Data Set 1. Biological analysis of the genes found to be significant in the endotoxin study. Pages 2 – 105: Q values, gene names and annotation on the genes significant at FDR = 0.1%. Pages 106 – 127: Global functional analysis of the down-regulated genes. Pages 128 – 169: Global functional analysis of the up-regulated genes. Probe Set q-value Direction Gene Annotation 117_at 9.60E-05 up HSPA6 heat shock 70kDa protein 6 (HSP70B') 1405_i_at 2.00E-06 down CCL5 chemokine (C-C motif) ligand 5 PRP8 pre-mRNA processing factor 8 200000_s_at 2.50E-05 down PRPF8 homolog (yeast) PRP8 pre-mRNA processing factor 8 200000_s_at 0.000712 down PRPF8 homolog (yeast) 200001_at 0.000658 down CAPNS1 calpain, small subunit 1 200002_at 2.00E-06 down RPL35 ribosomal protein L35 200002_at 2.00E-06 down RPL35 ribosomal protein L35 200003_s_at 1.10E-05 down RPL28 ribosomal protein L28 200003_s_at 1.10E-05 down RPL28 ribosomal protein L28 eukaryotic translation initiation factor 3, 200005_at 2.00E-06 down EIF3S7 subunit 7 zeta, 66/67kDa eukaryotic translation initiation factor 3, 200005_at 2.00E-06 down EIF3S7 subunit 7 zeta, 66/67kDa Parkinson disease (autosomal 200006_at 4.70E-05 down PARK7 recessive, early onset) 7 Parkinson disease (autosomal 200006_at 8.70E-05 down PARK7 recessive, early onset) 7 200008_s_at 5.40E-05 up GDI2 GDP dissociation inhibitor 2 200008_s_at 0.000361 up GDI2 GDP dissociation inhibitor 2 200009_at 0.000171 down GDI2 GDP dissociation inhibitor 2 200010_at 2.00E-06 down RPL11 ribosomal protein L11 200010_at 2.00E-06 down RPL11 ribosomal protein L11 200012_x_at 2.00E-06 down 200012_x_at 2.00E-06 down 200013_at 2.00E-06 down MAMDC2 MAM domain containing 2 200013_at 2.00E-06 down MAMDC2 MAM domain containing 2 neural precursor cell expressed, 200015_s_at 2.80E-05 down NEDD5 developmentally down-regulated 5 neural precursor cell expressed, 200015_s_at 0.000169 down NEDD5 developmentally down-regulated 5 heterogeneous nuclear 200016_x_at 2.00E-06 down HNRPA1 ribonucleoprotein A1 heterogeneous nuclear 200016_x_at 2.00E-06 down HNRPA1 ribonucleoprotein A1 200017_at 2.00E-06 down RPS27A ribosomal protein S27a 200017_at 1.10E-05 down RPS27A ribosomal protein S27a 200018_at 2.00E-06 down RPS13 ribosomal protein S13 200018_at 2.00E-06 down RPS13 ribosomal protein S13 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal 200019_s_at 2.00E-06 down FAU protein S30 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal 200019_s_at 2.90E-05 down FAU protein S30 200020_at 9.20E-05 down TARDBP TAR DNA binding protein 200022_at 2.00E-06 down RPL18 ribosomal protein L18 200022_at 2.00E-06 down RPL18 ribosomal protein L18 eukaryotic translation initiation factor 3, 200023_s_at 2.00E-06 down EIF3S5 subunit 5 epsilon, 47kDa eukaryotic translation initiation factor 3, 200023_s_at 2.00E-06 down EIF3S5 subunit 5 epsilon, 47kDa 200024_at 2.00E-06 down RPS5 ribosomal protein S5 200024_at 2.00E-06 down RPS5 ribosomal protein S5 200025_s_at 2.00E-06 down RPL27 ribosomal protein L27 200025_s_at 2.00E-06 down RPL27 ribosomal protein L27 200026_at 2.00E-06 down RPL34 ribosomal protein L34 200026_at 2.00E-06 down RPL34 ribosomal protein L34 200027_at 2.00E-06 down NARS asparaginyl-tRNA synthetase 200027_at 4.00E-06 down NARS asparaginyl-tRNA synthetase 200028_s_at 2.00E-06 down STARD7 START domain containing 7 200028_s_at 2.00E-06 down STARD7 START domain containing 7 200029_at 2.00E-06 down RPL19 ribosomal protein L19 200029_at 2.00E-06 down RPL19 ribosomal protein L19 solute carrier family 25 (mitochondrial 200030_s_at 2.00E-06 down SLC25A3 carrier; phosphate carrier), member 3 solute carrier family 25 (mitochondrial 200030_s_at 9.60E-05 down SLC25A3 carrier; phosphate carrier), member 3 200031_s_at 2.00E-06 down RPS11 ribosomal protein S11 200031_s_at 2.00E-06 down RPS11 ribosomal protein S11 200032_s_at 2.00E-06 down RPL9 ribosomal protein L9 200032_s_at 2.00E-06 down RPL9 ribosomal protein L9 200034_s_at 2.00E-06 down RPL6 ribosomal protein L6 200034_s_at 2.00E-06 down RPL6 ribosomal protein L6 200036_s_at 2.00E-06 down RPL10A ribosomal protein L10a 200036_s_at 2.00E-06 down RPL10A ribosomal protein L10a chromobox homolog 3 (HP1 gamma 200037_s_at 0.000716 down CBX3 homolog, Drosophila) 200038_s_at 2.00E-06 down RPL17 ribosomal protein L17 200038_s_at 2.00E-06 down RPL17 ribosomal protein L17 proteasome (prosome, macropain) 200039_s_at 3.80E-05 down PSMB2 subunit, beta type, 2 200041_s_at 0.000479 down BAT1 HLA-B associated transcript 1 200042_at 8.90E-05 down HSPC117 hypothetical protein HSPC117 200042_at 0.000676 down HSPC117 hypothetical protein HSPC117 enhancer of rudimentary homolog 200043_at 1.80E-05 down ERH (Drosophila) enhancer of rudimentary homolog 200043_at 2.80E-05 down ERH (Drosophila) 200050_at 2.00E-06 down ZNF146 zinc finger protein 146 200050_at 9.00E-06 down ZNF146 zinc finger protein 146 interleukin enhancer binding factor 2, 200052_s_at 2.00E-06 down ILF2 45kDa interleukin enhancer binding factor 2, 200052_s_at 5.00E-05 down ILF2 45kDa 200054_at 0.000485 down ZNF259 zinc finger protein 259 non-POU domain containing, octamer- 200057_s_at 2.00E-06 down NONO binding non-POU domain containing, octamer- 200057_s_at 2.00E-06 down NONO binding 200058_s_at 9.50E-05 down U5-200KD U5 snRNP-specific protein, 200-KD 200058_s_at 0.00039 down U5-200KD U5 snRNP-specific protein, 200-KD RNA binding protein S1, serine-rich 200060_s_at 2.00E-06 down RNPS1 domain RNA binding protein S1, serine-rich 200060_s_at 7.00E-06 down RNPS1 domain 200061_s_at 2.00E-06 down RPS24 ribosomal protein S24 200061_s_at 2.00E-06 down RPS24 ribosomal protein S24 200062_s_at 2.00E-06 down RPL30 ribosomal protein L30 200062_s_at 2.00E-06 down RPL30 ribosomal protein L30 nucleophosmin (nucleolar 200063_s_at 2.00E-06 down NPM1 phosphoprotein B23, numatrin) nucleophosmin (nucleolar 200063_s_at 2.00E-06 down NPM1 phosphoprotein B23, numatrin) 200067_x_at 9.80E-05 up SNX3 sorting nexin 3 200068_s_at 3.90E-05 down CANX calnexin 200068_s_at 0.000313 down CANX calnexin squamous cell carcinoma antigen 200069_at 4.00E-06 down SART3 recognised by T cells 3 squamous cell carcinoma antigen 200069_at 0.000177 down SART3 recognised by T cells 3 heterogeneous nuclear ribonucleoprotein D (AU-rich element 200073_s_at 2.00E-06 down HNRPD RNA binding protein 1, 37kDa) 200074_s_at 2.00E-06 down RPL14 ribosomal protein L14 200074_s_at 2.00E-06 down RPL14 ribosomal protein L14 200081_s_at 2.00E-06 down 200081_s_at 2.00E-06 down 200082_s_at 2.00E-06 down RPS7 ribosomal protein S7 200082_s_at 2.00E-06 down RPS7 ribosomal protein S7 200084_at 0.000965 down SMAP small acidic protein cytochrome c oxidase subunit IV 200086_s_at 7.70E-05 down COX4I1 isoform 1 cytochrome c oxidase subunit IV 200086_s_at 0.000548 down COX4I1 isoform 1 200088_x_at 2.00E-06 down RPL12 ribosomal protein L12 200088_x_at 2.00E-06 down RPL12 ribosomal protein L12 200089_s_at 2.00E-06 down RPL4 ribosomal protein L4 200089_s_at 2.00E-06 down RPL4 ribosomal protein L4 200090_at 0.000112 down FNTA farnesyltransferase, CAAX box, alpha 200091_s_at 2.00E-06 down RPS25 ribosomal protein S25 200091_s_at 0.000128 down RPS25 ribosomal protein S25 200092_s_at 2.00E-06 down RPL37 ribosomal protein L37 200092_s_at 3.80E-05 down RPL37 ribosomal protein L37 histidine triad nucleotide binding 200093_s_at 4.00E-06 down HINT1 protein 1 histidine triad nucleotide binding 200093_s_at 3.80E-05 down HINT1 protein 1 eukaryotic translation elongation factor 200094_s_at 2.00E-06 down EEF2 2 eukaryotic translation elongation factor *probe sets 200094_s_at 2.00E-06 down EEF2 2 200000_s_at - 200095_x_at 2.00E-06 down RPS10 ribosomal protein S10 200099_s_at are present on 200095_x_at 2.00E-06 down RPS10 ribosomal protein S10 both Human U133-A chip and 200098_s_at 2.00E-06 down ANAPC5 anaphase promoting complex subunit 5 U133-B chip. Therefore these 200098_s_at 2.00E-06 down ANAPC5 anaphase promoting complex subunit 5 probes are 200099_s_at 2.00E-06 down RPS3A ribosomal protein S3A measured twice 200099_s_at 2.00E-06 down RPS3A ribosomal protein S3A for each sample. eukaryotic translation initiation factor 3, 200595_s_at 4.70E-05 down EIF3S10 subunit 10 theta, 150/170kDa eukaryotic translation initiation factor 3, 200596_s_at 4.00E-06 down EIF3S10 subunit 10 theta, 150/170kDa 200599_s_at 0.00012 down TRA1 tumor rejection antigen (gp96) 1 200610_s_at 2.00E-06 down NCL nucleolin 200624_s_at 1.80E-05 down MATR3 matrin 3 200626_s_at 5.50E-05 down MATR3 matrin 3 200629_at 0.000553 up WARS tryptophanyl-tRNA synthetase SET translocation (myeloid leukemia- 200630_x_at 9.60E-05 down SET associated) SET translocation (myeloid leukemia- 200631_s_at 2.00E-06 down SET associated) 200634_at 2.80E-05 up PFN1 profilin 1 superoxide dismutase 1, soluble 200642_at 2.00E-06 down SOD1 (amyotrophic lateral sclerosis 1 (adult)) 200644_at 0.000459 down MLP MARCKS-like protein 200646_s_at 4.90E-05 up NUCB1 nucleobindin 1 eukaryotic translation initiation factor 3, 200647_x_at 2.00E-06 down EIF3S8 subunit 8, 110kDa 200649_at 1.90E-05 up NUCB1 nucleobindin 1 200650_s_at 4.20E-05 up LDHA lactate dehydrogenase A guanine nucleotide binding protein (G 200651_at 2.00E-06 down GNB2L1 protein), beta polypeptide 2-like 1 calmodulin 1 (phosphorylase kinase, 200655_s_at 0.000143 down CALM1 delta) solute carrier family 25 (mitochondrial carrier; adenine nucleotide 200657_at 2.00E-06 down SLC25A5 translocator), member 5 translocase of outer mitochondrial 200662_s_at 2.00E-06 down TOMM20 membrane 20