TABLE 2.

Significant genes up- or down-regulated by LeTx in RAW 264.7 murine macrophages from 0 to 3 h as determined by four separate analysis methods (grouped by function)a

Function and GenBank identificationGene or gene product nameResult by method:
GCOS (fold change)Spotfire (fold change)SAM (fold change)ANOVA (P value)LPS (GCOS; fold change)PA (GCOS; fold change)
Cell adhesion
    NM_020008.1C-type (calcium-dependent, carbohydrate recognition domain) lactin, superfamily member 122.1221.68E−05
Cell cycle
    BC003290.1Cyclin 1−2−2−1.60.000866
Cytoskeletal regulation
    AV148480Thymosin, beta 10−2.1−2.2−55.58E−05
    BB096368Thymosin, beta 10−2.4−2.3−3.50.000787
    NM_025284.1Thymosin, beta 10−2.4−2.5−2.50.001843
    NM_021278.1Thymosin, beta 4−2−2−4.70.000101
    NM_009405.1Troponin I, skeletal, fast 2−3.1−2.3−1.80.000574
    BG094946Cytoplasmic dynein light chain−2−2.1−6.34.98E−06
Energy production
    NM_025983.1ATP synthase epsilon chain, mitochondrial−2.5−2.7−3.50.000783
    NM_025650.1Ubiquinol-cytochrome c reductase (6.4-kDa) subunit−2.5−2.8−2.30.022367
    AW106975Ubiquinol-cytochrome c reductase complex 11-kDA protein (cDNA)−2.3−2.5−20.00247
    C88880NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 7−2.2−2−3.60.000554
    AK009614.1Cytochrome c oxidase subunit VIIa polypeptide 2-like−2.1−2−6.43.75E−06
    NM_010885.1NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 2−2−2−1.80.042225
Immune response- inflammation
    NM_009404.1CD137 ligand−2.6−2.3−1.80.006252
    AF128218.1Mip-1 beta2.22.21.70.0302233
    NM_011905.1Toll-like receptor 22.32.12.10.001
    NM_009856.1CD83 antigen3.54.14.50.0289762.51.6
    NM_030612.1Molecule possessing ankyrin repeats induced by LPS (mail; pending)4.33.740.0305239.8
    L38281.1Immune-responsive gene 1 (Irg1)6.57.33.50.02511518.4
    NM_009140.1Mip-29.48.98.40.03716121.12
    NM_008871.1Plasminogen activator inhibitor, type I9.66.13.80.00995
Protein metabolism
    AV216370Ribosomal protein L36−2.4−2.2−1.90.004075
    NM_009084.1Ribosomal protein L37a−2.4−2.4−1.90.012705
    NM_018730.1Ribosomal protein L36−2.3−2.3−20.002914
    NM_009079.1Ribosomal protein L22−2.1−2.1−1.80.017672
    NM_025592.1Ribosomal protein L35−2.1−2.2−2.20.002808
    NM_018860.1Ribosomal protein L41−2.1−2−20.003252
    NM_023133.1Ribosomal protein S19−2.1−2.2−1.90.026968
    BF237074Ubiquitin A-52 residue ribosomal protein fusion product 1 (Uba52)−2−2.4−2.20.002938
    BC004625.1Ubiquitin-like protein Nedd8−2−2.2−3.90.000394
    NM_016738.1Ribosomal protein L13−2−2.2−1.80.003931
    AV124660Ribosomal protein L26−2−2−1.70.021368
    NM_009082.1Ribosomal protein L29−2−2−1.80.02696
    AV124739Ribosomal protein L35−2−2−1.90.010129
    AV124680Ribosomal protein L35−2−2−1.70.027161
    NM_018730.1Ribosomal protein L36−2−2.1−2.10.002701
    NM_019865.1Ribosomal protein L44−2−2.3−2.20.006207
    NM_009091.1Ribosomal protein S15−2−2.1−1.80.038687
    AV151252Ribosomal protein S21−2−2.7−1.90.018089
    AV123577Ribosomal protein S21−2−2.6−20.054336
    AA208652Ribosomal protein S27−2−2−1.70.015819
    AA030209Ribosomal protein S17221.97.50E-06
Protein traffic king
    NM_024171.1Sec61 beta subunit−2.1−2−20.017967
    BO010487.1ADP ribosylation factor2.12.12.10.000341−4.3
Signaling
    AF260717.1Calcipressin 16.16.65.86.06E−07
    BC021599.1Guanine nucleotide binding protein (G protein), gamma 2 subunit−5.4−5.9−3.80.017082
    NM_026268.1Dual-specificity phosphatase 6 (Dusp6)−3.3−3.5−5.29.10E−06
    BC026550.1Protein kinase inhibitor gamma (PKI gamma)−2.6−2.3−2.10.021481
    BB780848Pleckstrin homology domain-containing, family A (phosphoinositide-binding-specific) member 3 (Fapp1)−2.2−2.4−1.80.001432−1.6
    AW495875Protein tyrosine phosphatase 4a2−2−2.1−1.90.04473
    BC011193.1Prostaglandin E2 receptor, EP4 subtype2.1220.000302
    NM_008979.1Protein tyrosine phosphatase, non-receptor type 82.12.32.30.000359
    NM_010907.1NF-κB inhibitor alpha2.221.98.61E-062.3
    AF326555.1Phosphodiesterase 4B, cAMP specific2.22.62.41.23E-064.3
    BB100249Regulator of G-protein signaling 16 (Rgs16)3.33.63.19.93E-071.5
    U94828.1Regulator of G-protein, signaling 16 (Rgs16)15.41814.91.48E−063.5
Stress-apoptosis
    AF274027.1Glutathione peroxidase 4−2.4−2.1−7.21.50E-06
    BF658806Ribosome-associated membrane protein 4 (Ramp4)−2.4−2.7−2.10.024068
    AK010420.1Growth arrest and DNA damage-inducible 45 beta (GADD45 beta)2.84.33.52.48E-063.7
    AI323528Growth arrest and DNA, damage-inducible 45 beta (GADD45 beta) (cDNA)32.92.86.43E−053.2
Transcription factor
    NM_011980.1Zinc finger protein 146 (Zfp146)−10.4−8.4−4.10.00246
    BC002081.1c-Jun−2.8−2.6−2.60.0230961.9
    BB031791Zinc finger protein 36, C3H type-like 2−2.4−2.2−2.20.004184
    NM_007913.1Early growth response 1 (Egr1)−2.2−2.7−4.59.00E−052.8
    BC019946.1Activating transcription factor 3 (ATF-3)2.12.71.70.030924
    AF155372.1Nuclear factor κB subunit p100 (Nfkb2)2.12.11.80.0001733
    NM_011498.1Basic helix-loop-helix domain, containing, class B22.321.70.019764
    NM_009046.1Oncogene-related B (Rel-B)2.52.62.32.01E−052.5
    NM_008452.1Kruppel-like factor 22.6330.00038
    AY061760.1Nuclear factor, interleukin-3, regulated (Nfil3)3.73.93.30.000462
    X06746.1Early growth response 2 (Egr2)3.87.83.90.0059772
    BE824605Orphan nuclear receptor Nr4a24.53.93.50.000169
    AF201289.1TSC22-related inducible leucine zipper 3c (TSC-22R)4.54.62.90.001233
    X06746.1Early growth response 2 (Egr2)55.446.98E−072.5
    NM_010444.1Orphan nuclear receptor Nr4a19.36.96.80.0016022
    NM_013613.1Orphan nuclear receptor Nr4a211.31030.001257
Transporter
    BB277461Neutral amino acid transporter A2.43.11.80.006518
Other
    NM_007763.1Cysteine-rich intestinal protein (Crip)−2.4−2.4−3.50.000937
    NM_010240.1Ferritin light chain 1−2.1−2.1−5.52.45E-05
    NM_015786.1Histone H1.22.22.22.20.00054
    BB533903Histone H1.22.22.32.30.011142−1.5
    W91024Histone H2A−2.1−2.1−4.87.56E−05
    U29539.1Lysosome-associated protein transmembrane 52224.63E-07
    AK004120.1Nucleolar protein family A, member 3 (Nola3)−2.1−2.3−2.10.019914
    BM210485Plectin 12.121.60.0099021.5
    U37500.1RNA polymerase II largest, subunit (RPB1)22.61.60.009562
    AA709993Small EDRK-rich factor 1 (Serf1)−2.2−2.4−1.80.011101
    NM_009121.1Spermidine supermine N1-acetyltransferase−2.1−2.1−1.70.0021821.5
    NM_009169.1Split hand foot deleted gene 1 (Shfdg1)−2.1−2−1.90.0168581.5
Unknown
    BE945188cDNA−2.2−2.4−20.010897
    AF353245.1D12 protein−2.1−2.2−2.20.001657
    AF353245.1D12 protein−2.1−2.6−2.10.001966
    AV012102cDNA−2.1−2.2−1.90.021583
    BC006603.1cDNA−2−2.1−1.80.004157
    W42220cDNA−2−2−1.90.008602
    BQ044335cDNA−2−2.5−1.80.009801
    AV170241cDNA−2−2.1−1.90.041788
    NM_138743.1cDNA−2−2.2−1.90.048444
    NM_022332.1Suppression of tumorigenicity22.520.000302
    AA049040cDNA2.121.90.0098611.6
    BB408147cDNA2.42.125.01E−07
    BB183628cDNA2.42.12.10.002364
    BC025169.1cDNA2.83.22.50.013931
    BG066184cDNA9.29.44.20.002088
    NM_008383.1Centrosomal protein 210.714.43.50.000368
  • a Genes listed twice were represented on the GeneChips by more than one probe set, and each was determined separately to be significantly up- or down-regulated by LeTx. A minus sign before the value indicates down-regulation of the gene.