TABLE S1 (Supplemental table 1) Complete list of selected for hierarchical clustering as shown in figure 2. GeneID name(1) Gene Cluster (2) Pvalue_B13 (3) B13.Ave.R (4) Y14737 IGHG3; IgG heavy chain B cells 0.02 0.68 NM_014239 EIF2B2; translation factor B cells 0.01 0.93 NM_013230 CD24 B cells 0.01 0.81 BC007782 IGL; lambda light chain B cells <0.005 3.29 NM_001060 TBXA2R; tromboxane rec. IFN-inducible <0.005 0.76 AB033094 KIAA1268 IFN-inducible 0.01 0.5 NM_001126 ADSS; adenylosuccinate synthet. IFN-inducible <0.005 1.11 NM_002773 PRSS8; serine protease IFN-inducible <0.005 1 NM_002462 MX1; myxovirus resistance 1 IFN-inducible <0.005 1.39 NM_005101 G1P2; ISG15 IFN-inducible <0.005 1.99 NM_002463 MX2; myxovirus resistance 2 IFN-inducible <0.005 0.95 NM_002432 MNDA; myeloid nuclear diff.ag. IFN-inducible 0.02 0.53 NM_001548 IFIT1; IFI56 IFN-inducible <0.005 1.31 NM_003113 SP100 IFN-inducible <0.005 0.64 NM_006153 NCK1; NCK tyrosine kinase IFN-inducible <0.005 0.63 NM_000433 NCF2; neutr cytosolic factor 2 myeloid* <0.005 0.78 NM_004454 ETV5 myeloid* <0.005 0.71 NM_000397 CYBB; cytochrome b 245 myeloid <0.005 1.13 NM_004244 CD163 myeloid* <0.005 1.05 NM_006762 LAPTM5; lysosomal protein myeloid* <0.005 0.95 NM_004106 FCER1G; FcR gamma chain myeloid* <0.005 1.17 NM_003890 FCGBP; FcgR binding myeloid* <0.005 0.99 NM_000560 CD53 myeloid* <0.005 1.44 NM_002110 HCK; hemopoetic cell kinase myeloid* <0.005 0.82 NM_004851 NAP1; pronapsin A myeloid <0.005 1.03 NM_004720 MAZ; myc ass. zink finger protein myeloid* <0.005 2.65 NM_003355 UCP2; uncoupling protein 2 myeloid* <0.005 0.78 NM_000582 SPP1; osteopontin myeloid* <0.005 1.76 NM_002872 RAC2; RAS family GTPase myeloid* <0.005 0.79 NM_003264 TLR2; Toll-like receptor 2 myeloid* <0.005 1.38 NM_000072 CD36 myeloid* 0.01 0.87 NM_005950 MT1G; metallothionein 1G myeloid 0.01 0.75 NM_002970 SAT; spermidine myeloid* <0.005 0.87 NM_001150 ANPEP; alanyl aminopeptidase myeloid 0.01 0.77 NM_006332 IFI30; GILT myeloid* <0.005 2.04 NM_003119 SPG7; spastic paraplegia 7 myeloid* <0.005 0.75 NM_001908 CTSB; cathepsin B myeloid* <0.005 1.37 NM_005211 CSF1R; colony stim fact 1 rec myeloid* <0.005 1.24 NM_001250 TNFRSF5; CD40 myeloid* <0.005 1.3 NM_004054 C3AR1; complement C3a rec myeloid* <0.005 1.1 NM_002350 LYN myeloid* <0.005 0.8 BC08004 LGMN; legumain myeloid <0.005 0.79 NM_004390 CTSH; cathepsin H myeloid <0.005 1.94 NM_004848 C1orf38; ICB-1 myeloid* <0.005 0.73 NM_002983 CCL3; MIP-1-alpha myeloid* <0.005 0.95 NM_016522 HNT; neurotrimin myeloid <0.005 1.27 NM_000211 ITGB2; CD18 myeloid* <0.005 1.62 NM_000591 CD14 myeloid* <0.005 0.82 NM_006282 STK4; serine/threonin kinase 4 myeloid <0.005 0.71 NM_002306 LGALS3; galectin 3 myeloid <0.005 1.02 NM_003878 GGH; gamma-glutamyl myeloid <0.005 0.76 NM_006984 CLDN10; claudin 10 myeloid 0.05 0.49 NM_001038 SCNN1A; myeloid <0.005 0.76 NM_002997 SDC1; syndecan 1 myeloid 0.01 0.65 NM_002371 MAL; T-cell differentiation protein myeloid <0.005 1.38 NM_002151 HPN; hepsin myeloid <0.005 0.67 NM_001353 AKR1C1;aldo-keto reductase myeloid <0.005 0.84 NM_003177 SYK; spleen tyrosine kinase myeloid <0.005 1.45 BG393100 novel myeloid <0.005 1.03 NM_015646 RAP1B; member RAS family myeloid <0.005 0.64 NM_004684 SPARCL1; hevin myeloid <0.005 0.97 NM_005720 ARPC1B; actin-related protein fibrosis <0.005 0.85 NM_004369 COL6A3; collagen VI fibrosis <0.005 1.57 NM_000064 C3; complement C3 fibrosis <0.005 1.7 NM_000224 KRT18; keratin 18 fibrosis <0.005 1.28 NM_000204 IF; I factor complement fibrosis <0.005 1 D43968 RUNX1; AML1b fibrosis 0.01 0.78 NM_003786 ABCC3;ATP-bind cassette fam3 fibrosis 0.05 1.01 NM_000089 COL1A2; collagen I fibrosis <0.005 1.51 NM_001629 ALOX5AP; FLAP fibrosis <0.005 0.78 NM_000861 HRH1;histamine H1 receptor fibrosis <0.005 0.98 AY007239 DKFZP564G202;monooxygenase fibrosis <0.005 0.71 NM_001508 GPR39;G-protein rec 39 fibrosis <0.005 1.26 NM_001095 ACCN2; ion channel fibrosis 0.01 0.86 NM_005878 TNRC3; mastermind-like3 fibrosis <0.005 0.98 NM_002982 CCL2; MCP-1 fibrosis 0.01 0.72 NM_004415 DSP; fibrosis <0.005 1.38 NM_001140 ALOX15;arachidonate-15 lipoxyg. fibrosis <0.005 0.76 NM_002423 MMP7;matrixmetalloproteinase7 fibrosis <0.005 1.65 NM_007173 SPUVE; serine protease 23 fibrosis <0.005 1.04 NM_001733 C1R; complement 1 receptor fibrosis 0.02 0.65 NM_003020 SGNE1;neuroendocrine protein 1 fibrosis <0.005 0.89 NM_001078 VCAM1 fibrosis 0.03 1.2 NM_004460 FAP; fibroblast activating protein fibrosis <0.005 0.88 NM_002345 LUM; lumican fibrosis <0.005 1.97 M35878 IGFBP3;insulin-like growth fac.BP fibrosis <0.005 0.95 NM_033209 THY1 fibrosis <0.005 1.43 NM_001814 CTSC; cathepsin C fibrosis <0.005 2.3 1833 Novel; retinoid BP gene decreased in SLE <0.005 -3.61 NM_004040 ARHB; ras homolog gene famB decreased in SLE <0.005 -1.91 NM_000602 SERPINE1, PAI-1 decreased in SLE <0.005 -1.77 NM_005225 E2F1; transcription factor decreased in SLE <0.005 -1.81 NM_006022 TSC-22; TGF-beta stim protein decreased in SLE <0.005 -1.4 U90902 Human clone 23612 decreased in SLE 0.001 -1.31 NM_001333 CTSL2; decreased in SLE 0.001 -1.39 D50683 TGFBRII; TGFβ receptor II decreased in SLE 0.001 -1.64 NM_005574 LMO2;rhombotin-like 1 decreased in SLE <0.005 -1.33 NM_000800 FGF1; fibroblast growth factor 1 decreased in SLE <0.005 -1.37 NM_002019 FLT1; vascular growth factor decreased in SLE <0.005 -1.23 NM_002736 cAMP-dep. PK subunit RII-beta decreased in SLE <0.005 -1.13 NM_006633 IQGAP2; GTPase activat protein decreased in SLE <0.005 -1.19 NM_014720 SLK; serine/threonin kinase decreased in SLE 0.001 -1.1 NM_013262 MYLIP; ERM-like protein decreased in SLE <0.005 -1.29 NM_000685 AGTR1; angiotensin receptor 1 decreased in SLE <0.005 -1.15 NM_005161 AGTRL1; angiotensin-like rec. 1 decreased in SLE 0.001 -0.67 NM_021643 TRB2; tribbles homolog 2 decreased in SLE 0.015 -0.7 AK000002 FLJ00002 decreased in SLE <0.005 -0.75 NM_000675 ADORA2A; adenosine A2a rec decreased in SLE 0.021 -0.78 AF119897 PRO2760 mRNA decreased in SLE <0.005 -0.88 NM_003651 CSDA;coldshock domain 2a decreased in SLE <0.005 -0.99 NM_004624 VIPR1;vasoactive intest peptide decreased in SLE <0.005 -0.98 NM_002037 FYN decreased in SLE <0.005 -0.94 AF022375 VEGF; vascular growth fact decreased in SLE <0.005 -1.09 NM_013281 FLRT3;fibronectin leu-rich protein decreased in SLE 0.002 -0.9 NM_018674 ASIC4; decreased in SLE <0.005 -0.88 NM_014380 NGFRAP1; nerve GF rec assoc. decreased in SLE <0.005 -0.94 NM_001748 CAPN2;calpain 2 decreased in SLE <0.005 -1.08 NM_006238 PPARD; peroxisome prolif act rec decreased in SLE 0.041 -0.91 NM_014767 KIAA0275 decreased in SLE <0.005 -0.9 NM_000674 ADORA1;adenosine A1 rec decreased in SLE 0.001 -0.74 NM_004492 GTF2A2;general transcription fact decreased in SLE <0.005 -0.94 NM_000724 CACNB2;calcium ion channel decreased in SLE <0.005 -1.15 NM_020529 NFKBIA; MAD3; IKBA decreased in SLE <0.005 -0.9 NM_004288 PSCDBP; pleckstring homology decreased in SLE 0.001 -0.82 NM_002473 MYH9; HC non-muscle decreased in SLE <0.005 -1.05 AK023505 FLJ13443 decreased in SLE <0.005 -1.13 AV712687 DCAAJG02 5' decreased in SLE <0.005 -0.91 NM_017526 HSOBRGRP decreased in SLE <0.005 -0.77 D86973 KIAA0219 decreased in SLE 0.001 -1.01 NM_000184 HBG2;hemoglobin gamma 2 decreased in SLE <0.005 -0.9 NM_000660 TGFB1; TGFβ1 decreased in SLE <0.005 -1.22 NM_002428 MMP15;matrix metalloproteinase decreased in SLE <0.005 -1.06 NM_001134 AFP; alpha-fetoprotein decreased in SLE <0.005 -0.91 AF103803 novel decreased in SLE 0.01 -0.75 NM_001798 CDK2; cyclin dependent kinase2 decreased in SLE 0.001 -0.69 BF968992 IMAGE:4358542 5' decreased in SLE <0.005 -0.93 NM_006471 MLCB; myosin regulatory LC decreased in SLE <0.005 -0.84 U97105 cDNA N2A3 decreased in SLE <0.005 -1.03 AK025431 FLJ21778 decreased in SLE 0.002 -0.89 NM_001329 CTBP2; C-terminal bind protein2 decreased in SLE <0.005 -0.91 AB002306 KIAA0308 decreased in SLE 0.001 -0.74 AK025902 FLJ22249 decreased in SLE <0.005 -0.89 NM_005520 HNRPH1; ribonuclear protein H1 decreased in SLE 0.002 -1.07 NM_001155 ANXA6; annexin A6 decreased in SLE <0.005 -1.04 NM_000165 GJA1; connexin 43 decreased in SLE <0.005 -1.19 H95354 IMAGE:234468 3' decreased in SLE <0.005 -1.28 NM_020357 PCNP; nuclear protein decreased in SLE 0.006 -0.63 NM_006330 LYPLA1; lysophospholipase1 decreased in SLE 0.005 -0.63 AF342989 PLAC3; placenta spec 3 decreased in SLE 0.001 -0.74 NM_000126 ETFA; electron transfer protein decreased in SLE 0.002 -0.71 NM_000333 SCA7;spinocerebellar ataxia7 decreased in SLE <0.005 -0.7 AA448691 Novel decreased in SLE <0.005 -0.57 NM_005667 RNF103; ring finger protein 3 decreased in SLE 0.018 -0.73 NM_003715 VDP; vesicle docking protein decreased in SLE 0.051 -0.56 NM_002752 MAPK9 decreased in SLE <0.005 -0.61 NM_006937 SMT3H2; sentrin decreased in SLE 0.006 -0.63 AK027793 TM4SF8;TSPAN-3; tetraspanin decreased in SLE 0.001 -0.81 D86962 KIAA0207 decreased in SLE 0.045 -0.64 NM_004622 TSN; translin decreased in SLE 0.002 -0.8 NM_007166 PICALM; clathrin assembly decreased in SLE 0.001 -0.73 NM_002609 PDGFRB decreased in SLE 0.04 -0.62 NM_004800 TM9SF2;transmembrane9 fam2 decreased in SLE 0.004 -0.63 NM_002290 LAMA4; laminin decreased in SLE 0.043 -0.45 NM_003373 VCL; decreased in SLE 0.02 -0.58 NM_019111 HLA-DRA decreased in SLE 0.028 -0.79 NM_006206 PDGFRA decreased in SLE 0.005 -0.65 NM_016441 CRIM1;cysteinrich motor neuron1 decreased in SLE <0.005 -1.46 NM_003243 TGFBR3 decreased in SLE 0.001 -1.5 NM_001936 DPP6; dipeptidylpeptidase 6 decreased in SLE <0.005 -1.46 NM_002775 PRSS11; serine protease decreased in SLE <0.005 -1.43 NM_002661 PLCG2; phospholipase C decreased in SLE <0.005 -1.06 NM_000597 IGFBP2;insulin-like GF BP2 decreased in SLE 0.026 -0.74 NM_001124 ADM; adrenomedullin decreased in SLE 0.025 -0.63 L27560 IGFBP5;insulin-like GF BP5 decreased in SLE <0.005 -1.43 NM_004417 DUSP1; phosphatase decreased in SLE <0.005 -2.25 NM_005252 FOS decreased in SLE 0.002 -1.64 NM_001964 EGR1; zink finger protein decreased in SLE 0.008 -1.48

(1) Genes are identified by their official gene name as assigned in LocusLink, if available. In addition a commonly known gene description or functional assignment has been listed for most genes. Abbreviations used: rec=receptor; synthet=synthetase; diff=differentiation; ag=antigen; neutr=neutrophil; ass=associated; fac=factor; HC=heavy chain; LC=light chain; GF=growth factor; BP=binding protein; (2) Gene clusters “B cells”, “IFN-inducible”, “myeloid” and “fibrosis” are increased in SLE glomeruli compared to controls and the cluster “decreased in SLE” is decreased in SLE glomeruli compared to controls. Genes indicated by an asterisk are included in the myeloid subcluster, as described in the text. (3) P values refer to the values obtained when comparing the expression of each gene in SLE glomeruli to the expression in controls. (4) Listed is the average of the log2 intensity of expression of each gene in all SLE glomeruli relative to the mean of the controls. These averages have been calculated for the use in this table to simplify data presentation and are not used in other calculations where instead the intensity of expression in each sample is used. A value of 1 is a 2-fold change.