Table 3.
Representative gene expression changes increased in BALBLps-d tumors.
| 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 | |||
| Ccr1 | 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 |
| F10 | coagulation factor X | 1449305_at | proteolysis |
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.
*Representative increased genes from the "Up-in-KO_tumor" profile that were higher in the BALBLpsd tumors 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 BALBLspd tumors 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).