GO:0060143 positive regulation of syncytium formation by plasma membrane fusion 35 MX1 Interferon-induced GTP-binding GO:0003374 dynamin family protein polymerization involved protein in mitochondrial fission;GO:0045071 negative regulation of viral genome replication;GO:0003373 dynamin family protein polymerization involved in membrane fission 36 LCK Lymphocyte-specific protein GO:0050862 positive regulation of T cell receptor signaling tyrosine kinase, assists signaling pathway;GO:0050857 positive regulation of antigen receptor- from the TCR into the T-cells mediated signaling pathway;GO:0051209 release of sequestered calcium ion into cytosol 37 ITGB4 Integrin
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  • Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease

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    Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................