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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).