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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

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BMC Bioinformatics

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