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Table 3 Representative gene expression changes increased in BALBLps-d tumors.

From: Transcriptomic analysis of pathways regulated by toll-like receptor 4 in a murine model of chronic pulmonary inflammation and carcinogenesis

Gene Symbol Gene Name Affymetrix Probe ID Major GO Category(ies)
Angiogenesis
Anpep alanyl aminopeptidase 1421424_a_at angiogenesis; proteolysis
Col18a1 procollagen, type XVIII, alpha 1 1418237_s_at angiogenesis
Nus1 nuclear undecaprenyl pyrophosphate synthase 1 homolog 1419915_at angiogenesis; multicellular organismal development
Apoptosis and cell death
Bcl2l14 bcl2-like 14 1424814_a_at apoptosis
Cideb cell death-inducing DNA fragmentation factor, alpha subunit-like effector B 1418976_s_at apoptosis; induction of apoptosis
Pglyrp1 peptidoglycan recognition protein 1 1449184_at apoptosis; immune response
Cell cycle and cell growth
Aspm asp-like, microcephaly associated 1422814_at cell cycle; mitosis
Ereg Epiregulin 1419431_at regulation of progression through cell cycle; angiogenesis
Cenpf centromere protein F 1427161_at G2 and M phase of mitotic cell cycle
Mycn v-myc myelocytomatosis viral related oncogene, neuroblastoma derived   regulation of progression through cell cycle; regulation of transcription, DNA-dependent
Immune response
Clcf1 cardiotrophin-like cytokine factor 1 1437270_a_at cell surface receptor linked signal transduction; JAK-STAT cascade
Flt3l FMS-like tyrosine kinase 3 ligand 1422115_a_at lymphocyte differentiation
H2-oa histocompatibility 2, O region alpha locus 1419297_at immune response; antigen processing and presentation
Klrb1b killer cell lectin-like receptor subfamily B member 1B 1420421_s_at negative regulation of natural killer cell mediated cytotoxicity
Raet1a retinoic acid early transcript 1, alpha 1420603_s_at positive regulation of immune response to tumor cell
Inflammatory response and chemotaxis
Ccr 1 chemokine (C-C motif) receptor 1 1419610_at inflammatory response; signal transduction
Cxcl4; Pf4 platelet factor 4; chemokine (C-X-C motif) ligand 4 1448995_at chemotaxis; immune response
Cxcl5, Ena-
78
chemokine (C-X-C motif) ligand 5 1419728_at chemotaxis; inflammatory response
Cxcl9, Mig chemokine (C-X-C motif) ligand 9 1418652_at inflammatory response; immune response
Cxcl11, Itac chemokine (C-X-C motif) ligand 11 1419697_at chemotaxis; inflammatory response
Kng1 kininogen 1 1416676_at inflammatory response; blood coagulation
Spp1 secreted phosphoprotein 1 1449254_at ossification; anti-apoptosis
Protein synthesis and turnover
Cdkn2a cyclin-dependent kinase inhibitor 2A 1450140_a_at regulation of cyclin-dependent protein kinase activity; cell cycle
Cfi †‡ Complement component factor i 1418724_at proteolysis; immune response
Gzme granzyme E 1421227_at proteolysis; cytolysis
F 10 coagulation factor X 1449305_at proteolysis
  1. These genes were identified in the "Up-in-KO_tumor" profile (A) and "Down in WT tumor" profile (B) that are below the p value set for the DAVID analysis (p < 0.0001); see Additional file 2, Table S1 for the complete profile gene lists.
  2. *Representative increased genes from the "Up-in-KO_tumor" profile that were higher in the BALBLpsdtumors compared to BALB mice. These genes were identified after bioinformatic analysis filtering first on biological patterns using both Genespring and Spotfire Software followed by filtering on GO biological categories using the DAVID Bioinformatics Database. Genes upregulated ≥ 1.5-2-fold in BALBLspdtumors vs. BALB tumors based on GeneSpring. Genes with significant interaction effects comparing strain (BALB vs BALBLspd) and treatment (MCA, MCA/BHT tumors, MCA/BHT uninvolved tissue) (p < 0.05). Bolded genes are those genes in common with the gene list identified for the 4BHT study (see Table 1).