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.
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

Yao et al. BMC Bioinformatics 2004 5:99   doi:10.1186/1471-2105-5-99