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Table 1 List of involution-specific genes clustered with the use of Pearson correlation clustering

From: Involution of the mouse mammary gland is associated with an immune cascade and an acute-phase response, involving LBP, CD14 and STAT3

DMT probe set Log ratio Gene description DMT probe set Log ratio Gene description
Cluster 1    Cluster 3   
100034_at 3.42 Maspin 102761_at 1.47 GrpE-like 2, mitochondrial
102712_at 3.27 Serum amyloid A3 162011_f_at 1.15 Ras homologue gene family, member U
98041_at 8.01 Ribonuclease 1, pancreatic 96747_at 1.16 Ras homologue gene family, member U
96056_at 1.42 RhoC 103065_at 1.66 Solute carrier family 20, member 1
160686_at 2.07 Hypothetical transcription factor 93435_at 8.41 Cytochrome P450, 24
101996_at 1.53 Protein tyrosine phosphatase, non-receptor type 2 95348_at 2.27 GRO1 chemokine (C-X-C motif) ligand 1, GRO1/CXCL1
95462_at 2.11 HFB2 homologue 95745_g_at 1.33 ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha 70 kDa, isoform 1
99633_at 1.65 Neurochondrin-1 94734_at 4.14 α1-acid glycoprotein 2, orosomucoid 2
101892_f_at 0.86 Fused toes 92312_at 1.33 Phosphatidylinositol 3-kinase p170
104340_at 1.4 Methyl-CpG binding protein, MBD1 98910_at 0.84 Homology to ETS-domain protein ELK-1 from rat
99582_at 1.27 Tumour-associated calcium signal transducer 1    
103059_at 1.44 MAT8, FXYD domain-containing ion-transport regulator 3 161139_f_at 1.8 DDEF1/development and differentiation enhancing 1
101583_at 0.89 B-cell translocation gene 2, anti-proliferative    
    Cluster 4   
100893_at 1.6 Serine palmitoyltransferase, long chain base subunit 2 100136_at 1.15 Lysosomal membrane glycoprotein 2
    101055_at 1.11 Protective protein for β-galactosidase
96657_at 1.81 Spermidine/spermine N1-acetyl transferase 103812_at 3.31 Chloride channel calcium activated 1
93017_at 2.16 Syntenin 101389_at 1.93 scavenger receptor class B, member 2
104725_at 2 Small ras-like GTPase Tc10 93728_at 2.73 Transforming growth factor β1 induced transcript 4, TSC-22
93220_at 2.33 Procollagen, type IV, α 5    
101995_at 1.59 Sequestosome 1 101587_at 4.37 Microsomal epoxide hydrolase (Eph1), allele b
160713_at 2.71 Arsenite inducible RNA-associated protein (Airap) 96119_s_at 3.32 Angiopoietin-like 4
    97420_at 4.04 Leucine-rich α2-glycoprotein
95674_r_at 2.71 Brain-abundant membrane-attached signal protein 1 102114_f_at 3.7 Angiopoietin-like 4/fasting-induced adipose factor FIAF
160894_at 2.48 CCAAT/enhancer binding protein (C/EBP), δ    
    Cluster 5   
95673_s_at 6.11 Brain-abundant membrane-attached signal protein 1 100513_at 2.39 DDEF1/development and differentiation enhancing
104701_at 2.42 Basic helix–loop–helix protein B2/DEC1 93281_at 0.89 Taipoxin-associated calcium-binding protein 49 mRNA, reticulocalbin2
Cluster 2      
95746_at 1.34 ATPase, H+ transporting, lysosomal (vacuolar proton pump), α 70 kDa, isoform 1 96738_at 1.61 Metalloprotease/disintegrin/cysteine-rich protein precursor (MDC9)
97492_at 1.41 Hypothetical protein with thioredoxin domain 100565_at 1.95 Glucosamine-6-phosphate deaminase
94850_at 1.17 Acyl-coenzyme A thioesterase 3, mitochondrial 103503_at 2.06 Phospholipase Cγ2 (phosphatidylinositol-specific)
95622_at 1 Host cell factor homologue 160127_at 1.01 Cyclin G1
101410_at 2.96 Claudin 4/mCPE receptor 97948_at 3.39 Retinoblastoma 1
160106_at 1.73 Capping protein (actin filament), gelsolin-like    
    Cluster 6   
103305_at 3.52 Integrin β4 162479_f_at 0.89 Ferritin light chain 1
98151_s_at 1.06 Catenin Src 97529_at 3.12 Annexin 8
93347_at 0.88 RAB24, member of Ras oncogene family    
Cluster 7    Cluster 8 (continued)   
102255_at 3.41 Oncostatin M receptor 99133_at 1.65 Solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2
162206_f_at 3.85 Suppressor of cytokine signalling 3 102049_at 4.25 Pyruvate dehydrogenase kinase, isoenzyme 4
104155_f_at 1.79 ATF3 (LRG-21) 94881_at 3.49 Cyclin-dependent kinase inhibitor 1A (p21)
93294_at 4.31 Fibroblast inducible secreted protein, connective tissue growth factor 161650_at 1.94 Secretory leukoprotease inhibitor
102362_i_at 3.57 JunB 92858_at 4.89 Secretory leukoprotease inhibitor
93536_at 1.61 Bcl2-associated X protein 96614_at 1.67 Hypothetical protein
103448_at 1.31 S100 calcium binding protein A8 (calgranulin A) 101963_at 1.61 Cathepsin L
    92851_at 2.06 Caeruloplasmin
95680_at 1.22 Protein phosphatase 1, regulatory (inhibitor) subunit 2 93753_at 1.58 LPS-induced TN factor
    98088_at 2.6 CD14 antigen
96953_at 1.49 Small inducible cytokine subfamily B (Cys-X-Cys), member 14 /BMAC 101287_s_at 4.71 Cytochrome P450, 2d11
99952_at 7.05 Chitinase 3-like 1 94384_at 1.28 Immediate early response 3
95681_f_at 2.09 Protein phosphatase 1, regulatory (inhibitor) subunit 2 99099_at 0.93 Acute-phase response factor APRF/STAT3
    102751_at 1.9 Transforming growth factor, β3
Cluster 8    102313_at 1.15 GTP cyclohydrolase 1
100313_at 1.54 Integrin α8    
    Cluster 9   
101306_f_at 3.34 Serum amyloid A pseudogene 96679_at 1.25 DnaJ (Hsp40) homologue, subfamily B, member 9
100333_at 2.34 Serum amyloid A2 (SAA-2)    
    Cluster 10   
96123_at 1.69 LPS-binding protein 103016_s_at 2.77 CD68 antigen
96766_s_at 2.2 Receptor tyrosine kinase, Tyro3 95706_at 4.15 Galectin 3
96940_at 0.99 TEA-domain family member 2 98543_at 2.69 Cathepsin S
100491_at 0.84 Solute carrier family 16 (monocarbox. acid transporters), member 2 99071_at 1.42 Macrophage-expressed gene 1, Mpeg1/MPS1
    104023_at 1.2 Immunoglobulin superfamily, member 7
96592_at 2.39 Phosphatidylinositol 3-kinase, reg. subunit, polypeptide 1 (p85α) 93318_at 2.59 Adhesion molecule ninjurin
  1. The genes are listed in their order of appearance in the gene tree after Pearson correlation clustering. The DMT probe set number refers to the number of the probe on the Affymetrix MG-U74Av2 chip. The log ratio describes the average change of signal intensity between lactation day 7 and the day of highest expression during involution, on a log2 scale. The gene description refers to the description of the probe set on the NetAffx website.