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Table 1 Representative gene expression changes increased in BALBLsp-d compared to BALB mice.

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)
Hbegf heparin-binding EGF-like growth factor 1418349_at angiogenesis; blastocyst growth
Mmp19 matrix metallopeptidase 19 1421977_at angiogenesis; peptidoglycan metabolic process
Timp1 tissue inhibitor of metallo-proteinase 1 1460227_at erythrocyte maturation
Cell cycle and cell growth
Cdkn1a cyclin-dependent kinase inhibitor 1A (P21) 1424638_at regulation of progression through cell cycle; response to DNA damage stimulus
Ereg †‡ epiregulin 1419431_at regulation of progression through cell cycle; angiogenesis
Mina myc induced nuclear antigen 1451042_a_at regulation of cell proliferation
Myc myelocytomatosis oncogene 1424942_a_at regulation of progression through cell cycle; release of cytochrome c from mitochondria
Socs3 suppressor of cytokine signaling 3 1455899_x_at regulation of cell growth; regulation of protein amino acid phosphorylation
Cell shape and morphogenesis
Krt19 keratin 19 1417156_at cytoskeleton organization and biogenesis
Tnc tenascin C 1416342_at cell adhesion
Tuba1c tubulin, alpha 1C 1416128_at microtubule-based process and movement
Inflammatory and immune response
Il6 interleukin 6 1450297_at neutrophil apoptosis
Lif leukemia inhibitory factor 1421207_at immune response; tyrosine phosphorylation of stat3 protein
Spp1 secreted phosphoprotein 1 1449254_at ossification; anti-apoptosis
Protein synthesis and turnover
Eif1a eukaryotic translation initiation factor 1A 1419736_a_at translation and initiation
Hras1 Harvey rat sarcoma virus oncogene 1 1422407_s_at translation; endocytosis
Nola1 nucleolar protein family A, member 1 1418305_s_at rRNA processing; ribosome biogenesis and assembly
Nola2 nucleolar protein family A, member 2 1416605_at rRNA processing; translation
Nol5A nucleolar protein 5 1450986_at ribosome biogenesis and assembly
Nmd3 NMD3 homolog 1437238_x_at ribosomal large subunit export from nucleus
Rps6ka3 ribosomal protein S6 kinase polypeptide 3 1427299_at protein amino acid phosphorylation; ribosome biogenesis and assembly
Protein targeting
Afp alpha fetoprotein 1416646_at ovulation; transport
Bcl3 B-cell leukemia/lymphoma 3 1418133_at protein import into nucleus, translocation; follicular dendritic cell differentiation
Bnip1 BCL2/adenovirus E1B interacting protein 1, NIP1 1427908_at ER to Golgi vesicle-mediated transport; apoptosis
Nup62 Nucleoporin 62 1438917_x_at protein targeting; transport
Transcription, processing, and chromatin structure
Bhlhb8 basic helix-loop-helix domain containing, class B, 8 1449233_at regulation of transcription, DNA-dependent
Ddx39 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 1423643_at mRNA processing; RNA splicing
Hmga1 high mobility group AT-hook 1 1416184_s_at DNA packaging; transcription
Lmna lamin A 1425472_a_at nuclear membrane organization and biogenesis
Pparg peroxisome proliferator activated receptor gamma 1420715_a_at negative regulation of transcription from RNA polymerase II promoter
  1. These genes were identified in profile "BHT-1day_up" (A) and profile "BHT-1day_down" (B) below the p value set for the DAVID analysis (p < 0.0003)*; see Additional file 2, Table S1 for the complete profile gene lists.
  2. *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. These genes were upregulated ≥ 2-fold in BALBLsp-dvs. BALB 1 day following protocol 1 (chronic BHT) (P < 0.05). Significant interaction effects between strain (BALB vs BALBLpsdmice) and treatment (oil, 1 or 3 days following 4BHT) (p < 0.05). Bolded genes are those genes in common with the gene list identified for Protocol 2 (see Table 2).