TABLE I.
GENES IN 4T1 TUMOR1
| Genbank Accession |
Signal ratio (log of 2) |
Change p-value | Gene description | Gene function |
|---|---|---|---|---|
| a. Genes that show enhanced expression in 4T1 tumor following IL-12 treatment in vivo | ||||
| AF0659473 | 3.20 | 0 | NOD/LtJ small inducible cytokine A5 (ScyA5) RANTES |
Chemoattractant for Mϕ/DC, T/NK/basophil/ eosinophil |
| AF061569 | 2.60 | 0.00001 | c-myc coding region determinant binding protein |
Stabilizes c-myc mRNA |
| L12029 | 2.30 | 0.000001 | Stromal cell derived factor 1-α | Chemoattractant |
| X064543 | 2.20 | 0 | Sex-limited protein Slp(w7) alpha-gamma chain |
Complement-like |
| U348813 | 2.10 | 0.000649 | CD8 antigen, alpha chain | Cytotoxic and DC marker |
| K027823 | 1.80 | 0.000008 | Complement component C3 mRNA, alpha and beta subunits |
Complement |
| X04673 | 1.80 | 0.000408 | Adipsin | Complement D activity, activates alternative pathway |
| M348153 | 1.80 | 0 | Monokine induced by gamma interferon (MIG); CXCL9 |
Chemoattractant for activated T cells |
| AB0234183 | 1.80 | 0 | monocyte chemoattractant protein-2 (MCP-2), CCL8 |
Chemoattractant for T/monocyte/basophil/ eosinophil |
| AL0786302 | 1.80 | 0.000388 | Mouse genomic DNA sequence from clone 573K1 (EST) |
Unknown |
| M63335 | 1.80 | 0.004863 | lipoprotein lipase | Hydrolyzes triglycerides in lipid metablism |
| X046533 | 1.70 | 0 | Ly-6 alloantigen (Ly-6E.1) | T-lymphocyte activation |
| AF0102543 | 1.50 | 0.000001 | Complement component 1 inhibitor | Inhibitor of C1 and several plasma serine proteases |
| X03505 | 1.50 | 0 | Serum amyloid A 3 | Acute stress response |
| M64085 | 1.50 | 0 | spi2 proteinase inhibitor (spi2/eb1) | Inhibitor of serine proteases |
| AW1243372 | 1.40 | 0.000002 | UI-M-BH2.1-apq-f-08-0-UI.s1 Mus musculus cDNA, 3 end |
Homologous to microsomal glutathione S- transferase 1 |
| AF0612603 | 1.40 | 0.000031 | Immunosuperfamily protein BI2, nectin-like protein 2 (Necl2) |
Cell-cell adhesion and transmembrane protein localization |
| U353303 | 1.40 | 0 | Histocompatibility 2, class II, locus Mb1 | Antigen presentation to CD4+/T cells |
| U069243 | 1.40 | 0 | Signal transducer and activator of transcription 1 (Stat1) |
IFN-γ signaling |
| AF071180 | 1.40 | 0.000001 | N-formylpeptide receptor-like 2 gene | Chemotactic for phagocytes (antibacterial and tissue repair) |
| X009583 | 1.30 | 0 | I-E (beta-b) gene | Antigen presentation to CD4+ T cells |
| Y08135 | 1.30 | 0 | Acid Sphingomyelinase-like phosphodiesterase 3a |
Novel binding protein of tumor suppressor DBCCR1 (deleted in bladder cancer chromosome region 1) |
| AA7903072 | 1.30 | 0 | vw17a10.r1 Mus musculus cDNA, 5′ end (Onzin) |
Unknown |
| U53219 | 1.30 | 0 | GTPase IGTP | Interferon induced GTP-binding protein |
| X78445 | 1.30 | 0.000001 | Cytochrome P450 | Detoxification by oxidation |
| X023393 | 1.30 | 0.000115 | CD3 antigen, delta polypeptide | T-lymphocyte marker |
| AI3860933 | 1.30 | 0.000008 | Similar to protein tyrosine kinase ZAP-70 | T-lymphocyte activation signaling |
| U88566 | 1.20 | 0.000001 | Secreted frizzled related protein sFRP-1 (Sfrp1) |
Inhibitor of Wnt, induces apoptosis |
| V008333 | 1.20 | 0 | E-alpha gene for immune response gene | Antigen presentation to CD4+/T cells |
| U353233 | 1.10 | 0 | H2-M chain, H2-M2, H2-M1, low molecular weight protein 2 (Lmp2) |
Antigen presentation to CD4+ T cells |
| M219323 | 1.10 | 0 | MHC class II H2-I-A-beta gene (k haplotype) | Antigen presentation to CD4+ T cells |
| M16238 | 1.10 | 0 | Fibrinogen-like protein 2 | Thrombosis, cytotoxic T-specific protein |
| D44464 | 1.10 | 0 | Uridine phosphorylase | Catalyzes the reversible phosphorolysis of uridine to uracil |
| M689033 | 1.10 | 0.000001 | Integrin beta 7, Ly69 | Lymphocyte homing and retention |
| AA914345 | 1.10 | 0.000001 | Interferon-inducible GTPase | Interferon induced GTP-binding protein |
| U434283 | 1.10 | 0.000018 | Nitric oxide synthase 2, inducible, macrophage | Synthesis of nitric oxide |
| M55544 | 1.10 | 0 | Guanylate nucleotide binding protein 1 | GTPase |
| AF084524 | 1.10 | 0.000018 | Cellular repressor of E1A-stimulated genes CREG |
Inhibits cell growth and/or promotes cell differentiation |
| AW049768 | 1.10 | 0 | Tubulointersititial nephritis antigen-related protein |
Unknown |
| U12884 | 1.00 | 0 | Vascular cell adhesion molecule-1 truncated form T-VCAM-1 |
Unknown |
| X526433 | 1.00 | 0 | Histocompatibility 2, class II antigen A, alpha | Antigen presentation to CD4+ T cells |
| AI8428282 | 1.00 | 0.000002 | EST UI-M-AP1-agi-h-10-0-UI.s1 Mus musculus cDNA (EST) |
Unknown |
| M55181 | 1.00 | 0.000311 | Preproenkephalin 2 | Five-amino-acid neuropeptide with morphin- like activity |
| AJ0079703 | 1.00 | 0 | GBP-2 protein | GTPase inducible by IFN-γ in macrophages |
| AJ007971 | 1.00 | 0 | IIGP protein | IFN-γ-inducible GTPase |
| M161183 | 1.00 | 0.000009 | T-cell receptor insulin (A-chain) reactive alpha chain VJC |
T-cell receptor |
| X75129 | 1.00 | 0 | Xanthine dehydrogenase | Catalyzes oxidation of hypoxanthine, xanthine, and purine. |
| AA9589032 | 1.00 | 0.000001 | EST: ua19f08.r1 Mus musculus cDNA (EST) | Unknown |
| AW0474762 | 1.00 | 0 | EST: UI-M-BH1-all-g-04-0-UI.s1 Mus musculus cDNA (EST) |
Unknown |
| D317883 | 1.00 | 0.000001 | BP-3 alloantigen, bone marrow stromal cell antigen 1 (BST-1) |
CD157 with ADP-ribosyl cyclase and NAD glycohydrolase activities |
| AJ006474 | 1.00 | 0.000004 | Carbonic anhydrase III | Protects proteins from oxidation catalyzed by iron-containing degradation products of haemoglobin and myoglobin |
| AV2396532 | 1.00 | 0.000006 | EST: Mus musculus cDNA, 3′ end/clone = 4732435F04 (EST) |
Unknown |
| b. Genes that show reduced expression in 4T1 tumor following IL-12 treatment | ||||
| AA592182 | −1.8 | 0 | Nephronectin | Extracellular matrix protein associated with integrin α8β1 |
| AW0478752 | −1.8 | 0 | EST, UI-M-BH1-als-g-03-0-UI.s1 | Unknown |
| Y13185 | −1.7 | 0.000002 | Matrix metalloproteinase 10 | Modulator of extracellular matrix composition and structure |
| M76124 | −1.6 | 0 | EGP314, epithelial glycoprotein | Involved in metastasis |
| Y17793 | −1.6 | 0.000063 | Roundabout homolog 1, mouse homologue of human DUTT1 |
Lung development |
| M83219 | −1.5 | 0 | MRP14, myeloid related protein | Neutrophil and monocyte activation |
| U43327 | −1.4 | 0 | Lamc2, Laminin, gamma 2 | Constituent of lamin-5, a major adhesion ligand of epithelial cells |
| AJ242625 | −1.4 | 0.000001 | Dmp-1, dentin matrix protein-1 | Involved in matrix mineralization |
| M83218 | −1.3 | 0 | MRP8, intracellular calcium-binding protein | Neutrophil and monocyte activation |
| U88064 | −1.3 | 0 | Basonuclin | Increases transcription of the ribosomal RNA genes |
| AF087825 | −1.3 | 0.000011 | Claudin 7 | A transmembrane protein that seals tight junctions |
| AA7169632 | −1.2 | 0 | EST, vu69f10.r1 | Unknown |
| AF017994 | −1.2 | 0.000008 | Peg1/MEST | Imprinted gene of unknown function expressed in mouse embryo |
| C766433 | −1.2 | 0.000002 | EST, D15Ertd30e | Unknown |
| X537983 | −1.1 | 0.000002 | MIP2, macrophage inflammatory protein-2 | Chemotactic for monocytes/macrophages |
| AJ2429123 | −1.1 | 0.000003 | Decysin, disintegrin metalloprotease | Expressed in macrophages and dendritic cells |
| AV112006 | −1.1 | 0.000025 | Procollagen, type XV | Precursor of constituent of skin and bone |
1
The signal ratios given (in log of 2) have been normalized as follows the 50th percentile of all measurements was used as a positive control for each sample; each measurement for each gene was divided by this synthetic positive control, assuming that this was at least 10. The bottom tenth percentile was used as a test for correct background subtraction. This was never less than the negative of the synthetic positive control. Each gene was normalized to itself by making a synthetic positive control for that gene and dividing all measurements for that gene by this positive control, assuming it was at least 0.01. This synthetic control was the median of the gene’s expression values over all the samples. Lastly, normalized values below 0 were set to 0. Change p values reflect statistical significance in differential expression between the 2 groups (IL-12-treated vs. PBS-treated).
2
EST clones.
3
Genes with primary immune cell origins.
The gene lists include only those that were reproduced in 2 separate experiments (72% reproducibility rate).