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Dolan Et Al SI Fig 1 Electronic Supplementary Material (ESI) for Molecular BioSystems This journal is © The Royal Society of Chemistry 2013 Dolan et al. SI Fig. 1 Keywords PFAM PANTHER MF PANTHER INTERPRO GO Molecular Function GO Cellular Component COG Ontology COG Name BLOCKS Electronic Supplementary Material (ESI) for Molecular BioSystems This journal is © The Royal Society of Chemistry 2013 Dolan et al SI Fig. 2 CYTOPLASMIC_PART CYTOPLASM EXTRACELLULAR_REGION EXTRACELLULAR_SPACE EXTRACELLULAR_REGION_PART GO.0005615.extracellular.space GO.0044421.extracellular.region.part INTRACELLULAR_ORGANELLE_PART ORGANELLE_PART CYTOSKELETON INTRACELLULAR_NON_MEMBRANE_BOUND_ORGANELLE NON_MEMBRANE_BOUND_ORGANELLE GO.0005856.cytoskeleton GO.0015630.microtubule.cytoskeleton GO.0005813.centrosome GO.0005815.microtubule.organizing.center CYTOSKELETAL_PART CENTROSOME MICROTUBULE_ORGANIZING_CENTER REACTOME_CELL_CYCLE REACTOME_CELL_CYCLE_MITOTIC REACTOME_MITOTIC_G2_G2_M_PHASES REACTOME_LOSS_OF_NLP_FROM_MITOTIC_CENTROSOMES REACTOME_RECRUITMENT_OF_MITOTIC_CENTROSOME_PROTEINS_AND_COMPLEXES NUCLEUS BIOPOLYMER_METABOLIC_PROCESS RNA_METABOLIC_PROCESS NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_NUCLEIC_ACID_METABOLIC_PROCESS SIGNAL_TRANSDUCTION COG1196..Smc..Chromosome.segregation.ATPases Cell.division.and.chromosome.partitioning ENDOPLASMIC_RETICULUM ANATOMICAL_STRUCTURE_MORPHOGENESIS MULTICELLULAR_ORGANISMAL_DEVELOPMENT SYSTEM_DEVELOPMENT ANATOMICAL_STRUCTURE_DEVELOPMENT PROTEIN_METABOLIC_PROCESS CELLULAR_PROTEIN_METABOLIC_PROCESS CELLULAR_MACROMOLECULE_METABOLIC_PROCESS REACTOME_IMMUNE_SYSTEM KEGG_COMPLEMENT_AND_COAGULATION_CASCADES REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT REACTOME_REGULATION_OF_COMPLEMENT_CASCADE REACTOME_COMPLEMENT_CASCADE PROTEIN_COMPLEX KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION KEGG_FOCAL_ADHESION REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING KEGG_REGULATION_OF_ACTIN_CYTOSKELETON ER_GOLGI_INTERMEDIATE_COMPARTMENT GO.0005793.ER.Golgi.intermediate.compartment REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL REACTOME_INTEGRIN_ALPHAIIB_BETA3_SIGNALING REACTOME_GRB2_SOS_PROVIDES_LINKAGE_TO_MAPK_SIGNALING_FOR_INTERGRINS_ REACTOME_P130CAS_LINKAGE_TO_MAPK_SIGNALING_FOR_INTEGRINS KEGG_SPLICEOSOME IPB002017.Spectrin.repeat ACTIN_CYTOSKELETON ACTIN_BINDING CYTOSKELETAL_PROTEIN_BINDING REACTOME_NEPHRIN_INTERACTIONS REACTOME_CELL_CELL_COMMUNICATION REACTOME_APOPTOSIS REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS REACTOME_APOPTOTIC_EXECUTION_PHASE PROTEIN_C_TERMINUS_BINDING REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE KEGG_THYROID_CANCER KEGG_PROSTATE_CANCER KEGG_ENDOMETRIAL_CANCER KEGG_COLORECTAL_CANCER DNA_BINDING GO.0016607.nuclear.speck NUCLEAR_PART MEMBRANE_ENCLOSED_LUMEN ORGANELLE_LUMEN MACROMOLECULAR_COMPLEX_ASSEMBLY PROTEIN_RNA_COMPLEX_ASSEMBLY RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS_AND_ASSEMBLY PROTEIN_HETERODIMERIZATION_ACTIVITY PROTEIN_DIMERIZATION_ACTIVITY CYTOSKELETON_ORGANIZATION_AND_BIOGENESIS ORGANELLE_ORGANIZATION_AND_BIOGENESIS REACTOME_HEMOSTASIS REACTOME_RESPONSE_TO_ELEVATED_PLATELET_CYTOSOLIC_CA2_ REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION GO.0030247.polysaccharide.binding GO.0001871.pattern.binding GO.0008201.heparin.binding GO.0005539.glycosaminoglycan.binding REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS GO.0005543.phospholipid.binding GO.0042627.chylomicron GO.0034358.plasma.lipoprotein.particle GO.0032994.protein.lipid.complex GO.0034361.very.low.density.lipoprotein.particle GO.0034385.triglyceride.rich.lipoprotein.particle RECEPTOR_BINDING ENDOCYTIC_VESICLE VESICLE CYTOPLASMIC_VESICLE CYTOPLASMIC_MEMBRANE_BOUND_VESICLE MEMBRANE_BOUND_VESICLE REACTOME_PPARA_ACTIVATES_GENE_EXPRESSION CELLULAR_LIPID_METABOLIC_PROCESS STEROL_BINDING STEROID_BINDING KEGG_PPAR_SIGNALING_PATHWAY LIPID_BINDING LIPID_TRANSPORT LIPID_HOMEOSTASIS CDC42_PROTEIN_SIGNAL_TRANSDUCTION REACTOME_HDL_MEDIATED_LIPID_TRANSPORT SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION RHO_PROTEIN_SIGNAL_TRANSDUCTION RAS_PROTEIN_SIGNAL_TRANSDUCTION GO.0034364.high.density.lipoprotein.particle PHOSPHOLIPID_BINDING GO.0070325.lipoprotein.receptor.binding REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT REACTOME_LIPOPROTEIN_METABOLISM DDX5 HSP APO APOE APO APOH APOB NPM1 PCNT SDCCA CEP6 PCM1 CTNNB IQGAP2 UTRN TPM4 SPT PIK3R1 FN TF FG NUCB1 NUCB2 R DST SMC1 CBX5 DDX2 COPS2 GA ZNF63 CFH C4 C3 SERPIND1 HRG TCF7L TRIP11 RNASET AD EIF4G2 PA CCDC88C ITSN2 SNX1 SESTD1 RL F EL SPG7 PDIA6 FBXO3 TSG101 HMGCR CUL7 A SCP2 SLMAP OPT KTN1 GA WBP1 MYH1 MYCBP2 IFT88 CALCOCO2 DDX3 STX8 MPHOSPH9 GLRX5 GOLGA2 NID1 LOC100133511 COPS3 TNFRSF10 AM123B GGF OCK1 IP AV A F T TM 1 AR B AD2 AN1 A8 N A1 A5 1 L1 3 4 4 X A 4 1 1 8 2 1 G8 A 2 B Electronic Supplementary Material (ESI) for Molecular BioSystems This journal is © The Royal Society of Chemistry 2013 Dolan et al. SI Fig. 3 FUNDC1 FUNDC2 (Khadka et al.) (Dolan et al.) GOLGB1 DENV M DDX24 HCV NS4B SNX14 LOC642846 KTN1 PDCD6IP APOH PRDX6 CFH MYCBP2 EMILIN1 HRG DENV NS3 HCV E2 DCTN2 PCM1 GREB1 UACA N4BP2L2 AKAP8L EIF4G2 ATXN2L ZBTB8OS CIC TCF7L2 RAI14 SMC1A PTBP1 FGB NUCB2 LAMB1 DENV NS1 CALCOCO2 UTRN C14orf94 GPR81 SRFBP1 WBP11 TAX1BP1 HCV NS5B NID1 RLF KIF1B NUCB1 FN1 ROCK1 LOC728047 DENV NS4A GOLGA2 WWC1 GORASP2 MAP3K7IP2 SERPIND1 COPS3 SPTBN2 APOE TRIM62 HMGCR ZNF688 ANKRD50 PIK3R1 KNG1 HCV NS5A RBM10 PECI AGGF1 IFT88 UBXD4 CBX5 CUL7 FYB ELAVL1 KPNA3 MPHOSPH9 DENV NS2B RILPL2 COL12A1 TSG101 FAM123B NUP50 HSPA8 PIAS1 SPTAN1 CNOT1 EHMT2 DDX5 CEP63 CAT SDCCAG8 SESTD1 CALR ITSN2 DCUN1D4 PCNT FBXO3 ALDH3A2 TF CROP RNASET2 SLMAP TP53BP2 MST1 LOC643696 CCDC66 SCP2 VPS37A TRIP11 TPM4 TTC1 HCV NS3 PDIA6 MATR3 MYH14 ZNF638 ERC1 ZNF195 AKAP9 SPG7 GATAD2A SYNE1 PAIP1 OPTN NUMA1 PHF14 EID1 CTNNB1 ADAR COBLL1 DENV NS5 HOOK1 DST C3 CEP135 NPM1 CGNL1 DDX3X HCV Core GLRX5 STAT2 APOB EIF3L UBE2I TNFRSF10B IQGAP2 SFRS11 GATM COPS2 PMS2L11 FGA HCV NS2 STX8 C4A GATC AKR7A3 LOC100133511 BMS1 APOA1 APOA5 SYNE2 CCDC88C SCLT1 DENV NS2A N = 56 GOLSYN N = 38 PSMD1 DSCR3 SEC31A GC AKAP1 DCTN1 KRT8 PGK1 DENV NS4B N = 67 Electronic Supplementary Material (ESI) for Molecular BioSystems This journal is © The Royal Society of Chemistry 2013 Dolan et al (Fig. 7B) SI Fig. 4 Comparison of Unique and Shared Host Functions DAVID Shared Targets Targets Targets HCV Unique DENV Unique DENV HCV (Fig. 7A) Flavi Targets All HCV Targets All Targets All DENV DAVID HCV Functional Profile Flaviviridae Functional Profile DENV Functional Profile (Fig. 7C) Electronic Supplementary Material (ESI) for Molecular BioSystems This journal is © The Royal Society of Chemistry 2013 Dolan et al. SI Fig. 5 A. Cellular ATP Levels (RLU) ATP Cellular B. 450) MTT (OD MTT.
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