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

Bauer, Alison K; Fostel, Jennifer; Degraff, Laura M; Rondini, Elizabeth A; Walker, Christopher; Grissom, Sherry F; Foley, Julie; Kleeberger, Steven R

doi:10.1186/1476-4598-8-107

Molecular Cancer

Table 4 Representative gene expression changes decreased in BALB 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
F 13a 1	coagulation factor XIII, A1 subunit	1448929_at	tRNA aminoacylation for protein translation; blood coagulation
Kdr ^†	kinase insert domain protein receptor	1449379_at	angiogenesis; ovarian follicle development
Tbx1 ^†	T-box 1	1425779_a_at	angiogenesis; blood vessel development
Apoptosis and cell death
Rassf5	ras association (RalGDS/AF-6) domain family 5	1422637_at	apoptosis; cell cycle
Unc5c	unc-5 homolog C	1449522_at	apoptosis; signal transduction
Immune response
Cd3d ^†	CD3 antigen, delta polypeptide	1422828_at	protein complex assembly; cell surface receptor linked signal transduction
Cd79a	CD79A antigen (immunoglobulin-associated alpha)	1418830_at	immune response; cell surface receptor linked signal transduction
Cr2 ^†	complement receptor 2	1425289_a_at	immune response; complement activation, classical pathway
Ltb	lymphotoxin B	1419135_at	immune response; lymph node development
Ppbp^†, Cxcl7	pro-platelet basic protein	1418480_at	immune response
Slamf1	signaling lymphocytic activation molecule family member 1	1425570_at	lymphocyte activation
Tnfrsf13c	tumor necrosis factor receptor superfamily, member 13c	1419307_at	B cell homeostasis; positive regulation of germinal center formation
Inflammatory response and chemotaxis
Ccl5 ^†	chemokine (C-C motif) ligand 5	1418126_at	chemotaxis; inflammatory response
Ccr2	chemokine (C-C motif) receptor 2	1421186_at	chemotaxis; inflammatory response
Chst1	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	1449147_at	carbohydrate and galactose metabolic process
Enpp2	ectonucleotide pyrophosphatase/phosphodiesterase 2	1415894_at	chemotaxis; metabolic process
S 100a 8	S100 calcium binding protein A8	1419394_s_at	chemotaxis
Protein synthesis and turnover
Cfd	complement factor D (adipsin)	1417867_at	proteolysis; immune response
Gzma	granzyme A	1417898_a_at	proteolysis; apoptosis
Transcription, processing, and chromatin structure
Hipk2	homeodomain interacting protein kinase 2	1429566_a_at	negative regulation of transcription from RNA polymerase II promoter
Myst3	MYST histone acetyltransferase 3	1436315_at	nucleosome assembly
SpiB	Spi-B transcription factor	1460407_at	regulation of transcription, DNA-dependent

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 decreased genes from the "Down in WT tumor" profile for genes BALB tumors compared to BALB^Lsp-dtumors. 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 down-regulated ≥ 50% in BALB tumors compared to BALB^Lspdtumors based on GeneSpring.

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ISSN: 1476-4598

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