TABLE 1.
Mean TLR4-dependent gene fold changes categorized by function
| Affymetrix probe ID | Gene symbol | Genbank accession no. | Change (fold) at 4 vs 0 h
|
Results in C3H/HeJ mice at 4 vs 0 ha | Description | ||
|---|---|---|---|---|---|---|---|
| C57BL/6 | 129/SvJ | C3H/HeN | |||||
| Cytokine/chemokine | |||||||
| 101160_at | Cxcl2 | X53798 | 51.27 | 41.9 | 13.18 | A | Chemokine (C-X-C motif) ligand 2/MIP-2 |
| 102218_at | IL-6 | X54542 | 26.91 | 4.89 | 25.11 | A | IL-6 |
| 102424_at | Ccl3 | J04491 | 8.51 | 3.05 | 3.05 | A | Chemokine (C-C motif) ligand 3/MIP-1α |
| 102629_at | Tnf | D84196 | 9.45 | 5.54 | 3.34 | A | TNF |
| 102736_at | Ccl2 | M19681 | 32.90 | 6.73 | 6.23 | A | Chemokine (C-C motif) ligand 2/MCP-1 |
| 103486_at | IL1b | M15131 | 21.56 | 6.68 | 4.82 | A | Interleukin 1β |
| 104388_at | Ccl9 | U49513 | 4.99 | 1.42 | 2.25 | A | Chemokine (C-C motif) ligand 9 |
| 94755_at | IL1a | M14639 | 9.45 | 5.10 | 4.82 | A | IL-1α |
| 95349_g_at | Cxc11 | J04596 | 61.39 | 25.99 | 25.63 | A | Chemokine (C-X-C motif)/KC-GRO |
| 98772_at | Cxc15 | U27267 | 28.05 | 3.46 | 12.64 | A | Chemokine (C-X-C motif) ligand 5 |
| 94142_at | G-CSF | M13926 | 2.83 | 2.13 | 3.97 | A | Granulocyte colony-stimulating factor |
| 102914_s_at | A1b | U23778 | 3.76 | 1.93 | 2.60 | A | Hematopoietic-specific early response A1-b |
| Receptors | |||||||
| 102658_at | IL-12 | X59769 | 12.38 | 3.39 | 8.63 | A | IL-1 receptor, type II |
| 931198_at | Csf3r | M58288 | 4.41 | 1.58 | 3.20 | A | Colony-stimulating factor 3 receptor (granulocyte) |
| 93430_at | Cmkor1 | AF000236 | 4.06 | 1.67 | 3.78 | A | Chemokine orphan receptor 1 |
| 93871_at | IL-1m | L32838 | 8.06 | 3.18 | 2.89 | A | IL-1 receptor antagonist |
| 102255_at | Osmr | AB015978 | 3.03 | 1.33 | 2.08 | Chg | Oncostatin receptor |
| 102663_at | Plaur | X62700 | 4.03 | 2.19 | 2.77 | NS | Urokinase plasminogen activator receptor |
| 101410_at | mCPE-R | AB000713 | 4.06 | 1.88 | 5.35 | A | CPE receptor |
| 98088_at | CD14 | X13333 | 7.84 | 2.82 | 4.17 | Fld<2 | LPS receptor |
| 99413_at | CCR1 | U29678 | 6.96 | 3.05 | 2.63 | *A | Chemokine (C-C) receptor 1 |
| Apoptosis | |||||||
| 101979_at | Gadd45g | AF055638 | 3.34 | 2.17 | 2.20 | A | Growth arrest and DNA damage-inducible 45 gamma |
| 99392_at | Tnfaip3 | U19463 | 17.75 | 9.45 | 3.76 | A | TNF-α-induced protein 3 |
| Signal/transduction | |||||||
| 102430_at | Myd88 | X51397 | 2.10 | 1.16 | 2.11 | A | Myeloid differentiation primary response gene 88 |
| 96747_at | Arhu | AW121294 | 2.48 | 1.56 | 3.12 | A | ras homolog gene family, member U |
| 98423_at | Gjb2 | M81445 | 2.14 | 2.41 | 4.89 | A | Gap junction membrane channel protein beta 2 |
| 92232_at | SOCS-3 | U88328 | 8.28 | 3.94 | 4.50 | A | Suppressor of cytokine signaling 3 |
| 92534_at | GEM | U10551 | 2.23 | 1.56 | 4.41 | A | GTP binding protein |
| Adhesion | |||||||
| 102805_at | Ceacam1 | M77196 | 2.89 | 1.11 | 3.53 | A | CEA-related cell adhesion molecule 1 |
| 103005_s_at | CD44 | X66084 | 3.07 | 1.48 | 2.08 | A | CD44 antigen |
| 96752_at | Icam1 | M90551 | 2.28 | 1.47 | 2.51 | Fld<2 | Intercellular adhesion molecule |
| Enzymes | |||||||
| 102905_at | Casp4 | Y13089 | 2.57 | 1.05 | 2.25 | A | Caspase 4, apoptosis-related cysteine protease |
| 103341_at | Ctps | U49350 | 2.89 | 1.40 | 2.01 | A | Cytidine 5′-triphosphate synthase |
| 104509_at | Ch25h | AF059213 | 9.25 | 2.19 | 2.75 | A | Cholesterol 25-hydroxylase |
| 104671_at | Ampd3 | D88994 | 3.05 | 1.67 | 2.22 | A | AMP deaminase 3 |
| 99985_at | TxNR | AB027565 | 3.70 | 1.92 | 3.56 | Chg | Thioredoxin reductase 1 |
| 98473_at | Arg2 | AF032466 | 4.20 | 2.39 | 3.89 | A | Arginase type II |
| 94297_at | FK506 binding protein 5 | U16959 | 6.02 | 2.57 | 2.81 | A | FK506 binding protein 5 |
| 103024_at | Adam8 | X13335 | 3.18 | 4.41 | 8.75 | A | A disintegrin and metalloprotease domain 8 |
| Transcriptional factors | |||||||
| 102955_at | NFIL3/E4BP4 | U83148 | 3.03 | 1.89 | 2.55 | A | Nuclear factor, IL-3 regulated |
| 104712_at | C-MYC | L00039 | 6.32 | 2.58 | 5.58 | A | Myelocytomatosis oncogene |
| Other | |||||||
| 102780_at | Tx01 | Z31362 | 3.81 | 3.03 | 3.11 | A | |
| 103887_at | MRP14 | M83219 | 5.86 | 6.36 | 5.03 | NS | Migration inhibitory factor-related protein 14 |
| 92315_at | Slfn4 | AF099977 | 4.20 | 1.13 | 2.17 | A | Schlafen4 |
| 93861_f_at | Endogenous murine leukemia virus modified polytropic provirus | M17327 | 3.05 | 1.16 | 2.33 | A | Endogenous murine leukemia virus modified polytropic provirus |
| 92471_i_at | Slfn2 | AF099973 | 2.36 | 1.95 | 2.30 | A | Schlafen2 |
| 103448_at | MRP8 | M83218 | 5.86 | 6.50 | 4.56 | NS | Intracellular Ca2+ binding protein |
| 93573_at | MT1 | V00835 | 7.89 | 5.70 | 6.23 | Fld<2 | Metallothionein I |
| 99915_at | SDGF | L41352 | 2.46 | 2.33 | 2.53 | A | Amphiregulin |
| 103328_at | I-TRAF | U59864 | 2.39 | 1.62 | 2.33 | A | TRAF-interacting activator |
| 93104_at | BTG1 | Z16410 | 2.07 | 1.48 | 2.38 | Fld<2 | B-cell-transclocation gene 1 protein |
| 98067_at | P21 | U09507 | 2.19 | 2.10 | 2.66 | A | Cyclin-dependent kinase inhibitor 1A |
| 97689_at | Coagulation factor III | M26071 | 3.36 | 3.39 | 2.35 | Chg | Coagulation factor III |
a
Fold changes were not shown for those genes that had detection calls of absent (A) in the 4-h treated group; that had an inappropriate change call (Chg), such that there was not a call of increased or marginally increased in greater than half of the comparisons made; that had a fold change less than 1 (Fld<2); or that were not determined to be significant (NS) by parametric and nonparametric tests with a P cutoff value of ≤0.05.