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Section III: Detailed Analysis

Hierarchical cluster analysis of diagnostic cases using all genes that passed the variation filter
Two-dimensional hierarchical clustering was performed using Pearson correlation coefficient and an unweighted pair group method using arithmetic averages (GeneMaths, version 1.5). The results of hierarchical clustering of the 327 diagnostic samples using genes selected by a variety of metrics are shown below.

Methods for gene selection
Discriminating genes for the various leukemia subtypes were selected using a variety of statistical metrics. The individual metrics used and the list of selected probe sets and corresponding genes are given below. Genes selected by Chi-square, T-statistics, Wilkins', and CFS, were chosen using the decision tree format shown in Figure 19 below. In this process, genes were selected that distinguished the class for all classes listed below it in the decision tree structure. For the selection of genes using SOM/DAV genes were selected that distinguished the class from all others. The degree of overlap between the lists of genes selected for each genetic subtype by the various metrics is discussed below.

Chi-square
The Chi-square method evaluates each gene individually by measuring the Chi-square statistics with respect to the classes. The method first discretizes the observed expression values of the gene into several intervals using an entropy-based discretization method. The Chi-square statistics of a gene is then calculated as X2 = ΣΣ(Aij - Eij)2/Eij, summing over intervals i = 1..m and classes j = 1..k. Aij is the number of samples in the ithinterval that are of the jth class. Eij is the expected frequency of Aij and is calculated as Eij = Ri * Ci/N, where Ri is the number of samples in the ith interval, Cj is the number of samples in the jth class, and N is the total number of samples. The genes are then sorted according to their Chi-square statistics---the larger the Chi-square statistics, the more important the gene. The 40 genes with the highest Chi-square statistics in each subtype are listed in Table 11. Generally, using anywhere from the top 20 to 40 genes did not result in significant differences in subtype prediction accuracy. Therefore, we used only the top 20 genes in subtype prediction, unless noted otherwise.


Table 11. Genes selected by Chi-square


  Affymetrix number Gene
Name
GeneSymbol Reference number
Chi-
square
value
Above/
Below
Mean


BCR-ABL

     
 

1

1637_at

mitogen-activated protein kinase-activated protein kinase 3

MAPKAPK3

U09578

62.75

Above

2

36650_at

cyclin D2

CCND2

D13639

59.79

Above

3

40196_at

HYA22 protein

HYA22

D88153

54.79

Above

4

1635_at

proto-oncogene tyrosine-protein kinase ABL gene

ABL

U07563

54.77

Above

5

33775_s_at

caspase 8 apoptosis-related cysteine protease

CASP8

X98176

49.70

Above

6

1636_g_at

proto-oncogene tyrosine-protein kinase ABL gene

ABL

U07563

48.29

Above

7

41295_at

GTT1 protein

GTT1

AL041780

42.60

Above

8

37600_at

extracellular matrix protein 1

ECM1

U68186

42.60

Above

9

37012_at

capping protein actin filament muscle Z-line beta

CAPZB

U03271

38.46

Above

10

39225_at

alkylglycerone phosphate synthase

AGPS

Y09443

38.46

Above

11

1326_at

caspase 10 apoptosis-related cysteine protease

CASP10

U60519

37.83

Above

12

34362_at

solute carrier family 2 facilitated glucose transporter member 5

SLC2A5

M55531

37.54

Above

13

33150_at

disrupter of silencing 10

SAS10

AI126004

36.95

Above

14

40051_at

TRAM-like protein

KIAA0057

D31762

36.95

Above

15

39061_at

bone marrow stromal cell antigen 2

BST2

D28137

36.95

Above

16

33172_at

hypothetical protein FLJ10849

FLJ10849

T75292

36.95

Above

17

37399_at

aldo-keto reductase family 1 member C3 3-alpha hydroxysteroid dehydrogenase type II

AKR1C3

D17793

36.95

Above

18

317_at

protease cysteine 1 legumain

PRSC1

D55696

36.95

Above

19

40953_at

calponin 3 acidic

CNN3

S80562

33.94

Above

20

330_s_at

tubulin, alpha 1, isoform 44

TUBA1

HG2259-HT2348

33.32

Above

21

40504_at

paraoxonase 2

PON2

AF001601

31.46

Above

22

38578_at

tumor necrosis factor receptor superfamily member 7

TNFRSF7

M63928

30.47

Above

23

39044_s_at

diacylglycerol kinase delta 130kD

DGKD

D73409

29.59

Below

24

36634_at

BTG family member 2

BTG2

U72649

29.16

Below

25

38119_at

glycophorin C Gerbich blood group

GYPC

X12496

29.16

Above

26

32562_at

endoglin Osler-Rendu-Weber syndrome 1

ENG

X72012

27.96

Above

27

33228_g_at

interleukin 10 receptor beta

IL10RB

AI984234

27.70

Below

28

37006_at

step II splicing factor SLU7

SLU7

AI660656

27.15

Above

29

38641_at

Homo sapiens mRNA for TSC-22-like protein

 

AJ133115

27.15

Above

30

38220_at

dihydropyrimidine dehydrogenase

DPYD

U20938

27.15

Above

31

1211_s_at

CASP2 and RIPK1 domain containing adaptor with death domain

CRADD

U84388

26.46

Above

32

39730_at

v-abl Abelson murine leukemia viral oncogene homolog 1

ABL1

X16416

25.90

Above

33

36591_at

tubulin alpha 1 testis specific

TUBA1

X06956

25.90

Above

34

36035_at

anchor attachment protein 1 Gaa1p yeast homolog

GPAA1

AB002135

25.34

Above

35

980_at

Niemann-Pick disease type C1

NPC1

AF002020

25.29

Above

36

671_at

secreted protein acidic cysteine-rich osteonectin

SPARC

J03040

25.29

Above

37

40698_at

C-type calcium dependent carbohydrate-recognition domain lectin superfamily member 2 activation-induced

CLECSF2

X96719

23.80

Above

38

39330_s_at

actinin alpha 1

ACTN1

M95178

23.70

Above

39

1983_at

cyclin D2

CCND2

X68452

23.70

Above

40

2001_g_at

ataxia telangiectasia mutated

ATM

U26455

22.60

Above

         
 

E2A-PBX1

     
 

1

41146_at

ADP-ribosyltransferase NAD poly ADP-ribose polymerase

ADPRT

J03473

187.00

Above

2

1287_at

ADP-ribosyltransferase NAD poly ADP-ribose polymerase

ADPRT

J03473

187.00

Above

3

32063_at

pre-B-cell leukemia transcription factor 1

PBX1

M86546

187.00

Above

4

33355_at

Homo sapiens cDNA FLJ12900 fis clone NT2RP2004321 (by CELERA serach of target sequence = PBX1)

PBX1

AL049381

187.00

Above

5

430_at

nucleoside phosphorylase

NP

X00737

187.00

Above

6

40454_at

FAT tumor suppressor Drosophila homolog

FAT

X87241

176.11

Above

7

753_at

nidogen 2

NID2

D86425

164.28

Above

8

33821_at

Human DNA sequence from clone RP3-483K16 on chromosome 6p12.1-21.1

HELO1

AL034374

155.00

Above

9

39614_at

KIAA0802 protein

KIAA0802

AB018345

153.46

Above

10

38340_at

huntingtin interacting protein-1-related

KIAA0655

AB014555

143.85

Above

11

1786_at

c-mer proto-oncogene tyrosine kinase

MERTK

U08023

142.34

Above

12

39929_at

KIAA0922 protein

KIAA0922

AB023139

139.97

Above

13

39379_at

Homo sapiens mRNA cDNA DKFZp586C1019 from clone DKFZp586C1019

 

AL049397

139.49

Above

14

717_at

GS3955 protein

GS3955

D87119

135.24

Above

15

362_at

protein kinase C zeta

PRKCZ

Z15108

131.36

Above

16

33513_at

signaling lymphocytic activation molecule

SLAM

U33017

131.36

Above

17

37225_at

KIAA0172 protein

KIAA0172

D79994

131.36

Above

18

854_at

B lymphoid tyrosine kinase

BLK

S76617

130.95

Above

19

35974_at

lymphoid-restricted membrane protein

LRMP

U10485

123.33

Above

20

36452_at

synaptopodin

KIAA1029

AB028952

123.33

Above

21

40648_at

c-mer proto-oncogene tyrosine kinase

MERTK

U08023

120.51

Above

22

38393_at

KIAA0247 gene product

KIAA0247

D87434

120.51

Above

23

38994_at

STAT induced STAT inhibitor-2

STATI2

AF037989

118.58

Below

24

34861_at

golgi autoantigen golgin subfamily a 3

GOLGA3

D63997

116.80

Above

25

38748_at

adenosine deaminase RNA-specific B1 homolog of rat RED1

ADARB1

U76421

114.13

Above

26

40113_at

GS3955 protein

GS3955

D87119

114.13

Above

27

36179_at

mitogen-activated protein kinase-activated protein kinase 2

MAPKAPK2

U12779

113.43

Above

28

37493_at

colony stimulating factor 2 receptor beta low-affinity granulocyte-macrophage

CSF2RB

H04668

113.04

Above

29

578_at

Human recombination acitivating protein (RAG2) gene

RAG2

M94633

111.32

Above

30

41017_at

myosin-binding protein H

MYBPH

U27266

109.73

Above

31

37625_at

interferon regulatory factor 4

IRF4

U52682

108.51

Above

32

38679_g_at

small nuclear ribonucleoprotein polypeptide E

SNRPE

AA733050

106.02

Above

33

1389_at

membrane metallo-endopeptidase neutral endopeptidase enkephalinase CALLA CD10

MME

J03779

105.65

Below

34

34783_s_at

BUB3 budding uninhibited by benzimidazoles 3 yeast homolog

BUB3

AF047473

103.87

Above

35

36959_at

ubiquitin-conjugating enzyme E2 variant1

UBE2V1

U49278

103.87

Above

36

39864_at

cold inducible RNA-binding protein

CIRBP

D78134

99.76

Below

37

41862_at

KIAA0056 protein

KIAA0056

D29954

99.76

Above

38

41425_at

Friend leukemia virus integration 1

FLI1

M98833

96.47

Above

39

37177_at

CD58 antigen lymphocyte function-associated antigen 3

CD58

Y00636

93.84

Above

40

37485_at

fatty-acid-Coenzyme A ligase very long-chain 1

FACVL1

D88308

93.17

Above

         
 

Hyperdiploid >50

   
 

1

36620_at

superoxide dismutase 1 soluble amyotrophic lateral sclerosis 1 adult

SOD1

X02317

52.43

Above

2

37350_at

Human DNA sequence from clone 889N15 on chromosome Xq22.1-22.3.

PSMD10

AL031177

48.71

Above

3

171_at

von Hippel-Lindau binding protein 1

VBP1

U56833

45.80

Above

4

37677_at

phosphoglycerate kinase 1

PGK1

V00572

45.80

Above

5

41724_at

accessory proteins BAP31/BAP29

DXS1357E

X81109

45.58

Above

6

32207_at

membrane protein palmitoylated 1 55kD

MPP1

M64925

44.07

Above

7

38738_at

SMT3 suppressor of mif two 3 yeast homolog 1

SMT3H1

X99584

43.57

Above

8

40480_s_at

FYN oncogene related to SRC FGR YES

FYN

M14333

43.57

Above

9

38518_at

sex comb on midleg Drosophila like 2

SCML2

Y18004

43.20

Above

10

41132_r_at

heterogeneous nuclear ribonucleoprotein H2 H

HNRPH2

U01923

43.15

Above

11

31492_at

muscle specific gene

M9

AB019392

43.01

Below

12

38317_at

transcription elongation factor A SII like 1

TCEAL1

M99701

41.10

Above

13

40998_at

trinucleotide repeat containing 11 THR-associated protein 230 kDa subunit

TNRC11

AF071309

40.88

Above

14

35688_g_at

mature T-cell proliferation 1

MTCP1

Z24459

40.52

Above

15

40903_at

ATPase H transporting lysosomal vacuolar proton pump membrane sector associated protein M8-9

APT6M8-9

AL049929

40.33

Above

16

36489_at

phosphoribosyl pyrophosphate synthetase 1

PRPS1

D00860

40.33

Above

17

1520_s_at

interleukin 1 beta

IL1B

X04500

40.29

Above

18

35939_s_at

POU domain class 4 transcription factor 1

POU4F1

L20433

38.74

Above

19

38604_at

neuropeptide Y

NPY

AI198311

38.26

Above

20

31863_at

KIAA0179 protein

KIAA0179

D80001

38.26

Above

21

890_at

ubiquitin-conjugating enzyme E2A RAD6 homolog

UBE2A

M74524

37.99

Above

22

39402_at

interleukin 1 beta

IL1B

M15330

37.92

Above

23

41490_at

phosphoribosyl pyrophosphate synthetase 2

PRPS2

Y00971

37.72

Above

24

34753_at

synaptobrevin-like 1

SYBL1

X92396

37.72

Above

25

40891_f_at

DNA segment on chromosome X unique 9879 expressed sequence

DXS9879E

X92896

37.15

Above

26

306_s_at

high-mobility group nonhistone chromosomal protein 14

HMG14

J02621

37.15

Above

27

37640_at

hypoxanthine phosphoribosyltransferase 1 Lesch-Nyhan syndrome

HPRT1

M31642

37.15

Above

28

34829_at

dyskeratosis congenita 1 dyskerin

DKC1

U59151

36.48

Above

29

36169_at

NADH dehydrogenase ubiquinone 1 alpha subcomplex 1 7.5kD MWFE

NDUFA1

N47307

36.48

Above

30

38968_at

SH3-domain binding protein 5 BTK-associated

SH3BP5

AB005047

35.95

Above

31

36128_at

transmembrane trafficking protein

TMP21

L40397

35.88

Above

32

37014_at

myxovirus influenza resistance 1 homolog of murine interferon-inducible protein p78

MX1

M33882

35.65

Above

33

34374_g_at

upstream regulatory element binding protein 1

UREB1

Z97054

35.55

Above

34

36542_at

solute carrier family 9 sodium/hydrogen exchanger isoform 6

SLC9A6

AF030409

35.55

Above

35

688_at

proteasome prosome macropain 26S subunit ATPase 1

PSMC1

L02426

35.55

Above

36

955_at

calmodulin type I

 

HG1862-HT1897

35.55

Above

37

35816_at

cystatin B stefin B

CSTB

U46692

35.27

Above

38

38459_g_at

Human cytochrome b5 (CYB5) gene

CYB5

L39945

35.18

Above

39

41288_at

matrix Gla protein

MGP

AL036744

35.18

Above

40

32251_at

hypothetical protein FLJ21174

FLJ21174

AA149307

35.14

Above

         
 

MLL

     
 

1

34306_at

muscleblind Drosophila like

MBNL

AB007888

64.07

Above

2

40797_at

a disintegrin and metalloproteinase domain 10

ADAM10

AF009615

62.85

Above

3

33412_at

LGALS1 Lectin, galactoside-binding, soluble, 1

LGALS1

AI535946

57.97

Above

4

39338_at

S100 calcium-binding protein A10 annexin II ligand calpactin I light polypeptide p11

S100A10

AI201310

57.97

Above

5

2062_at

insulin-like growth factor binding protein 7

IGFBP7

L19182

55.22

Above

6

32193_at

plexin C1

PLXNC1

AF030339

53.59

Above

7

40518_at

protein tyrosine phosphatase receptor type C

PTPRC

Y00062

53.40

Above

8

36777_at

DNA segment on chromosome 12 unique 2489 expressed sequence

D12S2489E

AJ001687

51.47

Above

9

32207_at

membrane protein palmitoylated 1 55kD

MPP1

M64925

50.73

Below

10

33859_at

sin3-associated polypeptide 18kD

SAP18

U96915

50.48

Above

11

38391_at

capping protein actin filament gelsolin-like

CAPG

M94345

50.26

Above

12

40763_at

Meis1 mouse homolog

MEIS1

U85707

50.26

Above

13

1126_s_at

cell surface glycoprotein CD44 gene

CD44

L05424

50.17

Above

14

34721_at

FK506-binding protein 5

FKBP5

U42031

50.17

Above

15

37809_at

homeo box A9

HOXA9

U41813

50.17

Above

16

34861_at

golgi autoantigen golgin subfamily a 3

GOLGA3

D63997

47.58

Below

17

38194_s_at

immunoglobulin kappa constant

IGKC

M63438

46.18

Below

18

657_at

protocadherin gamma subfamily C 3

PCDHGC3

L11373

46.05

Above

19

36918_at

guanylate cyclase 1 soluble alpha 3

GUCY1A3

Y15723

43.90

Above

20

32215_i_at

KIAA0878 protein

KIAA0878

AB020685

43.90

Above

21

38160_at

lymphocyte antigen 75

LY75

AF011333

43.90

Above

22

38413_at

defender against cell death 1

DAD1

D15057

43.90

Above

23

1389_at

membrane metallo-endopeptidase neutral endopeptidase enkephalinase CALLA CD10

MME

J03779

43.82

Below

24

34168_at

deoxynucleotidyltransferase terminal

DNTT

M11722

43.82

Below

25

2036_s_at

CD44 antigen homing function and Indian blood group system

CD44

M59040

42.55

Above

26

40522_at

glutamate-ammonia ligase glutamine synthase

GLUL

X59834

42.55

Above

27

854_at

B lymphoid tyrosine kinase

BLK

S76617

42.34

Above

28

40067_at

E74-like factor 1 ets domain transcription factor

ELF1

M82882

40.85

Above

29

39756_g_at

X-box binding protein 1

XBP1

Z93930

39.95

Below

30

36940_at

TGFB1-induced anti-apoptotic factor 1

TIAF1

D86970

39.82

Below

31

36935_at

RAS p21 protein activator GTPase activating protein 1

RASA1

M23379

38.77

Above

32

32134_at

testin

DKFZP586B2022

AL050162

38.77

Above

33

39379_at

Homo sapiens mRNA cDNA DKFZp586C1019 from clone DKFZp586C1019

 

AL049397

38.77

Above

34

40493_at

Human cell surface glycoprotein CD44

CD44

L05424

38.44

Above

35

769_s_at

annexin A2

ANXA2

D00017

37.61

Above

36

40415_at

acetyl-Coenzyme A acyltransferase 1 peroxisomal 3-oxoacyl-Coenzyme A thiolase

ACAA1

X14813

37.55

Above

37

35983_at

hypothetical protein R32184_1

R32184_1

AC004528

37.55

Above

38

40519_at

protein tyrosine phosphatase receptor type C

PTPRC

Y00638

36.56

Above

39

794_at

protein tyrosine phosphatase non-receptor type 6

PTPN6

X62055

36.56

Above

40

41234_at

DnaJ Hsp40 homolog subfamily B member 6

DNAJB6

AI540318

36.56

Above

         
 

Novel

     
 

1

37960_at

carbohydrate chondroitin 6/keratan sulfotransferase 2

CHST2

AB014679

175.82

Above

2

31892_at

protein tyrosine phosphatase receptor type M

PTPRM

X58288

172.85

Above

3

994_at

protein tyrosine phosphatase receptor type M

PTPRM

X58288

172.85

Above

4

995_g_at

protein tyrosine phosphatase receptor type M

PTPRM

X58288

172.85

Above

5

41074_at

G protein-coupled receptor 49

GPR49

AF062006

139.36

Above

6

41073_at

G protein-coupled receptor 49

GPR49

AI743745

139.36

Above

7

34676_at

KIAA1099 protein

KIAA1099

AB029022

137.71

Above

8

36139_at

DKFZP586G0522 protein

DKFZP586G0522

AL050289

127.05

Above

9

37542_at

lipoma HMGIC fusion partner-like 2

LHFPL2

D86961

120.79

Above

10

41159_at

clathrin heavy polypeptide Hc

CLTC

D21260

115.15

Above

11

40081_at

phospholipid transfer protein

PLTP

L26232

108.33

Above

12

32800_at

Human retinoid X receptor alpha mRNA, 3' UTR, partial sequence

RXR

U66306

107.39

Above

13

36906_at

cannabinoid receptor 1 brain

CNR1

U73304

107.39

Above

14

39878_at

protocadherin 9

PCDH9

AI524125

99.20

Above

15

41747_s_at

Human myocyte-specific enhancer factor 2A (MEF2A) gene, last coding  exon, and complete cds.

MEF2A

U49020

99.20

Above

16

33410_at

integrin alpha 6

ITGA6

S66213

96.17

Above

17

34947_at

phorbolin-like protein MDS019

MDS019

AA442560

93.59

Above

18

36029_at

chromosome 11 open reading frame 8

C11ORF8

U57911

93.59

Above

19

41708_at

KIAA1034 protein

KIAA1034

AB028957

92.60

Above

20

1664_at

insulin-like growth factor 2

IGF2

HG3543-HT3739

92.60

Above

21

32736_at

HSPC022 protein

HSPC022

W68830

91.62

Below

22

41266_at

integrin alpha 6

ITGA6

X53586

86.95

Above

23

36566_at

cystinosis nephropathic

CTNS

AJ222967

82.89

Above

24

1825_at

IQ motif containing GTPase activating protein 1

IQGAP1

L33075

81.20

Below

25

1731_at

platelet-derived growth factor receptor alpha polypeptide

PDGFRA

M21574

78.22

Above

26

37023_at

lymphocyte cytosolic protein 1 L-plastin

LCP1

J02923

78.22

Below

27

33037_at

carbohydrate N-acetylglucosamine 6-O sulfotransferase 7

CHST7

AL022165

76.00

Above

28

33411_g_at

integrin alpha 6

ITGA6

S66213

75.47

Above

29

538_at

CD34 antigen

CD34

S53911

74.86

Above

30

39108_at

lanosterol synthase 2 3-oxidosqualene-lanosterol cyclase

LSS

U22526

71.90

Above

31

38364_at

BCE-1 protein

BCE-1

AF068197

71.90

Above

32

40423_at

KIAA0903 protein

KIAA0903

AB020710

71.29

Above

33

35192_at

glycine dehydrogenase decarboxylating glycine decarboxylase glycine cleavage system protein P

GLDC

D90239

71.29

Above

34

39037_at

myeloid/lymphoid or mixed-lineage leukemia trithorax Drosophila homolog translocated to 2

MLLT2

L13773

71.29

Above

35

38747_at

Human CD34 gene, exon 8.

CD34

M81945

69.45

Above

36

37687_i_at

Fc fragment of IgG low affinity IIa receptor for CD32

FCGR2A

M31932

67.75

Above

37

1857_at

MAD mothers against decapentaplegic Drosophila homolog 7

MADH7

AF010193

66.28

Above

38

38618_at

Human PAC clone RP3-515N1 from 22q11.2-q22

LIMK2

AC002073

64.03

Above

39

31782_at

prostaglandin D2 receptor DP

PTGDR

U31099

61.92

Above

40

32842_at

B-cell CLL/lymphoma 7A

BCL7A

X89984

61.57

Above

         
 

T-ALL

     
 

1

38319_at

CD3D antigen delta polypeptide TiT3 complex

CD3D

AA919102

215.00

Above

2

1096_g_at

CD19 antigen

CD19

M28170

206.48

Below

3

38242_at

B cell linker protein

SLP65

AF068180

198.52

Below

4

32794_g_at

T cell receptor beta locus

TRB

X00437

197.71

Above

5

37988_at

CD79B antigen immunoglobulin-associated beta

CD79B

M89957

197.71

Below

6

38017_at

CD79A antigen immunoglobulin-associated alpha

CD79A

U05259

197.53

Below

7

35016_at

Human Ia-associated invariant gamma-

chain gene, exon 8, clones lambda-y(1,2,3).

M13560

M13560

Below

8

36277_at

Human membran protein (CD3-epsilon) gene, exon 9.

CD3E

M23323

197.53

Above

9

38095_i_at

major histocompatibility complex class II DP beta 1

HLA-DPB1

M83664

191.09

Below

10

39318_at

T-cell leukemia/lymphoma 1A

TCL1A

X82240

189.78

Below

11

38147_at

SH2 domain protein 1A Duncan s disease lymphoproliferative syndrome

SH2D1A

AL023657

189.78

Above

12

41723_s_at

major histocompatibility complex class II DR beta 1

HLA-DRB1

M32578

189.25

Below

13

38833_at

Human mRNA for SB classII histocompatibility antigen alpha-chain

 

X00457

189.03

Below

14

33238_at

Human T-lymphocyte specific protein tyrosine kinase p56lck (lck) abberant mRNA

lck

U23852

189.03

Above

15

37039_at

major histocompatibility complex class II DR alpha

HLA-DRA

J00194

188.93

Below

16

38051_at

mal T-cell differentiation protein

MAL

X76220

188.93

Above

17

37344_at

major histocompatibility complex class II DM alpha

HLA-DMA

X62744

187.25

Below

18

38096_f_at

major histocompatibility complex class II DP beta 1

HLA-DPB1

M83664

182.38

Below

19

2059_s_at

lymphocyte-specific protein tyrosine kinase

LCK

M36881

182.38

Above

20

1105_s_at

T cell receptor beta locus

TRB

M12886

180.45

Above

21

32649_at

transcription factor 7 T-cell specific HMG-box

TCF7

X59871

177.84

Above

22

38949_at

protein kinase C theta

PRKCQ

L01087

172.59

Below

23

39709_at

selenoprotein W 1

SEPW1

U67171

171.96

Above

24

41165_g_at

immunoglobulin heavy constant mu

IGHM

X67301

171.96

Below

25

36473_at

ubiquitin specific protease 20

USP20

AB023220

167.27

Above

26

266_s_at

CD24 antigen small cell lung carcinoma cluster 4 antigen

CD24

L33930

165.56

Below

27

40570_at

forkhead box O1A rhabdomyosarcoma

FOXO1A

AF032885

165.29

Below

28

40775_at

integral membrane protein 2A

ITM2A

AL021786

164.14

Above

29

37420_i_at

Human DNA sequence from clone RP3-377H14 on chromosome 6p21.32-22.1.

 

AL022723

164.14

Below

30

1085_s_at

phospholipase C gamma 2 phosphatidylinositol-specific

PLCG2

M37238

161.30

Below

31

38018_g_at

CD79A antigen immunoglobulin-associated alpha

CD79A

U05259

160.51

Below

32

35643_at

nucleobindin 2

NUCB2

X76732

160.07

Above

33

41166_at

immunoglobulin heavy constant mu

IGHM

X58529

158.50

Below

34

38415_at

protein tyrosine phosphatase type IVA member 2

PTP4A2

U14603

155.78

Above

35

38893_at

neutrophil cytosolic factor 4 40kD

NCF4

AL008637

155.78

Below

36

1241_at

protein tyrosine phosphatase type IVA member 2

PTP4A2

U14603

155.78

Above

37

32793_at

T cell receptor beta locus

TRB

X00437

155.43

Above

38

36571_at

topoisomerase DNA II beta 180kD

TOP2B

X68060

152.16

Below

39

37399_at

aldo-keto reductase family 1 member C3 3-alpha hydroxysteroid dehydrogenase type II

AKR1C3

D17793

151.93

Above

40

41097_at

telomeric repeat binding factor 2

TERF2

AF002999

151.86

Below

         
 

TEL-AML1

     
 

1

38652_at

hypothetical protein FLJ20154

FLJ20154

AF070644

137.92

Above

2

36239_at

POU domain class 2 associating factor 1

POU2AF1

Z49194

131.43

Above

3

41442_at

core-binding factor runt domain alpha subunit 2 translocated to 3

CBFA2T3

AB010419

130.17

Above

4

37780_at

piccolo presynaptic cytomatrix protein

PCLO

AB011131

126.79

Above

5

36985_at

isopentenyl-diphosphate delta isomerase

IDI1

X17025

125.47

Above

6

38578_at

tumor necrosis factor receptor superfamily member 7

TNFRSF7

M63928

115.72

Above

7

38203_at

potassium intermediate/small conductance calcium-activated channel subfamily N member 1

KCNN1

U69883

112.87

Above

8

35614_at

transcription factor-like 5 basic helix-loop-helix

TCFL5

AB012124

108.45

Above

9

32224_at

KIAA0769 gene product

KIAA0769

AB018312

107.08

Above

10

32730_at

Homo sapiens mRNA for KIAA1750 protein partial cds

 

AL080059

104.93

Above

11

35665_at

phosphoinositide-3-kinase class 3

PIK3C3

Z46973

104.83

Above

12

1077_at

recombination activating gene 1

RAG1

M29474

102.90

Above

13

36524_at

Rho guanine nucleotide exchange factor GEF 4

ARHGEF4

AB029035

100.67

Above

14

34194_at

Homo sapiens cDNA FLJ21697 fis clone COL09740

 

AL049313

98.31

Above

15

36937_s_at

PDZ and LIM domain 1 elfin

PDLIM1

U90878

96.91

Below

16

36008_at

protein tyrosine phosphatase type IVA member 3

PTP4A3

AF041434

96.68

Above

17

1299_at

telomeric repeat binding factor 2

TERF2

X93512

93.08

Above

18

41814_at

fucosidase alpha-L- 1 tissue

FUCA1

M29877

92.77

Above

19

41200_at

CD36 antigen collagen type I receptor thrombospondin receptor like 1

CD36L1

Z22555

90.86

Above

20

35238_at

TNF receptor-associated factor 5

TRAF5

AB000509

90.81

Above

21

880_at

FK506-binding protein 1A 12kD

FKBP1A

M34539

86.69

Above

22

33690_at

Homo sapiens mRNA cDNA DKFZp434A202 from clone DKFZp434A202

 

AL080190

86.69

Above

23

40272_at

collapsin response mediator protein 1

CRMP1

D78012

85.44

Above

24

35362_at

myosin X

MYO10

AB018342

83.60

Above

25

41819_at

FYN-binding protein FYB-120/130

FYB

U93049

83.25

Above

26

40279_at

KIAA0121 gene product

KIAA0121

D50911

81.66

Above

27

1488_at

protein tyrosine phosphatase receptor type K

PTPRK

L77886

81.66

Above

28

1325_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59423

81.17

Above

29

37908_at

guanine nucleotide binding protein 11

GNG11

U31384

80.37

Above

30

769_s_at

annexin A2

ANXA2

D00017

78.68

Below

31

33415_at

non-metastatic cells 2 protein NM23B expressed in

NME2

X58965

77.04

Below

32

1980_s_at

non-metastatic cells 2 protein NM23B expressed in

NME2

X58965

76.35

Below

33

32579_at

SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily a member 4

SMARCA4

D26156

76.35

Above

34

39425_at

thioredoxin reductase 1

TXNRD1

X91247

75.97

Above

35

755_at

inositol 1 4 5-triphosphate receptor type 1

ITPR1

D26070

75.56

Above

36

37343_at

inositol 1 4 5-triphosphate receptor type 3

ITPR3

U01062

75.11

Above

37

1336_s_at

protein kinase C beta 1

PRKCB1

X06318

73.96

Above

38

41097_at

telomeric repeat binding factor 2

TERF2

AF002999

73.84

Above

39

31786_at

Sam68-like phosphotyrosine protein T-STAR

T-STAR

AF051321

73.72

Above

40

160029_at

protein kinase C beta 1

PRKCB1

X07109

73.66

Above



Illustrated below are the results of a two-dimensional hierarchical clustering algorithm of the 327 diagnostic ALL cases using the top 40 probe sets for each of the 7 groups selected by the Chi-square metric. This represents 271 unique probe sets as some probe sets were selected for more than one diagnostic group.


Figure 14. Hierarchical cluster of 327 diagnostic ALL bone marrow samples and genes chosen by Chi-square metric.

Correlation-based Feature Selection (CFS)
The Correlation-based Feature Selection (CFS) is a method that evaluates subsets of genes rather than individual genes4. The core of the algorithm is a subset evaluation heuristic that takes into account the usefulness of individual features for predicting the class along with the level of intercorrelation among them with the belief that "good feature subsets contain features highly correlated with the class, yet uncorrelated with each other". The heuristic assigns a score Merits to a subset S containing k genes, defined as Merits = (k* rcf)/sqrt(k + k * (k - 1) * rff), where rcf is the average gene-class correlation and rff is the average gene-gene correlation. Like the Chi-square method, CFS first discretizes the gene expressions into intervals and then calculates a matrix of gene-class and gene-gene correlations from the training data for merit calculation. The correlation between two genes or a gene and a class is calculated as rxy = 2 * [H(X) + H(Y) - H(X,Y)]/[H(X) + H(Y)], where H(X) is the entropy of a gene X. CFS starts from an empty set of genes and uses the best-first search technique with a stopping criterion of 5 consecutive fully expanded non-improving subsets. The subset with the highest merit found during the search is selected. Table 12 lists the top gene subsets chosen by CFS for each subtype. For subtype prediction, each gene subset must be used in its entirety, as within each subset, all genes are equally ranked. A two-dimensional clustering of these genes is shown in Figure 15. Recall that in CFS, genes in a subset are chosen so that they have high correlation with the corresponding class and low correlation with each other. This characteristic is clearly visible in Figure 15.

 

Table 12. Genes selected by CFS


 

Affymetrix number

Gene Name

GeneSymbol

Reference number

Above/Below Mean


BCR-ABL        

1

36650_at

cyclin D2

CCND2

D13639

Above

2

40196_at

HYA22 protein

HYA22

D88153

Above

3

1635_at

proto-oncogene tyrosine-protein kinase (ABL) gene

ABL

U07563

Above

4

33775_s_at

caspase 8 apoptosis-related cysteine protease

CASP8

X98176

Above

5

1636_g_at

proto-oncogene tyrosine-protein kinase (ABL) gene

ABL

U07563

Above

6

41295_at

GTT1 protein

GTT1

AL041780

Above

7

1326_at

caspase 10 apoptosis-related cysteine protease

CASP10

U60519

Above

8

33150_at

disrupter of silencing 10

SAS10

AI126004

Above

9

40051_at

TRAM-like protein

KIAA0057

D31762

Above

10

39061_at

bone marrow stromal cell antigen 2

BST2

D28137

Above

11

33172_at

hypothetical protein FLJ10849

FLJ10849

T75292

Above

12

37399_at

aldo-keto reductase family 1 member C3 3-alpha hydroxysteroid dehydrogenase type II

AKR1C3

D17793

Above

13

317_at

protease cysteine 1 legumain

PRSC1

D55696

Above

14

330_s_at

tubulin, alpha 1, isoform 44

TUBA1

HG2259-HT2348

Above

15

38578_at

tumor necrosis factor receptor superfamily member 7

TNFRSF7

M63928

Above

16

39044_s_at

diacylglycerol kinase delta 130kD

DGKD

D73409

Below

17

32562_at

endoglin Osler-Rendu-Weber syndrome 1

ENG

X72012

Above

18

38641_at

Homo sapiens mRNA for TSC-22-like protein

 

AJ133115

Above

19

1211_s_at

CASP2 and RIPK1 domain containing adaptor with death domain

CRADD

U84388

Above

20

39730_at

v-abl Abelson murine leukemia viral oncogene homolog 1

ABL1

X16416

Above

21

36591_at

tubulin alpha 1 testis specific

TUBA1

X06956

Above

22

36035_at

anchor attachment protein 1 Gaa1p yeast homolog

GPAA1

AB002135

Above

23

980_at

Niemann-Pick disease type C1

NPC1

AF002020

Above

24

40698_at

C-type calcium dependent carbohydrate-recognition domain lectin superfamily member 2 activation-induced

CLECSF2

X96719

Above

25

39330_s_at

actinin alpha 1

ACTN1

M95178

Above

26

2001_g_at

ataxia telangiectasia mutated includes complementation groups A C and D

ATM

U26455

Above

27

39319_at

lymphocyte cytosolic protein 2 SH2 domain-containing leukocyte protein of 76kD

LCP2

U20158

Above

28

37685_at

Clathrin assembly lymphoid-myeloid leukemia gene

CLTH

U45976

Above

29

33813_at

tumor necrosis factor receptor superfamily member 1B

TNFRSF1B

AI813532

Above

30

33134_at

adenylate cyclase 3

ADCY3

AB011083

Above

31

36536_at

schwannomin interacting protein 1

SCHIP-1

AF070614

Above

32

36985_at

isopentenyl-diphosphate delta isomerase

IDI1

X17025

Below

33

35991_at

Sm protein F

LSM6

AA917945

Above

34

33774_at

caspase 8 apoptosis-related cysteine protease

CASP8

X98172

Above

35

37470_at

leukocyte-associated Ig-like receptor 1

LAIR1

AF013249

Above

36

39245_at

Human 40871 mRNA partial sequence

 

U72507

Above

37

40076_at

tumor protein D52-like 2

TPD52L2

AF004430

Below

38

39370_at

Microtubule-associated proteins 1A and 1B light chain 3

MAP1ALC3

W28807

Below

39

41594_at

Janus kinase 1 a protein tyrosine kinase

JAK1

M64174

Above

40

41338_at

amino-terminal enhancer of split

AES

AI969192

Below

41

32319_at

tumor necrosis factor ligand superfamily member 4 tax-transcriptionally activated glycoprotein 1 34kD

TNFSF4

AL022310

Above

42

33924_at

KIAA1091 protein

KIAA1091

AB029014

Above

43

37397_at

 platelet/endothelial cell adhesion molecule-1 (PECAM-1) gene

PECAM

L34657

Above

44

37190_at

WAS protein family member 1

WASF1

D87459

Below

45

39070_at

singed Drosophila like sea urchin fascin homolog like

SNL

U03057

Above

46

38994_at

STAT induced STAT inhibitor-2

STATI2

AF037989

Above

47

32621_at

down-regulator of transcription 1 TBP-binding negative cofactor 2

DR1

M97388

Above

48

40108_at

KIAA0005 gene product

KIAA0005

D13630

Below

49

35238_at

TNF receptor-associated factor 5

TRAF5

AB000509

Above

50

1558_g_at

p21/Cdc42/Rac1-activated kinase 1 yeast Ste20-related

PAK1

U24152

Above

51

1373_at

transcription factor 3 E2A immunoglobulin enhancer binding factors E12/E47

TCF3

M31523

Below

52

35731_at

integrin alpha 4 antigen CD49D alpha 4 subunit of VLA-4 receptor

ITGA4

X16983

Above

53

38659_at

suppressor of clear C. elegans homolog of

SHOC2

AB020669

Below

           

E2A-PBX1

       

1

33355_at

Homo sapiens cDNA FLJ12900 fis clone NT2RP2004321 (by CELERA search of target sequence = PBX1)

PBX1

AL049381

Above

           

Hyperdiploid >50

       

1

36620_at

superoxide dismutase 1 soluble amyotrophic lateral sclerosis 1 adult

SOD1

X02317

Above

2

37350_at

clone 889N15 on chromosome Xq22.1-22.3. Contains part of the gene for a novel protein similar to X. laevis Cortical Thymocyte Marker CTX

PSMD10

AL031177

Above

3

41724_at

accessory proteins BAP31/BAP29

DXS1357E

X81109

Above

4

38738_at

SMT3 suppressor of mif two 3 yeast homolog 1

SMT3H1

X99584

Above

5

40480_s_at

FYN oncogene related to SRC FGR YES

FYN

M14333

Above

6

38518_at

sex comb on midleg Drosophila like 2

SCML2

Y18004

Above

7

31492_at

muscle specific gene

M9

AB019392

Below

8

35688_g_at

mature T-cell proliferation 1

MTCP1

Z24459

Above

9

35939_s_at

POU domain class 4 transcription factor 1

POU4F1

L20433

Above

10

36128_at

transmembrane trafficking protein

TMP21

L40397

Above

11

37014_at

myxovirus influenza resistance 1 homolog of murine interferon-inducible protein p78

MX1

M33882

Above

12

34374_g_at

upstream regulatory element binding protein 1

UREB1

Z97054

Above

13

688_at

proteasome prosome macropain 26S subunit ATPase 1

PSMC1

L02426

Above

14

39878_at

protocadherin 9

PCDH9

AI524125

Below

15

38771_at

histone deacetylase 1

HDAC1

D50405

Below

16

865_at

ribosomal protein S6 kinase 90kD polypeptide 3

RPS6KA3

U08316

Above

17

41143_at

calmodulin (CALM1) gene

CALM1

U12022

Above

18

39867_at

Tu translation elongation factor mitochondrial

TUFM

S75463

Below

19

41470_at

prominin mouse like 1

PROML1

AF027208

Above

20

41503_at

KIAA0854 protein

KIAA0854

AB020661

Below

21

2039_s_at

FYN oncogene related to SRC FGR YES

FYN

M14333

Above

22

36845_at

KIAA0136 protein

KIAA0136

D50926

Above

23

36940_at

TGFB1-induced anti-apoptotic factor 1

TIAF1

D86970

Above

24

32236_at

ubiquitin-conjugating enzyme E2G 2 homologous to yeast UBC7

UBE2G2

AF032456

Above

25

36885_at

spleen tyrosine kinase

SYK

L28824

Below

26

40200_at

heat shock transcription factor 1

HSF1

M64673

Below

27

40842_at

 U1 snRNP-specific protein A gene

SNRPA

M60784

Below

28

40514_at

hypothetical 43.2 Kd protein

LOC51614

AF091085

Below

29

41222_at

signal transducer and activator of transcription 6 (STAT6) gene

STAT6

AF067575

Below

30

1294_at

ubiquitin-activating enzyme E1-like

UBE1L

L13852

Below

31

34315_at

AFG3 ATPase family gene 3 yeast like 2

AFG3L2

Y18314

Above

32

39806_at

DKFZP547E2110 protein

DKFZP547E2110

AL050261

Above

33

40875_s_at

small nuclear ribonucleoprotein 70kD polypeptide RNP antigen

SNRP70

X06815

Below

34

38458_at

cytochrome b5 (CYB5) gene

CYB5

L39945

Above

35

1817_at

prefoldin 5

PFDN5

D89667

Below

36

34709_r_at

stromal antigen 2

STAG2

Z75331

Above

37

33447_at

myosin light polypeptide regulatory non-sarcomeric 20kD

MLCB

X54304

Above

38

1077_at

recombination activating gene 1

RAG1

M29474

Below

39

1915_s_at

v-fos FBJ murine osteosarcoma viral oncogene homolog

FOS

V01512

Above

40

38854_at

KIAA0635 gene product

KIAA0635

AB014535

Above

41

37732_at

RING1 and YY1 binding protein

RYBP

AL049940

Above

42

35940_at

POU domain class 4 transcription factor 1

POU4F1

X64624

Above

43

34733_at

splicing factor 3a subunit 1 120kD

SF3A1

X85237

Below

44

245_at

selectin L lymphocyte adhesion molecule 1

SELL

M25280

Below

45

40146_at

RAP1B member of RAS oncogene family

RAP1B

AL080212

Below

46

40104_at

serine/threonine kinase 25 Ste20 yeast homolog

STK25

D63780

Below

47

430_at

nucleoside phosphorylase

NP

X00737

Above

48

36899_at

special AT-rich sequence binding protein 1 binds to nuclear matrix/scaffold-associating DNA s

SATB1

M97287

Below

49

35727_at

hypothetical protein FLJ20517

FLJ20517

AI249721

Below

50

38649_at

KIAA0970 protein

KIAA0970

AB023187

Below

51

36107_at

ATP synthase H transporting mitochondrial F0 complex subunit F6

ATP5J

AA845575

Above

52

38789_at

transketolase Wernicke-Korsakoff syndrome

TKT

L12711

Below

53

39301_at

calpain 3 p94

CAPN3

X85030

Below

54

41278_at

BAF53

BAF53A

AF041474

Below

55

41162_at

protein phosphatase 1G formerly 2C magnesium-dependent gamma isoform

PPM1G

Y13936

Below

56

37819_at

hypothetical protein

LOC54104

AF007130

Below

57

38717_at

DKFZP586A0522 protein

DKFZP586A0522

AL050159

Below

58

40019_at

ecotropic viral integration site 2B

EVI2B

M60830

Above

59

39489_g_at

protocadherin 9

PCDH9

W27720

Below

60

857_at

protein phosphatase 1A formerly 2C magnesium-dependent alpha isoform

PPM1A

S87759

Above

61

32804_at

RNA binding motif protein 5

RBM5

AF091263

Below

62

37676_at

phosphodiesterase 8A

PDE8A

AF056490

Below

63

1519_at

v-ets avian erythroblastosis virus E26 oncogene homolog 2

ETS2

J04102

Above

64

37680_at

A kinase PRKA anchor protein gravin 12

AKAP12

U81607

Below

65

548_s_at

spleen tyrosine kinase

SYK

S80267

Below

66

39797_at

KIAA0349 protein

KIAA0349

AB002347

Above

67

32789_at

nuclear cap binding protein subunit 2 20kD

NCBP2

AA149428

Below

68

38091_at

lectin galactoside-binding soluble 9 galectin 9

LGALS9

Z49107

Below

69

41223_at

cytochrome c oxidase subunit Va

COX5A

M22760

Below

70

933_f_at

zinc finger protein 91 HPF7 HTF10

ZNF91

L11672

Below

71

37012_at

capping protein actin filament muscle Z-line beta

CAPZB

U03271

Below

72

35214_at

UDP-glucose dehydrogenase

UGDH

AF061016

Above

73

32434_at

myristoylated alanine-rich protein kinase C substrate MARCKS 80K-L

MACS

D10522

Above

74

38345_at

centrosomal protein 1

CEP1

AF083322

Below

75

40404_s_at

CDC16 cell division cycle 16 S. cerevisiae homolog

CDC16

U18291

Below

76

39096_at

SON DNA binding protein

SON

AB028942

Above

77

33429_at

DKFZP586M1523 protein

DKFZP586M1523

AL050225

Above

78

40641_at

TBP-associated factor 172

TAF-172

AF038362

Above

79

41381_at

KIAA0308 protein

KIAA0308

AB002306

Below

80

35135_at

Homo sapiens Similar to CG15084 gene product clone MGC 10471 mRNA complete cds

 

X13956

Below

81

39421_at

runt-related transcription factor 1 acute myeloid leukemia 1 aml1 oncogene

RUNX1

D43969

Below

82

195_s_at

caspase 4 apoptosis-related cysteine protease

CASP4

U28014

Below

83

36898_r_at

primase polypeptide 2A 58kD

PRIM2A

X74331

Above

84

38792_at

spermine synthase

SMS

AD001528

Above

85

32643_at

glucan 1 4-alpha- branching enzyme 1 glycogen branching enzyme Andersen disease glycogen storage disease type IV

GBE1

L07956

Below

86

38808_at

cell membrane glycoprotein 110000M r surface antigen

GP110

D64154

Below

87

36062_at

Leupaxin

LPXN

AF062075

Below

88

300_f_at

transcription factor BTF3 homolog (GB:M90355)

 

HG4518-HT4921

Below

89

1979_s_at

nucleolar protein 1 120kD

NOL1

X55504

Below

90

32230_at

eukaryotic translation initiation factor 3 subunit 2 beta 36kD

EIF3S2

U39067

Below

91

39893_at

guanine nucleotide binding protein G protein gamma 7

GNG7

AB010414

Below

92

34651_at

catechol-O-methyltransferase

COMT

M58525

Above

93

1052_s_at

CCAAT/enhancer binding protein C/EBP delta

CEBPD

M83667

Below

94

36272_r_at

peripheral myelin protein 2

PMP2

X62167

Below

95

2044_s_at

retinoblastoma 1 including osteosarcoma

RB1

M15400

Below

96

32135_at

sterol regulatory element binding transcription factor 1

SREBF1

U00968

Below

           

MLL

       

1

34306_at

muscleblind Drosophila like

MBNL

AB007888

Above

2

40797_at

a disintegrin and metalloproteinase domain 10

ADAM10

AF009615

Above

3

33412_at

LGALS1 Lectin, galactoside-binding, soluble, 1 (galectin 1)

LGALS1

AI535946

Above

4

39338_at

S100 calcium-binding protein A10 annexin II ligand calpactin I light polypeptide p11

S100A10

AI201310

Above

5

2062_at

insulin-like growth factor binding protein 7

IGFBP7

L19182

Above

6

32193_at

plexin C1

PLXNC1

AF030339

Above

7

40518_at

protein tyrosine phosphatase receptor type C

PTPRC

Y00062

Above

8

36777_at

DNA segment on chromosome 12 unique 2489 expressed sequence

D12S2489E

AJ001687

Above

9

38391_at

capping protein actin filament gelsolin-like

CAPG

M94345

Above

10

40763_at

Meis1 mouse homolog

MEIS1

U85707

Above

11

34721_at

FK506-binding protein 5

FKBP5

U42031

Above

12

37809_at

homeo box A9

HOXA9

U41813

Above

13

32215_i_at

KIAA0878 protein

KIAA0878

AB020685

Above

14

38160_at

lymphocyte antigen 75

LY75

AF011333

Above

15

1389_at

membrane metallo-endopeptidase neutral endopeptidase enkephalinase CALLA CD10

MME

J03779

Below

16

34168_at

deoxynucleotidyltransferase terminal

DNTT

M11722

Below

17

40522_at

glutamate-ammonia ligase glutamine synthase

GLUL

X59834

Above

18

854_at

B lymphoid tyrosine kinase

BLK

S76617

Above

19

40067_at

E74-like factor 1 ets domain transcription factor

ELF1

M82882

Above

20

39756_g_at

X-box binding protein 1

XBP1

Z93930

Below

21

32134_at

Testing

DKFZP586B2022

AL050162

Above

22

39379_at

Homo sapiens mRNA cDNA DKFZp586C1019 from clone DKFZp586C1019

 

AL049397

Above

23

40415_at

acetyl-Coenzyme A acyltransferase 1 peroxisomal 3-oxoacyl-Coenzyme A thiolase

ACAA1

X14813

Above

24

40519_at

protein tyrosine phosphatase receptor type C

PTPRC

Y00638

Above

25

33847_s_at

cyclin-dependent kinase inhibitor 1B p27 Kip1

CDKN1B

U10906

Above

26

32696_at

pre-B-cell leukemia transcription factor 3

PBX3

X59841

Above

27

40417_at

KIAA0098 protein

 

D43950

Above

28

1644_at

eukaryotic translation initiation factor 3 subunit 2 beta 36kD

EIF3S2

U36764

Above

29

948_s_at

peptidylprolyl isomerase D cyclophilin D

PPID

D63861

Above

30

34337_s_at

putative DNA binding protein

M96

AJ010014

Below

31

41747_s_at

myocyte-specific enhancer factor 2A (MEF2A) gene

MEF2A

U49020

Above

32

39516_at

hypothetical protein

HSPC004

AI827793

Above

33

31820_at

hematopoietic cell-specific Lyn substrate 1

HCLS1

X16663

Above

34

33305_at

serine or cysteine proteinase inhibitor clade B ovalbumin member 1

SERPINB1

M93056

Above

35

40520_g_at

protein tyrosine phosphatase receptor type C

PTPRC

Y00638

Above

36

41222_at

signal transducer and activator of transcription 6 (STAT6) gene

STAT6

AF067575

Above

37

1718_at

actin related protein 2/3 complex subunit 2 34 kD

ARPC2

U50523

Above

38

38342_at

KIAA0239 protein

KIAA0239

D87076

Below

39

38805_at

TG-interacting factor TALE family homeobox

TGIF

X89750

Below

40

32089_at

sperm associated antigen 6

SPAG6

AF079363

Above

41

1950_s_at

Smad 3, exon 1

 

AB004922

Above

42

39410_at

development and differentiation enhancing factor 2

DDEF2

AB007860

Above

43

37280_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59912

Below

44

32607_at

brain acid-soluble protein 1

BASP1

AF039656

Above

45

39389_at

CD9 antigen p24

CD9

M38690

Below

46

40913_at

ATPase Ca transporting plasma membrane 4

ATP2B4

W28589

Below

47

1039_s_at

hypoxia-inducible factor 1 alpha subunit basic helix-loop-helix transcription factor

HIF1A

U22431

Below

48

35939_s_at

POU domain class 4 transcription factor 1

POU4F1

L20433

Below

49

963_at

ligase IV DNA ATP-dependent

LIG4

X83441

Below

50

39628_at

RAB9 member RAS oncogene family

RAB9

U44103

Below

51

38242_at

B cell linker protein

SLP65

AF068180

Below

52

37692_at

diazepam binding inhibitor GABA receptor modulator acyl-Coenzyme A binding protein

DBI

AI557240

Above

53

32166_at

KIAA1027 protein

KIAA1027

AB028950

Above

54

34800_at

DKFZP586O1624 protein

DKFZP586O1624

AL039458

Below

55

34386_at

methyl-CpG binding domain protein 4

MBD4

AF072250

Below

56

40296_at

hypothetical protein

753P9

AL023653

Below

57

40456_at

up-regulated by BCG-CWS

LOC64116

AL049963

Above

58

33943_at

ferritin heavy polypeptide 1

FTH1

L20941

Below

59

39049_at

 G18.1a and G18.1b proteins (G18.1a and G18.1b genes, located in the class III region of the major histocompatibility complex)

 

AJ243937

Below

60

38075_at

synaptophysin-like protein

SYPL

X68194

Above

61

932_i_at

zinc finger protein 91 HPF7 HTF10

ZNF91

L11672

Below

62

1825_at

IQ motif containing GTPase activating protein 1

IQGAP1

L33075

Above

63

34210_at

CDW52 antigen CAMPATH-1 antigen

CDW52

N90866

Below

64

39778_at

mannosyl alpha-1 3- glycoprotein beta-1 2-N-acetylglucosaminyltransferase

MGAT1

M55621

Below

65

34699_at

CD2-associated protein

CD2AP

AL050105

Below

66

40066_at

ubiquitin-activating enzyme E1C homologous to yeast UBA3

UBE1C

AF046024

Above

67

41177_at

hypothetical protein FLJ12443

FLJ12443

AW024285

Above

68

32736_at

HSPC022 protein

HSPC022

W68830

Above

69

1928_s_at

mad protein homolog Smad2 gene

Smad2

U78733

Below

70

1081_at

ornithine decarboxylase 1

ODC1

M33764

Above

71

37345_at

Calumenin

CALU

AF013759

Above

72

34099_f_at

nucleosome assembly protein 1-like 1

NAP1L1

W26056

Above

73

933_f_at

zinc finger protein 91 HPF7 HTF10

ZNF91

L11672

Below

74

32214_at

thioredoxin-like 32kD

TXNL

AF003938

Below

75

33501_r_at

SNC73 protein SNC73 mRNA complete cds

 

S71043

Below

76

950_at

translocation protein 1

TLOC1

D87127

Below

77

41161_at

death-associated protein 6

DAXX

AB015051

Below

78

41381_at

KIAA0308 protein

KIAA0308

AB002306

Below

79

38705_at

ubiquitin-conjugating enzyme E2D 2 homologous to yeast UBC4/5

UBE2D2

AI310002

Above

80

38617_at

LIM domain kinase 2

LIMK2

D45906

Below

81

34305_at

poly rC binding protein 1

PCBP1

Z29505

Above