Table 3.
Comparison of lipopolysaccharide (LPS)-mediated gene expression between type I and type II responders. Genes are grouped based on known or putative function as determined by GeneOntology classifications.
| Gene ID | GOMF | Type II SLR | Type I SLR | P-value |
|---|---|---|---|---|
| 1 | Transcription factor binding/// activity | |||
| 203973_s_at | CCAAT/enhancer binding protein (C/EBP), delta | 3·1 | 1·94 | 0·0068 |
| 201502_s_at | Nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha | 2·06 | 1·6 | 0·24 |
| 209636_at | Nuclear factor of kappa light polypeptide gene enhancer in B cells 2 (p49/p100) | 1·93 | 1·65 | 0·68 |
| 208436_s_at | Interferon regulatory factor 7 | 1·12 | ||
| 2 | Cytoskeletal protein binding | |||
| 202071_at | Syndecan 4 (amphiglycan, ryudocan) | 1·1 | ||
| 3 | GTP binding/// GTPase activity | |||
| 202086_at | Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) | 2·84 | ||
| 4 | ATP binding/// ATPase activity | |||
| 202307_s_at | Transporter 1, ATP-binding cassette B (MDR/TAP) | 1·22 | ||
| 204567_s_at | ATP-binding cassette G (WHITE) | 1·2 | 1·14 | 0·83 |
| 205552_s_at | 2′,5′-oligoadenylate synthetase 1, 40/46 kDa | 2·1 | ||
| 209545_s_at | Receptor-interacting serine–threonine kinase 2 | 1·27 | ||
| 218943_s_at | DEAD (Asp–Glu–Ala–Asp) box polypeptide 58 | 1·31 | ||
| 219209_at | Interferon induced with helicase C domain 1 | 1·89 | 1·2 | 0·21 |
| 5 | Complement activation | |||
| 202357_s_at | B-factor, properdin | 2·25 | 1·,93 | 0·5 |
| 208747_s_at | Complement component 1, s | 3·9 | 2·24 | 0·24 |
| 6 | Immune response | |||
| 202411_at | Interferon, alpha-inducible protein 27 | 1·55 | ||
| 203153_at | Interferon-induced protein with tetratricopeptide repeats | 3·85 | ||
| 203828_s_at | Natural killer cell transcript 4 | 2·02 | 2 | 0·93 |
| 204279_at | Proteasome subunit, beta type, 9 | 1·28 | ||
| 204415_at | Interferon, alpha-inducible protein | 1·5 | ||
| 207339_s_at | Lymphotoxin beta | 1·4 | 1·01 | 0·14 |
| 208729_x_at | Major histocompatibility complex, class I, B | 1·4 | ||
| 209795_at | CD69 antigen | 2·04 | 2·71 | 0·3 |
| 211911_x_at | Major histocompatibility complex, class IC/IB | 1·85 | ||
| 7 | Cathepsin K activity | |||
| 202450_s_at | Cathepsin K | 1·41 | 1·28 | 0·77 |
| 8 | Angiogenesis | |||
| 202510_s_at | Tumour necrosis factor, alpha-induced protein 2 | 1·12 | ||
| 9 | Protein binding/// transmembrane receptor activity | |||
| 202637_s_at | Intercellular adhesion molecule 1 (ICAM) | 3·3 | 2·15 | 0·0005 |
| 203868_s_at | Vascular cell adhesion molecule 1 (VCAM) | 3·05 | 2·1 | 0·06 |
| 205483_s_at | Interferon, alpha-inducible protein | 1·4 | ||
| 206211_at | Selectin E (endothelial adhesion molecule 1) | 5·66 | 4·28 | 0·041 |
| 207196_s_at | TNFAIP3 interacting protein 1 | 1·28 | ||
| 209417_s_at | Interferon-induced protein 35 | 1·13 | ||
| 214587_at | Collagen, type VIII, alpha 1 | 1·52 | ||
| 204105_s_at | Neuronal cell adhesion molecule | 1·16 | ||
| 214022_s_at | Interferon induced transmembrane protein 1 | 1·36 | ||
| 10 | DNA binding/// protein binding | |||
| 202643_s_at | Tumour necrosis factor,alpha-induced protein 3 | 2 | 1 | 0·0021 |
| 206321_at | Regulatory factor X, 1 (influences HLA class II) | 0·3 | ||
| 214290_s_at | Histone 2, H2aa | 0·92 | ||
| 11 | Chemokine activity | |||
| 202859_x_at | Interleukin 8 | 4·1 | 2·4 | 0·0062 |
| 203687_at | MCP-1 | 2·6 | 1·12 | 0·006 |
| 204470-at | Melanoma growth stimulating activity-alpha | 3·8 | 3 | 0·177 |
| 205476_at | Chemokine (C–C motif) ligand 20 | 4·46 | 3·56 | 0·42 |
| 207850_at | Chemokine (C–X–C motif) ligand 3 | 5 | 3·48 | 0·011 |
| 209774_x_at | Chemokine (C–X–C motif) ligand 2 | 3·95 | 2·78 | 0·017 |
| 211122_s_at | Fractalkine | 2 | 1·3 | 0·12 |
| 214974_x_at | Chemokine (C–X–C motif) ligand 5 | 4·45 | 4·1 | 0·43 |
| 215101_s_at | ENA-78 | 5·28 | 3·84 | 0·06 |
| 823_at | Chemokine (C–X3–C motif) ligand 1 | 1·9 | 1·05 | 0·08 |
| 204533_at | IP-10 | 1·7 | ||
| 206336_at | Granulocyte chemotactic protein 2 | 4·6 | 2·77 | 0·031 |
| 210163_at | Chemokine (C–X–C motif) ligand 11 | 2·39 | 1·54 | 0·01 |
| 12 | Cathepsin S activity | |||
| 202902_s_at | Cathepsin S | 1·87 | 1·2 | 0·077 |
| 13 | Ion transporter activity/// ion binding | |||
| 212067_s_at | Complement component 1, r | 1·7 | ||
| 203124_s_at | Solute carrier family 11, member 2 | 1 | ||
| 204404_at | Solute carrier family 12 member 2 | 1·5 | 2·8 | 0·04 |
| 205680_at | Stromelysin 2 | 1·72 | 1·34 | 0·29 |
| 216841_s_at | Superoxide dismutase 2, mitochondrial | 3·9 | 2·6 | 0·033 |
| 217873_at | Calcium binding protein 39 | 1·12 | ||
| 220091_at | Solute carrier family 2 | 1·33 | ||
| 14 | Blood coagulation | |||
| 203887_s_at | Thrombomodulin | −1·90 | ||
| 213506_at | Thrombin receptor-like 1 | 1·64 | 0·98 | 0·01 |
| 15 | Cell proliferation | |||
| 33304_at | Interferon stimulated gene 20 kDa | 1·54 | 1 | 0·07 |
| 16 | Phospholipase–cyclooxygenase–lipase pathway | |||
| 204748_at | Prostaglandin G/H synthase and cyclooxygenase | 2·56 | 1·22 | 0·003 |
| 209785_s_at | Phospholipase A2, group IVC | 2·08 | 2·15 | 0·75 |
| 219181_at | Lipase, endothelial | 2·2 | 1·08 | 0·01 |
| 17 | Transferase activity | |||
| 221765_at | UDP-glucose ceramide glucosyltransferase | 1·4 | ||
| 18 | Intercellular junction assembly | |||
| 204904_at | Connexin 37 | −2·15 | ||
| 19 | Cytokine activity | |||
| 205207_at | Interleukin 6 | 1·84 | 1·2 | 0·046 |
| 207442_at | Colony stimulating factor 3 (granulocyte) | 5·5 | 2·6 | 0·07 |
| 210229_s_at | Colony stimulating factor 2 (granulocyte-macrophage) | 4·68 | 3·4 | 0·26 |
| 211518_s_at | Bone morphogenetic protein 4 | −1·63 | ||
| 219424_at | Epstein–Barr virus induced gene 3 | 4·11 | 3·45 | 0·09 |
| 20 | Proteolysis and peptidolysis | |||
| 205890_s_at | Ubiquitin D | 6·12 | 4·3 | 0·05 |
| 21 | G-protein coupled receptor protein signalling pathway | |||
| 212977_at | Chemokine orphan receptor 1 | 1·8 | ||
| 22 | Transferase activity | |||
| 213988_s_at | Spermidine/spermine N1-acetyltransferase | 1·27 |
Bold type: enlisted are all the genes that were significantly up-regulated by lipolysaccharide (LPS) in all type I and all type II responders. Italic bold type: enlisted are all the genes that were expressed in both types I and II responders, but were expressed significantly more strongly in type II responders. Note that the P-value refers to the comparison between types I and II responders. Plain text: enlisted are genes that were significantly modulated by LPS in all type II responders only. The results are expressed as mean signal log ratio (SLR).