Supplementary Figure 1: Func8onal Network Analysis of Kinases Significantly Modulated by MERS CoV Infec8on and Conserved Across All Time Points

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James Bridges
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A. B. 8 4 Supplementary Figure : Func8onal Network Analysis of Kinases Significantly Modulated by MERS CoV Infec8on and Conserved Across All Time Points Examined.

B) Func>onal network analysis of 7 common kinases from the central intersec>on of (A).

1 A. B. 8 4 Supplementary Figure : Func8onal Network Analysis of Kinases Significantly Modulated by MERS CoV Infec8on and Conserved Across All Time Points Examined. A) Venn diagram analysis of kinases significantly modulated throughout the course of MERS CoV infec>on. B) Func>onal network analysis of 7 common kinases from the central intersec>on of (A). Network associated func>ons: Cellular movement, cell death and survival, cell cycle. Grey shading designates nodes that were conserved across all data sets. Non highlighted nodes were not found to be conserved across the data sets in this study but are predicted by IPA to form part of the pathway/network presented.

A. B. Supplementary Figure : Inhibitory Ac8vi8es of FDA Licensed Kinase

Following infec>on and washing, media supplemented without (A) or with (B)

2 A. B. Supplementary Figure : Inhibitory Ac8vi8es of FDA Licensed Kinase Inhibitors Targe8ng ERK/MAPK or PIK/AKT Signaling Against MERS CoV Infec8on by Plaque Reduc8on Assay. Kinase inhibitors (0 μm) were added prior to ( hr) MERS CoV infec>on. Following infec>on and washing, media supplemented without (A) or with (B) fresh kinase inhibitors were added back to the cells. Results are presented as mean ± SD. The results represent three experimental repeats (mean ± SD, n=).

3 Supplemental Table : InnateDB Analysis of Temporal Kinome Datasets From MERS- CoV Infections A. Pathways modulated hr post-infection Upregulated Pathways: Pten dependent cell cycle arrest and apoptosis Focal adhesion Bacterial invasion of epithelial cells Direct p5 effectors Erk and pi- kinase are necessary for collagen binding in corneal epithelia Integrin signaling pathway Notch-mediated HES/HEY network Pathways in cancer AP- transcription factor network AndrogenReceptor Renal cell carcinoma EPHA forward signaling EPHB forward signaling HGF signaling pathway Hypoxia and p5 in the cardiovascular

4 system Integrin signaling pathway Nectin adhesion pathway Netrin-mediated signaling events PDGFR-alpha signaling pathway SHP signaling Vegf hypoxia and angiogenesis Signaling events mediated by Hepatocyte Growth Factor Receptor (c-met) Axon guidance Melanoma Wnt signaling pathway p75(ntr)-mediated signaling Fc-epsilon receptor I signaling in mast cells Regulation of actin cytoskeleton Amyotrophic lateral sclerosis (ALS) Ccr signaling in eosinophils Endocytosis Signaling events mediated by VEGFR and VEGFR

5 Down-Regulated Pathways: Glypican network The 4bb-dependent immune response Signal transduction through ilr Nfkb activation by nontypeable hemophilus influenzae ATR signaling pathway Regulation of Androgen receptor activity Tnf/stress related signaling Toll-like receptor pathway Keratinocyte differentiation TGF-beta signaling p5 pathway Cytokine-cytokine receptor interaction Osteoclast differentiation Chagas disease (American trypanosomiasis) IL- signaling pathway Toll-like receptor signaling pathway

6 B. Pathways modulated 6 hr post-infection Up-Regulated Pathways: Calcineurin-regulated NFAT-dependent transcription in lymphocytes GMCSF-mediated signaling events Beta integrin cell surface interactions Downstream signaling in naïve CD8+ T cells FOXM transcription factor network Trk receptor signaling mediated by the MAPK pathway Cytokine-cytokine receptor interaction Cyclins and cell cycle regulation Destabilization of mrna by KSRP Ras signaling in the CD4+ TCR pathway Down-Regulated Pathways: Downregulated of mta- in er-negative breast tumors 4

7 Adherens junction Calcium signaling pathway Stabilization and expansion of the E cadherin adherens junction Bacterial invasion of epithelial cells HGF signaling pathway Signaling mediated by p8-alpha and p beta SHP signaling Leptin C. Pathways modulated 4 hr post-infection Up-Regulated Pathways: Noncanonical Wnt signaling pathway Wnt Adherens junction MTOR signaling pathway Tight junction Wnt signaling pathway TGF-beta signaling pathway Tgf beta signaling pathway

8 Wnt signaling pathway Insulin receptor signaling Class I PIK signaling events mediated by Akt Regulation of nuclear SMAD/ signaling Down-Regulated Pathways: IL- signaling Leishmaniasis Stat signaling pathway p7 transcription factor network Interleukin-6 signaling Axon guidance Toxoplasmosis Regulation of actin dynamics for phagocytic cup formation Endogenous TLR signaling IL7-mediated signaling events IL ATM pathway Activation of Rac

9 IFN alpha signaling IL-0 signaling IL- signaling Il soluble receptor signaling pathway Interferon alpha/beta signaling Interferon gamma signaling No-dependent il- pathway in nk cells InnateDB is a publically available pathway analysis tool. Based on levels of differential expression or phosphorylation InnateDB is able to predict pathways that are consistent with the experimental data. Pathways are assigned a probability value (p) based on the number of proteins present for a particular pathway. It also provides the number of uploaded pathways associated with a particular pathway as well as the subset of individual proteins that are differentially phosphorylated. 8 9 Supplemental Table : Conserved Kinases Across all MERS-CoV Kinome Data Sets Molecule Name BRAF CHUK GNBL HIFA MET NFATC 7

10 PAK PIKR PRKAA SMAD STAT STMN VIM YWHAZ

Additional file 2 List of pathway from PID

Additional file 2 List of pathway from PID Pathway ID Pathway name # components # enriched GO terms a4b1_paxdep_pathway Paxillin-dependent events mediated by a4b1 20 179 a4b1_paxindep_pathway Paxillin-independent