Supplementary Files to Töröcsik et al. Factor XIII-A is involved in the regulation of
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1 Supplementary Files to Töröcsik et al. Factor XIII-A is involved in the regulation of gene expression in alternatively activated human macrophages (Thromb Haemost 2010; 104.3) A Protein synthesis Cell morphology Nervous system Immune response Cellular movement Hematological system RNA post-transcription modification Immunological disease Psychological disorders Amino acid metabolism B Connective tissue disorders Inflammatory disease Skeletal and molecular disorders Immunological disease Immune response Cellular movement Hematological system Cellular compromise Immune and lymphatic Cell-to-cell signaling and interaction Supplement Figure. Functional clustering of the genes up- (A) or down- (B) regulated by at least two-fold in DEF versus WT macrophages at 48 hours of IL4-induced differentiation by the Ingenuity Pathways Analysis program. 1
2 Supplementary Table 1. The fifteen most strongly up-regulated probes in DEF macrophages vs. WT cells at 48 hours after IL4-induced differentiation as revealed by DEF/WT fold-change ratios. PROBE ID Fold change in WT DEF Ratio of expression levels DEF/WT common name annotated gene name _at CD180 CD180 molecule _at DSU dilute suppressor _at CDR2 cerebellar degeneration-related protein 2, 62kDa _a_at CCL5 chemokine (C-C motif) ligand _at CTSC cathepsin C _s_at IL1R2 interleukin 1 receptor, type II _s_at GALM galactose mutarotase (aldose 1-epimerase) _at GGTA1 Glycoprotein, alpha-galactosyltransferase _at HLA-DPA1 major histocompatibility complex, class II, DP alpha _at SMAD1 SMAD, mothers against DPP homolog 1 (Drosophila) _at FGL2 fibrinogen-like _at PRRG4 Proline rich Gla (G-carboxyglutamic acid) _at FLJ10847 hypothetical protein FLJ _at BZW2 basic leucine zipper and W2 domains _at C17orf58 chromosome 17 open reading frame 58 2
3 Supplementary Table 2. The fifteen most strongly down-regulated probes in DEF macrophages vs. WT cells at 48 hours after IL4-induced differentiation, as revealed by DEF/WT type fold-change ratios. PROBE ID Fold change in WT DEF Ratio of expression levels DEF/WT common name annotated gene name _s_at CXCL5 chemokine (C-X-C motif) ligand _at CA12 carbonic anhydrase XII _at FLJ20701 Hypothetical protein FLJ _at KCNJ15 potassium inwardly-rectifying channel. subf. J. m _at SLC11A1 solute carrier family 11. member _s_at CCL7 chemokine (C-C motif) ligand _s_at PPBP pro-platelet basic protein (chemokine ligand 7) _at SERPINB2 serpin peptidase inhibitor. clade B (ovalbumin). m _x_at CSPG2 chondroitin sulfate proteoglycan 2 (versican) _at INDO indoleamine-pyrrole 2.3 dioxygenase _at BCL2A1 BCL2-related protein A _at IL1B interleukin 1. beta _at PAPLN papilin. proteoglycan-like sulfated glycoprotein _at OLIG1 oligodendrocyte transcription factor1 3
4 Supplementary Table 3. Functional clustering of the genes expressed differentially by at least two-fold in DEF vs. WT monocytes at 0 time point as revealed by the Cytoscape/BiNGO program using DEF/WT expression values. Description membranebound organelle p-value corr p- value# selected Total number of genes Genes in test set 4.33E NDUFA10, OLIG1, GTF2H1, ERCC5, RREB1, ZNF331, RBPSUH, ANAPC10, NUDT9, ZNF275, ALDH1B1, THRAP3, TSNAX, MYCL1, STK38, CHD1, NUMA1, LMNB1, ERF, DNMBP, HIST1H1C, NFX1, CLGN, B4GALT1, ZNF264, SLC33A1, TRA1, MGC26963, PSIP1, UBE2J1, CHD2, ZNF24, TLOC1, H2AFY, WDR33, COX4I1, ZFYVE1, NEDD9, RYBP, LPIN2, OGT, OPTN, SLC25A29, ZF, CBX5, PPIG, PHC1, HIST1H2AC, ATP2A2, MECP2, RRBP1, HIC2, BCOR, PRDM2, FBXL10, MEF2D, ENO1, NFATC3, NEK6, COX17, HOXA5, SMAD1, CYB5, PPARD, ICMT, JARID2, TFRC, NDUFA5, HIST1H2BC, CBX6, CDC14A, PRDM15, IDS, SMURF2, SFRS7, PEX6, ZNF395, HERC1, HNRPA1, POLS, RIF1, SP1, NR3C1, AP1GBP1, SMAD4, PNN, CTNND1, SS18, ZNF304, KLF5, SIAH1, HNRPH1, PPHLN1, SNRPN, BRD3, MGST3, ZNF398, ARID3A, TIPARP, NFE2L2, PRDM1, ARID2, FOXO1A, BTAF1, NKX31, BRD1, NRF1, FGD6, TTRAP, HSF2, NAPB, RBM12, CYP4F3, CLN8, SFRS5, AFTIPHILIN, FOSL2, SLC17A5 metabolism 6.62E NDUFA10, OLIG1, GTF2H1, ERCC5, RREB1, ZNF331, RBPSUH, ULK1, MAP3K8, ANAPC10, MTHFR, CASP3, SMURF1, MME, ZNF275, ALDH1B1, MARS, THRAP3, IL1RAP, PDLIM1, PGS1, MYCL1, STK38, ATP2B1, CHD1, ERF, CHKA, HIST1H1C, UBE2H, NFX1, CLGN, GNMT, B4GALT1, FNBP1, ZNF264, TRA1, MGC26963, MARK2, SYNJ1, PSIP1, UBE2J1, CHD2, ELA2, ZNF24, H2AFY, ITIH4, ALPL, WDR33, CYP4F3, SLC20A1, COX4I1, RYBP, CSNK1E, USP42, OGT, ZF, CBX5, PPIG, COL4A3BP, SFRS5, HIST1H2AC, ATP2A2, SLC23A2, MECP2, RRBP1, NALP12, HIC2, MTMR4, MSH5, C13ORF7, BCOR, PRDM2, CDC42EP2, ACVR1B, DNAJC5, FBXL10, MEF2D, ENO1, DICER1, FBXO9, GFPT1, NFATC3, MOCS2, NP, NEK6, COX17, IREB2, HOXA5, SLK, CHI3L1, TOLLIP, ATP8B1, UGDH, SMAD1, CYB5, PPARD, ICMT, JARID2, STK38L, TFRC, NDUFA5, HIST1H2BC, CDC14A, AGPAT3, RNF5, CBX6, PRDM15, IDS, DAG1, SMURF2, SFRS7, ZNF395, HERC1, HNRPA1, POLS, GFOD1, NR3C1, SP1, SMAD4, NKTR, PNN, ABCA1, ZNF304, RNASET2, KLF5, SIAH1, HNRPH1, SNRPN, PPM1B, ACSL4, NQO1, ARID3A, MGST3, ZNF398, CSNK1D, TIPARP, FOSL2, PTPRE, NFE2L2, PRDM1, ARID2, FOXO1A, RNASE2, NKX31, BTAF1, SLC2A3, LDLR, EIF5A, CAMK2G, NRF1, BRD1, IBRDC2, MKKS, HSF2, TUBB4, CHURC1, DNAJB6 DNA binding 8.82E MSH5, PRDM2, OLIG1, ERCC5, RREB1, ZNF331, RBPSUH, FBXL10, ENO1, MEF2D, NFATC3, ZNF275, HOXA5, SLK, TSNAX, ZBED4, SMAD1, MYCL1, CHD1, PPARD, ERF, JARID2, HIST1H1C, NFX1, HIST1H2BC, PRDM15, ZNF264, PSIP1, ZNF395, CHD2, ZNF24, POLS, SP1, NR3C1, H2AFY, SMAD4, PNN, ZNF304, KLF5, ZNF398, ARID3A, RYBP, NFE2L2, PRDM1, 4
5 FOXO1A, ARID2, BTAF1, NKX3-1, NRF1, ZF, HSF2, PHC1, HIST1H2AC, MECP2, HIC2, FOSL2 negative regulation of transcription nucleobase, nucleoside, nucleotide and nucleic acid metabolism 9.06E NFX1, BTAF1, BCOR, ZNF24, ZF, MECP2, HIC2, RBPSUH, PRDM1, SMURF2, PPARD 9.47E MSH5, NDUFA10, BCOR, PRDM2, OLIG1, ERCC5, GTF2H1, RREB1, ZNF331, RBPSUH, FBXL10, MEF2D, ENO1, DICER1, NFATC3, NP, ZNF275, HOXA5, MARS, THRAP3, SLK, UGDH, MYCL1, SMAD1, CHD1, PPARD, ERF, JARID2, HIST1H1C, HIC2, NFX1, HIST1H2BC, CBX6, PRDM15, ZNF264, SMURF2, PSIP1, SFRS7, CHD2, NF395, NRPA1, ZNF24, POLS, NR3C1, SP1, H2AFY, SMAD4, PNN, ZNF304, FOSL2, RNASET2, KLF5, HNRPH1, WDR33, SNRPN, ARID3A, ZNF398, CSNK1D, RYBP, NFE2L2, PRDM1, CSNK1E, ARID2, FOXO1A, RNASE2, BTAF1, NKX31, NRF1, BRD1, ZF, CBX5, HSF2, PPIG, CHURC1, HIST1H2AC, SLC23A2, MECP2, SFRS5 5
6 Supplementary Table 4. Functional clustering of the genes expressed differentially by at least two-fold in DEF vs. WT non-treated macrophages at 48 hours as revealed by the Cytoscape/BiNGO program using DEF/WT expression values. Description p-value corr p- value# selected Total number of genes Genes in test set mitochondrion 3.08E OPA1, NDUFA10, PCCA, DLAT, IDH2, MRPS16, PCCB, MRPS27, LARS2, GPAM, MRPS28, DNAJA3, HSPA9B, NLN, MRPL12, TRAP1, UQCRC2, C10ORF70, FH HSPD1, MRPS25, COX15, cellular biosynthesis structural constituent of ribosomes defense responses programmed cell death HADHSC, UQCRB, UNG, SCO2, NDUFS7, SUCLG1, MRPS17, ACADM, ETFA, TOMM22, MRPL11, NDUFS8, SFXN4, GLS, SUCLG2, ATP5G3, RTN4IP1, AFG3L2, AKAP1,HIBADH, ATP5G2, NDUFB2, FECH, WARS2, TFAM, LRPPRC, DUT, C14ORF159, SHMT2, NDUFB5, MRPS18B, BIT1, MCART1, MMAA, NDUFV3, PET112L, SLC25A6, C6ORF149, SH3BP5, TIMM23, ENDOG, C18ORF22, ACAT1, GLUD1, SCP2, MTHFD1, COQ7, MIPEP, RAF1, HSPE1, C1QBP, SLC25A12, MRPS30, GK, ALDH6A1, TIMM8B, MRPL3, ATP5G1, MRPL44, NNT, MRPL19, PRDX5, TOP1MT, PDCD8, TRNT1, NDUFS3, SYNJ2BP, ABCE1, AK2, AMACR, GBAS, FDX1 4.12E RPL14, LGTN, MRPS16, RPL36AL, JTV1, LARS2, MIF, GFPT1, RPL10A, KIAA1970, EEF2K, MRPL12, PDE4DIP, GLMN, SCD, RPL3, PGGT1B, RPL29, CAD, MRPS25, EIF3S9, RPS18, PFAS, AGL, RPL7A, KYNU, RPL4, HSPB1, RPLP0, MRPS17, RPL12, RPL15, RPS4X, MRPL11, RPS16, RPL18, PIGB, ADK, ATP5G3, ADORA2A, DHFR, PRPS2, PPAT, MTR, ATP5G2, FECH, RPS5, WARS2, SRM, RPL13, RPL5, DDT, EIF5, LARS, ADSL, ATIC, MRPS18B, ACACA, RPS7, GMDS, UMPS, MGST2, PET112L, ADM, NME2, CDC91L1, EPM2A, RPL23, EPRS, IARS, MTHFD1, COQ7, RPL17, OGT, RPL18A, CDR2, HS3ST3B1, MRPS30, RPL10L, RPL22, MRPL3, ATP5G1, YARS, QDPR, RPL36A, PAICS, IL18, RPL31, RPS19, PBEF1, MRPL19, CTPS2, RPL10, EEF1B2, RPS21, MRPL E RPL13, RPS8, RPL5, RPL14, MRPS18B, RPS7, MRPS16, MRPS27, RPL36AL, MRPS28, RPL10A, MRPL12, RPL23, PDE4DIP, RPL3, RPL29, MRPS25, RPL17, RPS18, RPL7A, RPL18A, RPL4, MRPS30, RPLP0, MRPS17, RPL10L, RPL22, RPL12, MRPL3, RPL36A, MRPL44, RPL15, RPS4X, MRPL11, RPS16, RPL18, RPL31, RPS19, MRPL19, RPL10, RPS21, RPS5, MRPL E CXCL16, S100A12, TRGV9, IRAK2, HHEX, C1QR1, FN1, CD226, MIF, IL21R, RGS1, LILRA2, CXCL5, GLMN, RNF125, CD84, GBP3, IL24, C1QB, MNDA, DAF, IL1B, LILRA1, TNFSF10, TNFSF13B, CYSLTR1, CCR7, LILRB3, NALP1, CX3CR1, ADORA2A, CHST2, NFIL3, INDO, B2M, LAT, BCL6, PDCD1LG2, TNFSF8, HLA-DPB1, HLADPA1, CST7, CXCL3, TRIM22, MGST2, TNFAIP6, NCK1, PSMB10, PSME2, IFIT5, LILRB1, CTSC, HLADRB3, OAS1, C1QBP, MAP4K2, PSMB9, FCAR, CCL4, CXCL2, C3, IL8, AQP9, IL18, PRDX5, LTB4R, FCGR2A, IL7 2.97E IGF1R, OPA1, TRIB3, TNFSF8, IER3, BIT1, CUL4A, MIF, DNAJA3, RYBP, TNFRSF10B, RAF1, IL24, BTG1, FAF1, BCL2A1, IL1B, MRPS30, P2RX1, YARS, TNFSF10, FAIM, SPHK1, VEGF, BCLAF1, IL18, GADD45G, NALP1, STK17B, ADORA2A, PDCD8, SERPINB2, MAGEH1, SOCS2, 6
7 BAG2, DNM2, NOL3, STK17A, ERCC2 cytokine activity 4.07E CXCL16, IL24, CTF1, TNFSF8, IL1B, CXCL2, CCL4, IL8, ECGF1, YARS, TNFSF10, CXCL3, TNFSF13B, MIF, VEG, IL18, PBEF1, TRAP1, IL7, GLMN, CXCL5, SOCS2 7
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