Skip to main content

Table 1 List of identified genes. Gene accession numbers, gene descriptions, fold-changes, and p-values for genes identified by the dye-swap method with ANOVA and regularized t-test analysis and the control correction method (CCM). Genes are broadly classified into three groups: proliferation-related, differentiation-related and unclassified.

From: Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells

Proliferation-Related Genes       
Classification Acc# Gene Description CCM fold CCM p-value Dye-Swap fold Dye-Swap p-value Regularized fold Regularized p-value
Heat shock proteins NM_006597 heat shock 70 kDa protein 8 -2.8 9.5E-6 -2.9 4.2E-7 -2.9 8.4E-13
  M34664 heat shock 60 kDa protein 1 (chaperonin)    -1.9 3.9E-6 -1.9 4.8E-10
  L15189 heat shock 70 kDa protein 9B (mortalin-2) -2.2 1.4E-3 -1.8 1.8E-6 -1.8 6.5E-6
  M22382 Human mitochondrial matrix protein P1    -1.8 1.5E-5 -1.7 2.9E-9
  M94859 Human calnexin mRNA, complete cds -1.8 4.1E-3     
  L27706 Human chaperonin protein (Tcp20) gene complete cds -2.1 3.8E-4     
Transcription and translation D29677 helicase with zinc finger domain    -1.9 3.1E-5 -1.9 2.8E-10
  X91257 seryl-tRNA synthetase -1.8 1.2E-3 -1.8 4.5E-8 -1.9 2.0E-11
  D30655 eukaryotic translation initiation factor 4A, isoform 2    -1.7 5.5E-5   
  U76111 Human translation repressor NAT1 mRNA, complete cds -1.7 8.9E-3     
  M74719 transcription factor 4 -1.9 2.0E-3     
  X13293 Human mRNA for B-myb gene      1.7 4.2E-9
  U00968 Human SREBP-1 mRNA      -1.7 8.4E-9
  L41490 eukaryotic translation elongation factor 1 alpha 1-like 14 -1.8 1.4E-5 -1.7 5.3E-5 -1.8 5.0E-12
Fatty acid and sugar metabolism D16481 Homo sapiens mRNA for mitochondrial 3-ketoacyl-CoA thiolase beta-subunit of trifunctional protein, complete cds    -1.8 5.6E-5   
  Y00711 Human mRNA for lactate dehydrogenase B (LDH-B)    -1.8 6.9E-5 -1.7 2.4E-8
  D78130 Homo sapiens mRNA for squalene epoxidase, complete cds    -1.9 1.2E-5 -1.8 9.5E-7
  M37154 Human glutamate dehydrogenase (GDH) mRNA, complete cds -1.8 4.0E-3 -1.7 8.0E-4   
  U62961 3-oxoacid CoA transferase -2.0 1.2E-4     
  Y13647 Homo sapiens mRNA for stearoyl-CoA desaturase -1.9 1.5E-6     
GTPase Y13286 Homo sapiens mRNA for GDP dissociation inhibitor beta    -1.8 1.8E-5 -1.7 1.3E-6
  X51408 Human mRNA for n-chimaerin 2.1 1.8E-2     
Cell cycle U47413 Human cyclin G1 mRNA, complete cds    -1.7 9.6E-7   
  AF139897 Homo sapiens BASS1 (BASS1) mRNA, partial cds -1.8 1.8E-3     
  D00265 Homo sapiens mRNA for cytochrome c, partial cds -2.0 2.0E-2     
  X68836 H. sapiens mRNA for S-adenosylmethionine synthetase -2.2 8.3E-6     
  U19251 Homo sapiens neuronal apoptosis inhibitory protein mRNA, complete cds 1.8 1.1E-2     
  S45630 alpha B-crystallin=Rosenthal fiber component [human, glioma cell line, mRNA, 691 nt] 2.1 2.7E-3     
  X86779 H. sapiens mRNA for FAST kinase 1.7 1.9E-2     
Oncogenes X03541 Human mRNA of trk oncogene -1.8 3.1E-3     
  M19722 Human fgr proto-oncogene encoded p55-c-fgr protein, complete cds -1.9 5.0E-3     
  X77548 H. sapiens cDNA for RFG -2.1 1.5E-3     
Proliferation D63390 platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30 kDa -1.8 4.4E-4     
  U62739 Human branched-chain amino acid aminotransferase (ECA40) mRNA, complete cds 1.7 1.2E-2     
  L12350 Human thrombospondin 2 (THBS2) mRNA, complete cds 1.9 2.2E-3     
  X06614 Human mRNA for receptor of retinoic acid 1.7 2.8E-2     
  Y07921 Human mRNA for serine protease      -1.7 1.1E-6
Differentiation-Related Genes       
Tumor suppressor AF042857 Homo sapiens lung cancer antigen NY-LU-12 variant A mRNA, complete cds 2.1 4.4E-3     
Differentiation M21300 Human small proline rich protein (sprI) mRNA, clone 15B 1.7 2.0E-4     
ECM and vesicle trafficking M15395 Human leukocyte adhesion protein (LFA-1/Mac-1/p150,95 family) beta subunit mRNA 2.0 2.8E-2     
  S72869 H4(D10S170) = putative cytoskeletal protein [human, thyroid, mRNA, 3011 nt] -1.9 3.2E-2     
  D21267 SNAP25 synaptosomal-associated protein, 25 kDa 1.9 1.7E-2     
  U95735 Human thrombospondin 2 (THBS2) mRNA, complete cds -1.8 1.5E-5     
  X68194 H. sapiens h-Sp1 mRNA -1.7 4.2E-2     
  Z74615 collagen, type I, alpha 1 2.5 5.3E-3     
Immune-response U68030 chemokine (C-C motif) receptor 6 1.8 5.8E-3     
  X04701 Human mRNA for complement component C1r -2.4 3.3E-2     
DNA repair D79983 ring finger protein 144 1.7 2.3E-2     
  D29013 Homo sapiens mRNA for DNA polymerase beta, complete cds 1.8 7.3E-3     
Unclassified Genes       
  J02854 myosin, light polypeptide 9, regulatory 2.6 4.5E-2     
  X58141 Human mRNA for erythrocyte adducin alpha subunit 2.1 3.2E-2     
  AJ224442 Homo sapiens mRNA for putative methyltransferase 1.8 3.4E-3     
  X06661 Human mRNA for 27-kDa calbindin 2.1 9.0E-3     
  U24266 aldehyde dehydrogenase 4 family, member A1 1.7 2.5E-3     
  U62432 Human nicotinic acetylcholine receptor alpha3 subunit precursor, mRNA, complete cds 1.8 7.0E-3     
  U79259 Human clone 23945 mRNA, complete cds -1.7 4.2E-3     
  M18533 Homo sapiens dystrophin (DMD) mRNA, complete cds -2.5 1.1E-2     
  J05401 Human sarcomeric mitochondrial creatine kinase(MtCK) gene, complete cds 2.2 1.5E-2     
  D13315 Human mRNA for lactoyl glutathione lyase      -1.7 4.6E-7
  AB001740 Homo sapiens mRNA for p27      1.8 8.6E-4
  M15661 Human ribosomal protein mRNA      -1.7 1.3E-4