Table 1.

Selected gene list defining the TAM transcriptome

Feature ID
Gene
Description
Average log ratio
Up-regulated genes    
   Receptors/surface molecules     
      IMAGE:534886  Ly6a*  Lymphocyte antigen 6 complex, locus A   8.70  
      IMAGE:582679  Ly6e  Lymphocyte antigen 6 complex, locus E   7.05  
      IMAGE:775893  Cd81*  CD81 antigen   5.05  
      IMAGE:1477073  Msr2*  Macrophage scavenger receptor 2   5.50  
      IMAGE:1367026  Sema4d  Sema domain, (semaphorin) 4D   3.85  
      IMAGE:597157  C1qa*  Complement component 1, q subcomponent, alpha polypeptide   4.69  
      IMAGE:426010  C1qg  Complement component 1, q subcomponent, gamma polypeptide   2.95  
      IMAGE:524391  Axl  AXL receptor tyrosine kinase   3.60  
      IMAGE:1382670  H2-DMa  Histocompatibility 2, class II, locus DMa   2.95  
      IMAGE:1092081  H2-Eb1*  Histocompatibility 2, class II, antigen E beta 1   2.70  
      IMAGE:406272  Crabp1  Cellular retinoic acid binding protein I   3.10  
      IMAGE:576062  Fegr1  Fe receptor, IgG, high affinity I   4.30  
   Chemokines     
      IMAGE:1446589  Cxcl10*  Chemokine (C-X-C motif) ligand 10   4.10  
      IMAGE:832342  Ccl5*  Chemokine (C-C motif) ligand 5   2.75  
      IMAGE:573898  Ccl2*  Chemokine (C-C motif) ligand 2   2.51  
   Transcriptional factors     
      IMAGE:1430219  Irf7  Interferon regulatory factor 7   5.40  
      IMAGE:521100  Idb3  Inhibitor of DNA binding 3   3.10  
      IMAGE:1446422  Tbx6  T-box 6   2.90  
      IMAGE:1222882  Hdac6  Histone deacetylase 6   3.20  
      IMAGE:934509  Hist2h2aa1  Histone 2, H2aa1   3.10  
   Growth factors/miscellaneous     
      IMAGE:734101  Tgfbi*  Transforming growth factor, beta induced   4.70  
      IMAGE:315447  Mif*  Macrophage migration inhibitory factor   6.00  
      IMAGE:1382096  Aif1  Allograft inflammatory factor 1   3.50  
      IMAGE:819851  Gstp2  Glutathioņe S-transferase, pi 2   3.10  
      IMAGE:570994  Igfbp4  Insulin-like growth factor binding protein 4   2.70  
      IMAGE:1228288  Ucp2  Uncoupling protein 2, mitochondrial   2.60  
      IMAGE:537489  Ccnd1  Cyclin D1   2.93  
      IMAGE:440572  Col13a1  Procollagen, type XIII, alpha 1   4.00  
      IMAGE:864318  Lst1  Leukocyte-specific transcript 1   2.80  
      IMAGE:581981    Unknown   3.20  
      IMAGE:1247540  Dapk3  Death associated protein kinase 3   5.80  
      IMAGE:1210036  Ifit3  Interferon-induced protein with tetratricopeptide repeats 3   2.50  
   Proteases and their inhibitors     
      IMAGE:1227398  Spint1  Serine protease inhibitor, Kunitz type 1   2.80  
      IMAGE:1077734  Serpinh1  Serine (or cysteine) proteinase inhibitor, clade H, member 1   2.50  
Down-regulated genes    
   Receptors/surface molecules     
      IMAGE:764624  Cd5l  CD5 antigen-like   0.18  
      IMAGE:440614  Gp49b  Glycoprotein 49 B   0.29  
      IMAGE:404131  Plaur  Urokinase plasminogen activator receptor   0.25  
      IMAGE:518979  Hbb-y  Hemoglobin Y, beta-like embryonic chain   0.28  
      IMAGE:1617481  Cd83  CD83 antigen   0.30  
      IMAGE:437512  Tnfrsf1b  Tumor necrosis factor receptor superfamily, member 1b   0.50  
      IMAGE:1068952  Folr2  Folate receptor 2 (fetal)   0.21  
      IMAGE:366999  Il11ra1  Interleukin 11 receptor, alpha chain 1   0.49  
      IMAGE:1349690  Il11ra2  Interleukin 11 receptor, alpha chain 2   0.43  
      IMAGE:405832  P2ry2  Purinergic receptor P2Y, G-protein coupled 2   0.39  
      IMAGE:1227418  C4  Complement component 4 (within H-2S)   0.35  
      IMAGE:1224549  Igf2r  Insulin-like growth factor 2 receptor   0.43  
      IMAGE:533799  Lbp  Lipopolysaccharide binding protein   0.36  
   Chemokines     
      IMAGE:751833  Ccl3*  Chemokine (C-C motif) ligand 3   0.44  
      IMAGE:1078018  Ccl4  Chemokine (C-C motif) ligand 4   0.47  
      IMAGE:1077529  Ccl6  Chemokine (C-C motif) ligand 6   0.14  
      IMAGE:1148463  Ccl9  Chemokine (C-C motif) ligand 9   0.38  
   Transcriptional factors     
      IMAGE:403789
 		Idb2
 		 Inhibitor of DNA binding 2
 		 0.26
 
Growth factors/miscellaneous     
   IMAGE:1139544  Il1b*  Interleukin 1 beta   0.43  
   IMAGE:1327679  Tnf*  Tumor necrosis factor   0.32  
   IMAGE:1001011  Fcna  Ficolin A   0.07  
   IMAGE:1195776  Retnla  Resistin-like alpha (Fizzl)   0.06  
   IMAGE:1264951  Saa3  Serum amyloid A 3   0.04  
   IMAGE:990152  Fabp5  Fatty acid binding protein 5, epidermal   0.21  
   IMAGE:523460  Fabp4  Fatty acid binding protein 4, adipocyte   0.22  
   IMAGE:368778  Pmp22  Peripheral myelin protein   0.21  
   IMAGE:368524  Mfge8  Milk fat globule-EGF factor 8 protein   0.19  
   IMAGE:1001588  Pltp  Phospholipid transfer protein   0.19  
   IMAGE:1227378  Lpl  Lipoprotein lipase   0.05  
   IMAGE:819960  Arhb  ras homolog gene family, member B   0.22  
   IMAGE:2101183  Arhc  ras homolog gene family, member C   0.26  
Proteases and their inhibitors     
   IMAGE:976659  Ctsl  Cathepsin L   0.34  
   IMAGE:437755  Ctsb  Cathepsin B   0.33  
   IMAGE:1077399  Sdc1  Syndecan 1   0.16  
   IMAGE:1367299  Slpi  Secretory leukocyte protease inhibitor   0.04  
   IMAGE:622732  Timp1  Tissue inhibitor of metalloproteinase 1   0.47  
   IMAGE:1037661
 		Mmp12
 		 Matrix metalloproteinase 12
 		 0.25
 
Feature ID
Gene
Description
Average log ratio
Up-regulated genes    
   Receptors/surface molecules     
      IMAGE:534886  Ly6a*  Lymphocyte antigen 6 complex, locus A   8.70  
      IMAGE:582679  Ly6e  Lymphocyte antigen 6 complex, locus E   7.05  
      IMAGE:775893  Cd81*  CD81 antigen   5.05  
      IMAGE:1477073  Msr2*  Macrophage scavenger receptor 2   5.50  
      IMAGE:1367026  Sema4d  Sema domain, (semaphorin) 4D   3.85  
      IMAGE:597157  C1qa*  Complement component 1, q subcomponent, alpha polypeptide   4.69  
      IMAGE:426010  C1qg  Complement component 1, q subcomponent, gamma polypeptide   2.95  
      IMAGE:524391  Axl  AXL receptor tyrosine kinase   3.60  
      IMAGE:1382670  H2-DMa  Histocompatibility 2, class II, locus DMa   2.95  
      IMAGE:1092081  H2-Eb1*  Histocompatibility 2, class II, antigen E beta 1   2.70  
      IMAGE:406272  Crabp1  Cellular retinoic acid binding protein I   3.10  
      IMAGE:576062  Fegr1  Fe receptor, IgG, high affinity I   4.30  
   Chemokines     
      IMAGE:1446589  Cxcl10*  Chemokine (C-X-C motif) ligand 10   4.10  
      IMAGE:832342  Ccl5*  Chemokine (C-C motif) ligand 5   2.75  
      IMAGE:573898  Ccl2*  Chemokine (C-C motif) ligand 2   2.51  
   Transcriptional factors     
      IMAGE:1430219  Irf7  Interferon regulatory factor 7   5.40  
      IMAGE:521100  Idb3  Inhibitor of DNA binding 3   3.10  
      IMAGE:1446422  Tbx6  T-box 6   2.90  
      IMAGE:1222882  Hdac6  Histone deacetylase 6   3.20  
      IMAGE:934509  Hist2h2aa1  Histone 2, H2aa1   3.10  
   Growth factors/miscellaneous     
      IMAGE:734101  Tgfbi*  Transforming growth factor, beta induced   4.70  
      IMAGE:315447  Mif*  Macrophage migration inhibitory factor   6.00  
      IMAGE:1382096  Aif1  Allograft inflammatory factor 1   3.50  
      IMAGE:819851  Gstp2  Glutathioņe S-transferase, pi 2   3.10  
      IMAGE:570994  Igfbp4  Insulin-like growth factor binding protein 4   2.70  
      IMAGE:1228288  Ucp2  Uncoupling protein 2, mitochondrial   2.60  
      IMAGE:537489  Ccnd1  Cyclin D1   2.93  
      IMAGE:440572  Col13a1  Procollagen, type XIII, alpha 1   4.00  
      IMAGE:864318  Lst1  Leukocyte-specific transcript 1   2.80  
      IMAGE:581981    Unknown   3.20  
      IMAGE:1247540  Dapk3  Death associated protein kinase 3   5.80  
      IMAGE:1210036  Ifit3  Interferon-induced protein with tetratricopeptide repeats 3   2.50  
   Proteases and their inhibitors     
      IMAGE:1227398  Spint1  Serine protease inhibitor, Kunitz type 1   2.80  
      IMAGE:1077734  Serpinh1  Serine (or cysteine) proteinase inhibitor, clade H, member 1   2.50  
Down-regulated genes    
   Receptors/surface molecules     
      IMAGE:764624  Cd5l  CD5 antigen-like   0.18  
      IMAGE:440614  Gp49b  Glycoprotein 49 B   0.29  
      IMAGE:404131  Plaur  Urokinase plasminogen activator receptor   0.25  
      IMAGE:518979  Hbb-y  Hemoglobin Y, beta-like embryonic chain   0.28  
      IMAGE:1617481  Cd83  CD83 antigen   0.30  
      IMAGE:437512  Tnfrsf1b  Tumor necrosis factor receptor superfamily, member 1b   0.50  
      IMAGE:1068952  Folr2  Folate receptor 2 (fetal)   0.21  
      IMAGE:366999  Il11ra1  Interleukin 11 receptor, alpha chain 1   0.49  
      IMAGE:1349690  Il11ra2  Interleukin 11 receptor, alpha chain 2   0.43  
      IMAGE:405832  P2ry2  Purinergic receptor P2Y, G-protein coupled 2   0.39  
      IMAGE:1227418  C4  Complement component 4 (within H-2S)   0.35  
      IMAGE:1224549  Igf2r  Insulin-like growth factor 2 receptor   0.43  
      IMAGE:533799  Lbp  Lipopolysaccharide binding protein   0.36  
   Chemokines     
      IMAGE:751833  Ccl3*  Chemokine (C-C motif) ligand 3   0.44  
      IMAGE:1078018  Ccl4  Chemokine (C-C motif) ligand 4   0.47  
      IMAGE:1077529  Ccl6  Chemokine (C-C motif) ligand 6   0.14  
      IMAGE:1148463  Ccl9  Chemokine (C-C motif) ligand 9   0.38  
   Transcriptional factors     
      IMAGE:403789
 		Idb2
 		 Inhibitor of DNA binding 2
 		 0.26
 
Growth factors/miscellaneous     
   IMAGE:1139544  Il1b*  Interleukin 1 beta   0.43  
   IMAGE:1327679  Tnf*  Tumor necrosis factor   0.32  
   IMAGE:1001011  Fcna  Ficolin A   0.07  
   IMAGE:1195776  Retnla  Resistin-like alpha (Fizzl)   0.06  
   IMAGE:1264951  Saa3  Serum amyloid A 3   0.04  
   IMAGE:990152  Fabp5  Fatty acid binding protein 5, epidermal   0.21  
   IMAGE:523460  Fabp4  Fatty acid binding protein 4, adipocyte   0.22  
   IMAGE:368778  Pmp22  Peripheral myelin protein   0.21  
   IMAGE:368524  Mfge8  Milk fat globule-EGF factor 8 protein   0.19  
   IMAGE:1001588  Pltp  Phospholipid transfer protein   0.19  
   IMAGE:1227378  Lpl  Lipoprotein lipase   0.05  
   IMAGE:819960  Arhb  ras homolog gene family, member B   0.22  
   IMAGE:2101183  Arhc  ras homolog gene family, member C   0.26  
Proteases and their inhibitors     
   IMAGE:976659  Ctsl  Cathepsin L   0.34  
   IMAGE:437755  Ctsb  Cathepsin B   0.33  
   IMAGE:1077399  Sdc1  Syndecan 1   0.16  
   IMAGE:1367299  Slpi  Secretory leukocyte protease inhibitor   0.04  
   IMAGE:622732  Timp1  Tissue inhibitor of metalloproteinase 1   0.47  
   IMAGE:1037661
 		Mmp12
 		 Matrix metalloproteinase 12
 		 0.25
 

The values corresponding to each gene represent its expression levels in terms of the averaged log 2 ratio of Cy5/Cy3 intensities across all the microarray experiments. Stringency limits for significant gene modulation were as follows: mean ratio of Cy5/Cy3 intensity ≥2.5 for up-regulated genes and ≤0.4 for down-regulated genes.

*

Genes were validated by RT-PCR. Data are representative of 4 independent experiments

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