Section III: Detailed Analysis (cont.)


T-statistics
T-statistics is a classical feature selection approach. The t-statistics of a gene is defined as T = |μ1 - μ2|/sqrt(σ12/n1 + σ22/n2), where μi is the mean expression of that gene in the ith class, σi2 is the variance of that gene in the ith class and ni is the size of the ith class. This formula assigns higher value to a gene that has larger mean difference between two classes and has smaller variance within both classes. Data was log transformed prior to the application of the metric. The 40 top ranked genes for each diagnostic group are listed in Table 13. Generally, using the top 20-40 genes did not result in significant changes to subtype prediction accuracy. So we used only the top 20 genes for subtype prediction, unless noted otherwise.

Table 13. Genes Selected by T statistics


 

 

Affymetrix number

Gene Name

 

Gene Symbol

Reference number

T-stat value

Above/ Below
Mean

BCR-ABL

         

1

32319_at

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

 

TNFSF4

AL022310

12.0346

Above

2

36194_at

low density lipoprotein-related protein-associated protein 1 alpha-2-macroglobulin receptor-associated protein 1

LRPAP1

M63959

-11.3077

Below

3

1211_s_at

CASP2 and RIPK1 domain containing adaptor with death domain

CRADD

U84388

10.6627

Above

4

37397_at

Homo sapiens platelet/endothelial cell adhesion molecule-1 (PECAM-1) gene, exon 16 and complete cds.

PECAM

L34657

10.2460

Above

5

330_s_at

tubulin, alpha 1, isoform 44

TUBA1

HG2259-HT2348

10.0540

Above

6

33774_at

caspase 8 apoptosis-related cysteine protease

CASP8

X98172

9.9147

Above

7

202_at

heat shock transcription factor 2

HSF2

M65217

-9.7639

Below

8

1558_g_at

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

PAK1

U24152

9.6562

Above

9

39691_at

SH3-containing protein SH3GLB1

SH3GLB1

AB007960

9.5307

Above

10

2045_s_at

hemopoietic cell kinase

HCK

M16592

-9.3898

Below

11

36591_at

tubulin alpha 1 testis specific

TUBA1

X06956

9.3382

Above

12

1386_at

protein tyrosine phosphatase non-receptor type 9

PTPN9

M83738

-9.2414

Below

13

35991_at

Sm protein F

LSM6

AA917945

9.0298

Above

14

41273_at

FK506 binding protein 12-rapamycin associated protein 1

FRAP1

AL046940

8.9732

Above

15

35970_g_at

M-phase phosphoprotein 9

MPHOSPH9

N23137

8.6474

Above

16

38636_at

immunoglobulin superfamily containing leucine-rich repeat

ISLR

AB003184

8.4291

Above

17

36683_at

matrix Gla protein

MGP

AI953789

-8.3872

Below

18

39070_at

singed Drosophila like sea urchin fascin homolog like

SNL

U03057

8.2583

Above

19

40798_s_at

a disintegrin and metalloproteinase domain 10

ADAM10

Z48579

8.2283

Above

20

41649_at

FOXJ2 forkhead factor

LOC55810

AF038177

8.2275

Above

21

38966_at

glycoprotein synaptic 2

GPSN2

AF038958

8.2080

Above

22

34759_at

Human hbc647 mRNA sequence

 

U68494

8.1863

Above

23

1434_at

phosphatase and tensin homolog mutated in multiple advanced cancers 1

PTEN

U92436

8.1671

Above

24

40167_s_at

CS box-containing WD protein

LOC55884

AF038187

8.1655

Above

25

40264_g_at

zinc finger protein-like 1

ZFPL1

AF001891

8.1384

Above

26

36129_at

KIAA0397 gene product

KIAA0397

AB007857

8.0041

Above

27

551_at

E1A binding protein p300

EP300

U01877

-7.7578

Below

28

38345_at

centrosomal protein 1

CEP1

AF083322

-7.7431

Below

29

41137_at

myosin phosphatase target subunit 2

MYPT2

AB007972

-7.7301

Below

30

39068_at

protein phosphatase 2 regulatory subunit B B56 delta isoform

PPP2R5D

L76702

-7.6161

Below

31

38160_at

lymphocyte antigen 75

LY75

AF011333

7.5830

Above

32

34314_at

ribonucleotide reductase M1 polypeptide

RRM1

X59543

7.5778

Above

33

39519_at

KIAA0692 protein

KIAA0692

AB014592

7.4662

Above

34

32788_at

RAN binding protein 2

RANBP2

D42063

7.4114

Above

35

34882_at

nucleolar protein KKE/D repeat

NOP56

Y12065

7.3622

Above

36

2064_g_at

excision repair cross-complementing rodent repair deficiency complementation group 5

ERCC5

L20046

7.3597

Above

37

41836_at

protein with polyglutamine repeat
calcium ca2 homeostasis endoplasmic reticulum protein

ERPROT213-21

U94836

7.3350

Above

38

1563_s_at

tumor necrosis factor receptor superfamily member 1A

TNFRSF1A

M58286

7.3039

Above

39

37047_at

Niemann-Pick disease type C1

NPC1

AF002020

7.2357

Above

40

32724_at

phytanoyl-CoA hydroxylase Refsum disease

PHYH

AF023462

-7.2252

Below

             

E2A-PBX1

         

1

32063_at

pre-B-cell leukemia transcription
factor 1

PBX1

M86546

126.7442

Above

2

33355_at

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

PBX1

AL049381

36.6116

Above

3

40454_at

FAT tumor suppressor Drosophila homolog

FAT

X87241

30.7577

Above

4

717_at

GS3955 protein

GS3955

D87119

23.7813

Above

5

39070_at

singed Drosophila like sea urchin fascin homolog like

SNL

U03057

-22.8956

Below

6

33641_g_at

nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1

NFKBIL1

Y14768

-20.4637

Below

7

36536_at

schwannomin interacting protein 1

SCHIP-1

AF070614

-20.1554

Below

8

854_at

B lymphoid tyrosine kinase

BLK

S76617

19.6467

Above

9

37625_at

interferon regulatory factor 4

IRF4

U52682

18.8419

Above

10

39614_at

KIAA0802 protein

KIAA0802

AB018345

17.8214

Above

11

37099_at

arachidonate 5-lipoxygenase-activating protein

ALOX5AP

AI806222

-17.7944

Below

12

38994_at

STAT induced STAT inhibitor-2

STATI2

AF037989

-17.6553

Below

13

37641_at

Human gene for hepatitis C-associated microtubular aggregate protein p44,
exon 9 and complete cds.

 

D28915

-17.3074

Below

14

40113_at

GS3955 protein

GS3955

D87119

16.7288

Above

15

2031_s_at

cyclin-dependent kinase inhibitor 1A p21 Cip1

CDKN1A

U03106

-14.9826

Below

16

330_s_at

tubulin, alpha 1, isoform 44

TUBA1

HG2259-HT2348

-14.8016

Below

17

38340_at

huntingtin interacting protein-1-related

KIAA0655

AB014555

14.7180

Above

18

38510_at

Homo sapiens mRNA cDNA DKFZp586B0220

 

AL049435

-14.4522

Below

19

268_at

Homo sapiens platelet/endothelial cell adhesion molecule-1 (PECAM-1) gene, exon 16 and complete cds.

PECAM

L34657

-13.7540

Below

20

2062_at

insulin-like growth factor binding protein 7

IGFBP7

L19182

13.6403

Above

21

37893_at

protein tyrosine phosphatase non-receptor type 2

PTPN2

AI828880

13.5099

Above

22

38580_at

guanine nucleotide binding protein G protein q polypeptide

GNAQ

U43083

-12.8525

Below

23

40049_at

death-associated protein kinase 1

DAPK1

X76104

-12.3837

Below

24

38393_at

KIAA0247 gene product

KIAA0247

D87434

12.3436

Above

25

39379_at

Homo sapiens mRNA cDNA DKFZp586C1019

 

AL049397

12.2102

Above

26

430_at

nucleoside phosphorylase

NP

X00737

12.1307

Above

27

37975_at

cytochrome b-245 beta polypeptide chronic granulomatous disease

CYBB

X04011

-12.0743

Below

28

34862_at

CGI-49 protein

LOC51097

AA005018

12.0264

Above

29

39756_g_at

X-box binding protein 1

XBP1

Z93930

-11.9796

Below

30

307_at

arachidonate 5-lipoxygenase

ALOX5

J03600

-11.9492

Below

31

37304_at

chromobox homolog 1 Drosophila HP1 beta

CBX1

U35451

11.9422

Above

32

1287_at

ADP-ribosyltransferase NAD poly ADP-ribose polymerase

ADPRT

J03473

11.9051

Above

33

1520_s_at

interleukin 1 beta

IL1B

X04500

11.7327

Above

34

596_s_at

colony stimulating factor 3 receptor granulocyte

CSF3R

M59820

-11.6814

Below

35

37493_at

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

CSF2RB

H04668

11.6620

Above

36

36452_at

synaptopodin

KIAA1029

AB028952

11.4021

Above

37

1081_at

ornithine decarboxylase 1

ODC1

M33764

11.2865

Above

38

1563_s_at

tumor necrosis factor receptor superfamily member 1A

TNFRSF1A

M58286

-11.1361

Below

39

39069_at

AE-binding protein 1

AEBP1

AF053944

11.0984

Above

40

36203_at

ornithine decarboxylase 1

ODC1

X16277

10.9475

Above

             

Hyperdiploid >50

       

1

36620_at

superoxide dismutase 1 soluble amyotrophic lateral sclerosis 1 adult

SOD1

X02317

9.1574

Above

2

39878_at

protocadherin 9

PCDH9

AI524125

-6.9008

Below

3

37543_at

Rac/Cdc42 guanine exchange factor GEF 6

ARHGEF6

D25304

6.8366

Above

4

41470_at

prominin mouse like 1

PROML1

AF027208

6.7290

Above

5

31492_at

muscle specific gene

M9

AB019392

-6.6885

Below

6

38968_at

SH3-domain binding protein 5 BTK-associated

SH3BP5

AB005047

6.4051

Above

7

1915_s_at

v-fos FBJ murine osteosarcoma viral oncogene homolog

FOS

V01512

6.4008

Above

8

37677_at

phosphoglycerate kinase 1

PGK1

V00572

6.2865

Above

9

39867_at

Tu translation elongation factor mitochondrial

TUFM

S75463

-6.2299

Below

10

36795_at

prosaposin variant Gaucher disease and variant metachromatic leukodystrophy

PSAP

J03077

6.1812

Above

11

40875_s_at

small nuclear ribonucleoprotein 70kD polypeptide RNP antigen

SNRP70

X06815

-6.0877

Below

12

306_s_at

high-mobility group nonhistone chromosomal protein 14

HMG14

J02621

6.0804

Above

13

41724_at

accessory proteins BAP31/BAP29

DXS1357E

X81109

6.0244

Above

14

39168_at

Ac-like transposable element

ALTE

AB018328

5.9336

Above

15

955_at

calmodulin type I

CALM1

HG1862-HT1897

5.8650

Above

16

38604_at

neuropeptide Y

NPY

AI198311

5.8313

Above

17

39147_g_at

alpha thalassemia/mental retardation syndrome X-linked RAD54 S. cerevisiae homolog

ATRX

U72936

5.8181

Above

18

39069_at

AE-binding protein 1

AEBP1

AF053944

-5.6901

Below

19

37014_at

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

MX1

M33882

5.6688

Above

20

1520_s_at

interleukin 1 beta

IL1B

X04500

5.6605

Above

21

1488_at

protein tyrosine phosphatase receptor type K

PTPRK

L77886

-5.5877

Below

22

32553_at

MYC-associated zinc finger protein
purine-binding transcription factor

MAZ

M94046

-5.5000

Below

23

36169_at

NADH dehydrogenase ubiquinone 1 alpha subcomplex 1 7.5kD MWFE

NDUFA1

N47307

5.4376

Above

24

1817_at

prefoldin 5

PFDN5

D89667

-5.4110

Below

25

578_at

Human recombination acitivating protein (RAG2) gene, last exon

RAG2

M94633

-5.4026

Below

26

1556_at

RNA binding motif protein 5

RBM5

U23946

-5.3032

Below

27

40998_at

trinucleotide repeat containing 11 THR-associated protein 230 kDa subunit

TNRC11

AF071309

5.2349

Above

28

37294_at

B-cell translocation gene 1 anti-proliferative

BTG1

X61123

-5.1877

Below

29

1447_at

proteasome prosome macropain subunit beta type 1

PSMB1

D00761

5.1699

Above

30

35940_at

POU domain class 4 transcription factor 1

POU4F1

X64624

5.1200

Above

31

33307_at

kraken-like

BK126B4.1

AL022316

-5.0984

Below

32

1081_at

ornithine decarboxylase 1

ODC1

M33764

-5.0822

Below

33

34336_at

lysyl-tRNA synthetase

KARS

D32053

-5.0692

Below

34

41143_at

Human calmodulin (CALM1) gene, exons 2,3,4,5 and 6, and complete cds

CALM1

U12022

5.0543

Above

35

32251_at

hypothetical protein FLJ21174

FLJ21174

AA149307

5.0373

Above

36

35298_at

eukaryotic translation initiation factor 3 subunit 7 zeta 66/67kD

EIF3S7

U54558

-4.9499

Below

37

38649_at

KIAA0970 protein

KIAA0970

AB023187

-4.9228

Below

38

36629_at

glucocorticoid-induced leucine zipper

GILZ

AI635895

4.8061

Above

39

39721_at

ephrin-B1

EFNB1

U09303

4.7968

Above

40

2094_s_at

v-fos FBJ murine osteosarcoma viral oncogene homolog

FOS

K00650

4.7446

Above

             

MLL

         

1

307_at

arachidonate 5-lipoxygenase

ALOX5

J03600

-16.8244

Below

2

37280_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59912

-15.4460

Below

3

1520_s_at

interleukin 1 beta

IL1B

X04500

-13.6764

Below

4

36908_at

Human macrophage mannose receptor (MRC1) gene, exon 30.

MRC1

M93221

-11.8629

Below

5

33412_at

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

LGALS1

AI535946

11.0223

Above

6

2062_at

insulin-like growth factor binding
protein 7

IGFBP7

L19182

10.4318

Above

7

35940_at

POU domain class 4 transcription
factor 1

POU4F1

X64624

-10.1815

Below

8

39721_at

ephrin-B1

EFNB1

U09303

-9.6158

Below

9

39402_at

interleukin 1 beta

IL1B

M15330

-9.5998

Below

10

1737_s_at

insulin-like growth factor-binding
protein 4

IGFBP4

M62403

-9.4119

Below

11

37413_at

dipeptidase 1 renal

DPEP1

J05257

-9.4101

Below

12

40519_at

protein tyrosine phosphatase receptor type C

PTPRC

Y00638

9.3163

Above

13

1971_g_at

fragile histidine triad gene

FHIT

U46922

-9.2257

Below

14

1983_at

cyclin D2

CCND2

X68452

-9.2213

Below

15

38869_at

KIAA1069 protein

KIAA1069

AB028992

-9.1951

Below

16

40520_g_at

protein tyrosine phosphatase receptor type C

PTPRC

Y00638

9.1099

Above

17

1718_at

actin related protein 2/3 complex subunit 2 34 kD

ARPC2

U50523

9.0435

Above

18

34237_at

HBS1 S. cerevisiae like

HBS1L

AB028961

-8.8208

Below

19

1726_at

DNA polymerase, epsilon, catalytic subunit

 

HG919-HT919

-8.4664

Below

20

36643_at

discoidin domain receptor family member 1

DDR1

L20817

-8.4627

Below

21

1325_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59423

-8.3762

Below

22

39379_at

Homo sapiens mRNA cDNA DKFZp586C1019

 

AL049397

8.2974

Above

23

36536_at

schwannomin interacting protein 1

SCHIP-1

AF070614

-8.1177

Below

24

564_at

guanine nucleotide binding protein G protein alpha 11 Gq class

GNA11

M69013

-8.1107

Below

25

39705_at

KIAA0700 protein

KIAA0700

AB014600

-7.9334

Below

26

36105_at

Human nonspecific crossreacting antigen mRNA, complete cds.

NCA

M18728

-7.6911

Below

27

174_s_at

intersectin 2

ITSN2

U61167

7.5752

Above

28

39114_at

decidual protein induced by
progesterone

DEPP

AB022718

-7.4767

Below

29

40436_g_at

solute carrier family 25 mitochondrial carrier adenine nucleotide translocator member 6

SLC25A6

J03592

7.3952

Above

30

794_at

protein tyrosine phosphatase non-receptor type 6

PTPN6

X62055

7.2192

Above

31

38032_at

KIAA0736 gene product

KIAA0736

AB018279

-7.0718

Below

32

40518_at

protein tyrosine phosphatase receptor type C

PTPRC

Y00062

6.9829

Above

33

41762_at

TIA1 cytotoxic granule-associated RNA-binding protein-like 1

TIAL1

D64015

-6.9118

Below

34

1389_at

membrane metallo-endopeptidase
neutral endopeptidase enkephalinase CALLA CD10

MME

J03779

-6.7734

Below

35

39967_at

leucine zipper down-regulated in cancer 1

LDOC1

AB019527

-6.7415

Below

36

188_at

ephrin-B1

EFNB1

U09303

-6.5964

Below

37

160033_s_at

X-ray repair complementing defective repair in Chinese hamster cells 1

XRCC1

NM_006297

-6.5936

Below

38

40913_at

ATPase Ca transporting plasma membrane 4

ATP2B4

W28589

-6.5774

Below

39

37398_at

platelet/endothelial cell adhesion
molecule CD31 antigen

PECAM1

AA100961

-6.5675

Below

40

1488_at

protein tyrosine phosphatase receptor type K

PTPRK

L77886

-6.5584

Below

             

Novel

         

1

41734_at

KIAA0870 protein

KIAA0870

AB020677

-40.5168

Below

2

31892_at

protein tyrosine phosphatase receptor type M

PTPRM

X58288

33.4654

Above

3

995_g_at

protein tyrosine phosphatase receptor type M

PTPRM

X58288

24.7557

Above

4

34676_at

KIAA1099 protein

KIAA1099

AB029022

14.0491

Above

5

37908_at

guanine nucleotide binding protein 11

GNG11

U31384

11.4548

Above

6

37960_at

carbohydrate chondroitin 6/keratan sulfotransferase 2

CHST2

AB014679

10.9971

Above

7

33410_at

integrin alpha 6

ITGA6

S66213

10.0370

Above

8

40585_at

adenylate cyclase 7

ADCY7

D25538

-9.5897

Below

9

33284_at

myeloperoxidase

MPO

M19507

-9.4724

Below

10

41159_at

clathrin heavy polypeptide Hc

CLTC

D21260

9.4489

Above

11

36591_at

tubulin alpha 1 testis specific

TUBA1

X06956

-9.1387

Below

12

37712_g_at

MADS box transcription enhancer
factor 2 polypeptide C myocyte enhancer factor 2C

MEF2C

S57212

-9.1225

Below

13

38576_at

H2B histone family member B

H2BFB

AJ223353

-9.0869

Below

14

38408_at

transmembrane 4 superfamily member 2

TM4SF2

L10373

-8.7026

Below

15

33907_at

eukaryotic translation initiation factor 4 gamma 3

EIF4G3

AF012072

-8.3540

Below

16

41273_at

FK506 binding protein 12-rapamycin associated protein 1

FRAP1

AL046940

-8.3212

Below

17

402_s_at

intercellular adhesion molecule 3

ICAM3

X69819

-7.9741

Below

18

35112_at

regulator of G-protein signalling 9

RGS9

AF071476

7.8348

Above

19

34850_at

ubiquitin-conjugating enzyme E2E 3 homologous to yeast UBC4/5

UBE2E3

AB017644

7.8197

Above

20

37030_at

KIAA0887 protein

KIAA0887

AB020694

-7.6343

Below

21

36322_at

fucosyltransferase 7 alpha 1 3 fucosyltransferase

FUT7

AB012668

-7.6240

Below

22

39509_at

Homo sapiens cDNA FLJ22071

 

AI692348

-7.6232

Below

23

40091_at

B-cell CLL/lymphoma 6 zinc finger
protein 51

BCL6

U00115

-7.6171

Below

24

37280_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59912

7.5991

Above

25

1325_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59423

7.5824

Above

26

831_at

DEAD/H Asp-Glu-Ala-Asp/His box polypeptide 10 RNA helicase

DDX10

U28042

7.4276

Above

27

37600_at

extracellular matrix protein 1

ECM1

U68186

-7.2991

Below

28

41266_at

integrin alpha 6

ITGA6

X53586

7.2985

Above

29

36958_at

zyxin

ZYX

X95735

-7.2889

Below

30

36564_at

Human DNA sequence from clone RP5-1174N9 on chromosome 1p34.1-35.3

 

W27419

-7.2848

Below

31

32174_at

solute carrier family 9 sodium/hydrogen exchanger isoform 3 regulatory factor 1

SLC9A3R1

AF015926

-7.2749

Below

32

619_s_at

membrane-spanning 4-domains
subfamily A member 2 Fc fragment of
IgE high affinity I receptor for beta polypeptide

MS4A2

M27394

-7.2325

Below

33

40749_at

membrane-spanning 4-domains
subfamily A member 2 Fc fragment of
IgE high affinity I receptor for beta polypeptide

MS4A2

X07203

-7.2063

Below

34

31894_at

centromere protein C 1

CENPC1

M95724

6.9679

Above

35

32319_at

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

TNFSF4

AL022310

6.8225

Above

36

38259_at

syntaxin binding protein 2

STXBP2

AB002559

-6.6992

Below

37

35629_at

hypothetical protein

DJ1042K10.2

AL022238

-6.6968

Below

38

38700_at

cysteine and glycine-rich protein 1

CSRP1

M33146

-6.6962

Below

39

37397_at

Homo sapiens platelet/endothelial cell adhesion molecule-1 (PECAM-1) gene, exon 16 and complete cds.

PECAM

L34657

-6.6934

Below

40

41127_at

solute carrier family 1 glutamate/neutral amino acid transporter member 4

SLC1A4

L14595

-6.6892

Below

             

T -ALL

         

1

38242_at

B cell linker protein

SLP65

AF068180

-115.8362

Below

2

38319_at

CD3D antigen delta polypeptide TiT3 complex

CD3D

AA919102

27.6995

Above

3

37988_at

CD79B antigen immunoglobulin-associated beta

CD79B

M89957

-23.7294

Below

4

38147_at

SH2 domain protein 1A Duncan s disease lymphoproliferative syndrome

SH2D1A

AL023657

22.4501

Above

5

38522_s_at

CD22 antigen

CD22

X52785

-21.2795

Below

6

35350_at

B cell RAG associated protein

BRAG

AB011170

-19.1460

Below

7

36277_at

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

CD3E

M23323

19.0859

Above

8

38604_at

neuropeptide Y

NPY

AI198311

-18.8194

Below

9

33705_at

phosphodiesterase 4B cAMP-specific dunce Drosophila homolog phosphodiesterase E4

PDE4B

L20971

-18.6383

Below

10

36878_f_at

major histocompatibility complex class II DQ beta 1

HLA-DQB1

M60028

-18.5620

Below

11

36638_at

connective tissue growth factor

CTGF

X78947

-18.2772

Below

12

32794_g_at

T cell receptor beta locus

TRB

X00437

17.9081

Above

13

32174_at

solute carrier family 9 sodium/hydrogen exchanger isoform 3 regulatory factor 1

SLC9A3R1

AF015926

17.4427

Above

14

160041_at

protein tyrosine phosphatase non-receptor type 18 brain-derived

PTPN18

X79568

-17.3412

Below

15

38521_at

CD22 antigen

CD22

X59350

-17.0388

Below

16

38018_g_at

CD79A antigen immunoglobulin-associated alpha

CD79A

U05259

-16.7948

Below

17

36571_at

topoisomerase DNA II beta 180kD

TOP2B

X68060

-16.7508

Below

18

1096_g_at

CD19 antigen

CD19

M28170

-16.4583

Below

19

39318_at

T-cell leukemia/lymphoma 1A

TCL1A

X82240

-16.2017

Below

20

41710_at

hypothetical protein

LOC54103

AL079277

-15.9099

Below

21

599_at

H2.0 Drosophila like homeo box 1

HLX1

M60721

-15.5425

Below

22

266_s_at

CD24 antigen small cell lung carcinoma cluster 4 antigen

CD24

L33930

-15.0123

Below

23

36502_at

PFTAIRE protein kinase 1

PFTK1

AB020641

-14.9972

Below

24

39114_at

decidual protein induced by progesterone

DEPP

AB022718

-14.9886

Below

25

37539_at

RalGDS-like gene KIAA0959 protein

KIAA0959

AB023176

-14.6872

Below

26

40775_at

integral membrane protein 2A

ITM2A

AL021786

14.5666

Above

27

34033_s_at

leukocyte immunoglobulin-like receptor subfamily A with TM domain member 2

LILRA2

AF025531

-14.3809

Below

28

2031_s_at

cyclin-dependent kinase inhibitor 1A p21 Cip1

CDKN1A

U03106

-14.1071

Below

29

38051_at

mal T-cell differentiation protein

MAL

X76220

14.0743

Above

30

35794_at

KIAA0942 protein

KIAA0942

AB023159

-13.9659

Below

31

41156_g_at

catenin cadherin-associated protein alpha 1 102kD

CTNNA1

U03100

-13.8135

Below

32

32979_at

GRB2-associated binding protein 1

GAB1

U43885

-13.5842

Below

33

32562_at

endoglin Osler-Rendu-Weber
syndrome 1

ENG

X72012

-13.4209

Below

34

36536_at

schwannomin interacting protein 1

SCHIP-1

AF070614

-13.4172

Below

35

36108_at

major histocompatibility complex
class II DQ beta 1

HLA-DQB1

M16276

-13.3518

Below

36

41734_at

KIAA0870 protein

KIAA0870

AB020677

-13.2672

Below

37

41153_f_at

Homo sapiens alphaE-catenin (CTNNA1) gene, exon 18 and complete cds.

CTNNA1

AF102803

-12.7927

Below

38

37710_at

MADS box transcription enhancer
factor 2 polypeptide C myocyte enhancer factor 2C

MEF2C

L08895

-12.7716

Below

39

39893_at

guanine nucleotide binding protein G protein gamma 7

GNG7

AB010414

-12.7696

Below

40

37908_at

guanine nucleotide binding protein 11

GNG11

U31384

-12.7353

Below

             

TEL-AML1

         

1

38578_at

tumor necrosis factor receptor superfamily member 7

TNFRSF7

M63928

15.2209

Above

2

38203_at

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

KCNN1

U69883

15.0804

Above

3

36524_at

Rho guanine nucleotide exchange factor GEF 4

ARHGEF4

AB029035

14.9774

Above

4

37780_at

piccolo presynaptic cytomatrix protein

PCLO

AB011131

14.1405

Above

5

35614_at

transcription factor-like 5 basic helix-loop-helix

TCFL5

AB012124

12.9369

Above

6

160029_at

protein kinase C beta 1

PRKCB1

X07109

12.5429

Above

7

1980_s_at

non-metastatic cells 2 protein NM23B expressed in

NME2

X58965

-12.5035

Below

8

1488_at

protein tyrosine phosphatase receptor type K

PTPRK

L77886

12.3871

Above

9

34194_at

Homo sapiens cDNA FLJ21697

 

AL049313

12.1089

Above

10

37908_at

guanine nucleotide binding protein 11

GNG11

U31384

11.4322

Above

11

40272_at

collapsin response mediator protein 1

CRMP1

D78012

11.0625

Above

12

41097_at

telomeric repeat binding factor 2

TERF2

AF002999

11.0133

Above

13

33690_at

Homo sapiens mRNA cDNA DKFZp434A202

 

AL080190

10.8763

Above

14

32730_at

Homo sapiens mRNA for KIAA1750

 

AL080059

10.7439

Above

15

1325_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59423

10.5332

Above

16

41819_at

FYN-binding protein FYB-120/130

FYB

U93049

10.3692

Above

17

1299_at

telomeric repeat binding factor 2

TERF2

X93512

10.2921

Above

18

35665_at

phosphoinositide-3-kinase class 3

PIK3C3

Z46973

10.0568

Above

19

36537_at

Rho-specific guanine nucleotide exchange factor p114

P114-RHO-GEF

AB011093

9.8824

Above

20

37280_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59912

9.8662

Above

21

1936_s_at

proto-oncogene c-myc, alt. transcript 3, ORF 114

 

HG3523-HT4899

-9.6621

Below

22

1077_at

recombination activating gene 1

RAG1

M29474

9.4563

Above

23

38763_at

Human (clone D21-1) L-iditol-2 dehydrogenase gene, exon 9 and complete cds.

 

L29254

-9.2719

Below

24

41295_at

GTT1 protein

GTT1

AL041780

-9.1813

Below

25

36008_at

protein tyrosine phosphatase type IVA member 3

PTP4A3

AF041434

9.1682

Above

26

38570_at

major histocompatibility complex class II DO beta

HLA-DOB

X03066

9.0394

Above

27

32163_f_at

EST

 

AA216639

9.0392

Above

28

40570_at

forkhead box O1A rhabdomyosarcoma

FOXO1A

AF032885

8.9931

Above

29

32724_at

phytanoyl-CoA hydroxylase Refsum disease

PHYH

AF023462

8.9571

Above

30

932_i_at

zinc finger protein 91 HPF7 HTF10

ZNF91

L11672

8.8075

Above

31

37343_at

inositol 1 4 5-triphosphate receptor
type 3

ITPR3

U01062

8.7321

Above

32

33447_at

myosin light polypeptide regulatory non-sarcomeric 20kD

MLCB

X54304

-8.6848

Below

33

35362_at

myosin X

MYO10

AB018342

8.6700

Above

34

38906_at

spectrin alpha erythrocytic 1
elliptocytosis 2

SPTA1

M61877

8.5010

Above

35

324_f_at

basic transcription factor 3

BTF3

HG1515-HT1515

-8.4705

Below

36

39329_at

actinin alpha 1

ACTN1

X15804

-8.3219

Below

37

577_at

midkine neurite growth-promoting factor 2

MDK

M94250

8.2693

Above

38

40729_s_at

nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1

NFKBIL1

Y14768

8.2000

Above

39

41442_at

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

CBFA2T3

AB010419

8.0604

Above

40

36275_at

Homo sapiens mRNA from chromosome 5q21-22 clone FBR89

 

AB002438

7.8550

Above

Illustrated below are the results of a two-dimensional hierarchical clustering algorithm of the 327 diagnostic ALL cases using the top 280 probe sets selected by the T-statistics method. Some probe sets were chosen for more than one diagnostic group, and thus there are only 248 unique probe sets represented.

Figure 16. Hierarchical cluster of 327 Diagnostic ALL samples with genes selected by the T-statistics method.


Wilkins'
This method of selecting genes uses the weighted sum of three components to estimate the discriminative value of each gene. The higher the score, the better the gene is at discriminating between the two classes. The input to the scoring method is preprocessed and normalized data. The idea of the metric is that a gene is a good discriminator if (1) it is expressed in one class and not in the other, or if the gene is expressed in both classes, but significantly more so in one than the other, or (2) the gene is present in most samples, and the data are pure, in the sense that there is a threshold expression value for the gene where the gene generally has expression levels larger than the threshold in one class, and smaller than the threshold in the other class. The components of the metric were quantified as follows. For a gene, assume PR1 is the ratio of "present" samples to all samples in class 1, where present means that the gene's expression value was not preprocessed to a constant (1). Assume PR2 is defined similarly for class 2. The first component of the metric, M1,
is estimated as the absolute difference between PR1 and PR2. This value is between 0 (when the gene is equally present in both classes) and 1 (when the gene is expressed in one class and not in the other). The second component of the metric, M2, measures the extent to which the gene is present overall, and is defined as the average of PR1 and PR2. The final component, M3, estimates the "purity", or existence of a threshold value. The gene expression values for the present samples are sorted into ascending order and a vector of their class labels is built, for example {+, +, +, -, -, -, +, -, -, +, -}. The next step is to find the best place to partition the samples so that the expression values for one class (maybe +) are less than the partition point, and the values from the other class are larger. Let LC1 and LC2 be the number of class 1 and class 2 samples on the left side of the partition, respectively. Assume R1 and RC2 are defined similarly for the right side of the partition. Then the purity is estimated as: max {LC1 - LC2 + RC2 - RC1, LC2 - LC1 + RC1 - RC2} / number of total present samples. Each possible partition is checked. In the example above, the partition {+, +, +, || -, -, -, +, -, -, +, -} is the best partition, with a purity value of M3 = 7 / 11 = 0.64. The score for the gene is the weighted sum of 0.5*M1 + 0.25*M2 + 0.25*M3. The top 50 genes for each subgroup selected by this metric are listed in Table 14. For class prediction all 50 genes were used, unless otherwise stated.


Table 14. Genes Selected by Wilkins'


 

       
 

Affymetrix number

Gene Name

Gene
Symbol

Reference number

Train set score

Above/
Below Mean

BCR-ABL

         

1

32319_at

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

TNFSF4

AL022310

0.6354

Above

2

37479_at

CD72 antigen

CD72

M54992

0.6352

Below

3

1211_s_at

CASP2 and RIPK1 domain containing adaptor with death domain

CRADD

U84388

0.6265

Above

4

37397_at

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

PECAM

L34657

0.6161

Above

5

33162_at

insulin receptor

INSR

X02160

0.6118

Below

6

39691_at

SH3-containing protein SH3GLB1

SH3GLB1

AB007960

0.6089

Above

7

1558_g_at

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

PAK1

U24152

0.6087

Above

8

34759_at

Human hbc647 mRNA sequence

 

U68494

0.6061

Above

9

33774_at

caspase 8 apoptosis-related cysteine protease

CASP8

X98172

0.6040

Above

10

1326_at

caspase 10 apoptosis-related cysteine protease

CASP10

U60519

0.6021

Above

11

38312_at

DKFZp564O222 from clone DKFZp564O222

 

AL050002

0.6010

Above

12

35970_g_at

M-phase phosphoprotein 9

MPHOSPH9

N23137

0.5989

Above

13

41273_at

FK506 binding protein 12-rapamycin associated protein 1

FRAP1

AL046940

0.5989

Above

14

40798_s_at

a disintegrin and metalloproteinase domain 10

ADAM10

Z48579

0.5980

Above

15

40953_at

calponin 3 acidic

CNN3

S80562

0.5972

Above

16

1434_at

phosphatase and tensin homolog mutated in multiple advanced cancers 1

PTEN

U92436

0.5963

Below

17

38966_at

glycoprotein synaptic 2

GPSN2

AF038958

0.5953

Above

18

35991_at

Sm protein F

LSM6

AA917945

0.5938

Above

19

330_s_at

tubulin, alpha 1, isoform 44

TUBA1

HG2259-HT2348

0.5938

Above

20

38032_at

KIAA0736 gene product

KIAA0736

AB018279

0.5934

Above

21

1983_at

cyclin D2

CCND2

X68452

0.5927

Above

22

36194_at

low density lipoprotein-related protein-associated protein 1 alpha-2-macroglobulin receptor-associated protein 1

LRPAP1

M63959

0.5914

Below

23

34460_at

peripheral benzodiazepine receptor-associated protein 1

PRAX-1

AB014512

0.5911

Above

24

2001_g_at

ataxia telangiectasia mutated includes complementation groups A C and D

ATM

U26455

0.5910

Above

25

31443_at

AML1

AML1

S76346

0.5896

Above

26

33410_at

integrin alpha 6

ITGA6

S66213

0.5896

Above

27

37472_at

mannosidase beta A lysosomal

MANBA

U60337

0.5887

Below

28

36099_at

splicing factor arginine/serine-rich 1 splicing factor 2 alternate splicing factor

SFRS1

M69040

0.5877

Below

29

38636_at

immunoglobulin superfamily containing leucine-rich repeat

ISLR

AB003184

0.5858

Above

30

34314_at

ribonucleotide reductase M1 polypeptide

RRM1

X59543

0.5858

Below

31

36129_at

KIAA0397 gene product

KIAA0397

AB007857

0.5858

Above

32

40264_g_at

zinc finger protein-like 1

ZFPL1

AF001891

0.5858

Above

33

37399_at

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

AKR1C3

D17793

0.5852

Above

34

38160_at

lymphocyte antigen 75

LY75

AF011333

0.5832

Above

35

41649_at

FOXJ2 forkhead factor

LOC55810

AF038177

0.5832

Above

36

36591_at

tubulin alpha 1 testis specific

TUBA1

X06956

0.5832

Above

37

40167_s_at

CS box-containing WD protein

LOC55884

AF038187

0.5832

Above

38

2064_g_at

excision repair cross-complementing rodent repair deficiency complementation group

ERCC5

L20046

0.5832

Above

39

39729_at

Human natural killer cell enhancing factor (NKEFB) mRNA, complete

cds.

NKEFB

L19185

0.5829

Below

40

38270_at

poly ADP-ribose glycohydrolase

PARG

AF005043

0.5828

Below

41

40613_at

uncharacterized hypothalamus protein HT012

HT012

AL031775

0.5819

Below

42

39070_at

singed Drosophila like sea urchin fascin homolog like

SNL

U03057

0.5813

Above

43

40782_at

short-chain dehydrogenase/reductase 1

SDR1

AF061741

0.5813

Above

44

34256_at

sialyltransferase 9 CMP-NeuAc lactosylceramide alpha-2 3-sialyltransferase GM3 synthase

SIAT9

AB018356

0.5797

Above

45

41836_at

protein with polyglutamine repeat calcium ca2 homeostasis endoplasmic reticulum protein

ERPROT213-21

U94836

0.5777

Above

46

35681_r_at

zinc finger homeobox 1B

ZFHX1B

AB011141

0.5759

Below

47

37190_at

WAS protein family member 1

WASF1

D87459

0.5759

Below

48

32788_at

RAN binding protein 2

RANBP2

D42063

0.5756

Above

49

828_at

prostaglandin E receptor 2 subtype EP2 53kD

PTGER2

U19487

0.5740

Above

50

38220_at

dihydropyrimidine dehydrogenase

DPYD

U20938

0.5737

Above

             

E2A-PBX1

         

1

32063_at

pre-B-cell leukemia transcription factor 1

PBX1

M86546

0.8750

Above

2

38994_at

STAT induced STAT inhibitor-2

STATI2

AF037989

0.8252

Below

3

33355_at

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

PBX1

AL049381

0.8040

Above

4

40454_at

FAT tumor suppressor Drosophila homolog

FAT

X87241

0.7899

Above

5

753_at

nidogen 2

NID2

D86425

0.7368

Above

6

717_at

GS3955 protein

GS3955

D87119

0.7306

Above

7

1786_at

c-mer proto-oncogene tyrosine kinase

MERTK

U08023

0.7300

Above

8

39070_at

singed Drosophila like sea urchin fascin homolog like

SNL

U03057

0.7271

Below

9

1065_at

fms-related tyrosine kinase 3

FLT3

U02687

0.7160

Below

10

36650_at

cyclin D2

CCND2

D13639

0.7151

Below

11

33513_at

signaling lymphocytic activation molecule

SLAM

U33017

0.7096

Above

12

33748_at

minor histocompatibility antigen HA-1

KIAA0223

D86976

0.7084

Below

13

37225_at

KIAA0172 protein

KIAA0172

D79994

0.7033

Above

14

38717_at

DKFZP586A0522 protein

DKFZP586A0522

AL050159

0.7003

Below

15

854_at

B lymphoid tyrosine kinase

BLK

S76617

0.6982

Above

16

33641_g_at

nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1

NFKBIL1

Y14768

0.6975

Below

17

40468_at

KIAA0554 protein

KIAA0554

AB011126

0.6971

Below

18

41266_at

integrin alpha 6

ITGA6

X53586

0.6965

Below

19

36536_at

schwannomin interacting protein 1

SCHIP-1

AF070614

0.6938

Below

20

362_at

protein kinase C zeta

PRKCZ

Z15108

0.6904

Above

21

755_at

inositol 1 4 5-triphosphate receptor type 1

ITPR1

D26070

0.6877

Below

22

307_at

arachidonate 5-lipoxygenase

ALOX5

J03600

0.6875

Below

23

39614_at

KIAA0802 protein

KIAA0802

AB018345

0.6863

Above

24

1563_s_at

tumor necrosis factor receptor superfamily member 1A

TNFRSF1A

M58286

0.6837

Below

25

38748_at

adenosine deaminase RNA-specific B1 homolog of rat RED1

ADARB1

U76421

0.6763

Above

26

41409_at

basement membrane-induced gene

ICB-1

AF044896

0.6757

Below

27

34892_at

tumor necrosis factor receptor superfamily member 10b

TNFRSF10B

AF016266

0.6726

Below

28

40648_at

c-mer proto-oncogene tyrosine kinase

MERTK

U08023

0.6710

Above

29

38408_at

transmembrane 4 superfamily member 2

TM4SF2

L10373

0.6667

Below

30

34583_at

fms-related tyrosine kinase 3

FLT3

U02687

0.6665

Below

31

36900_at

stromal interaction molecule 1

STIM1

U52426

0.6650

Below

32

37625_at

interferon regulatory factor 4

IRF4

U52682

0.6636

Above

33

38340_at

huntingtin interacting protein-1-related

KIAA0655

AB014555

0.6609

Above

34

1830_s_at

transforming growth factor beta 1

TGFB1

M38449

0.6608

Below

35

37099_at

arachidonate 5-lipoxygenase-activating protein

ALOX5AP

AI806222

0.6605

Below

36

38254_at

KIAA0882 protein

KIAA0882

AB020689

0.6539

Below

37

37641_at

Human gene for hepatitis C-associated microtubular aggregate protein p44, exon 9 and complete cds.

 

D28915

0.6531

Below

38

33865_at

adenovirus 5 E1A binding protein

BS69

AA127624

0.6515

Below

39

40729_s_at

nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1

NFKBIL1

Y14768

0.6502

Below

40

40113_at

GS3955 protein

GS3955

D87119

0.6476

Above

41

32979_at

GRB2-associated binding protein 1

GAB1

U43885

0.6457

Below

42

36591_at

tubulin alpha 1 testis specific

TUBA1

X06956

0.6427

Below

43

38739_at

v-ets avian erythroblastosis virus E26 oncogene homolog 2

ETS2

AF017257

0.6424

Below

44

37485_at

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

FACVL1

D88308

0.6363

Above

45

538_at

CD34 antigen

CD34

S53911

0.6326

Below

46

37893_at

protein tyrosine phosphatase non-receptor type 2

PTPN2

AI828880

0.6318

Above

47

41017_at

myosin-binding protein H

MYBPH

U27266

0.6297

Above

48

37967_at

lymphocyte antigen 117

LY117

AF000424

0.6260

Below

49

37281_at

KIAA0233 gene product

KIAA0233

D87071

0.6250

Below

50

35675_at

vinexin beta SH3-containing adaptor molecule-1

SCAM-1

AF037261

0.6229

Below

             

Hyperdiploid > 50

       

1

39878_at

protocadherin 9

PCDH9

AI524125

0.5838

Below

2

41470_at

prominin mouse like 1

PROML1

AF027208

0.5616

Above

3

39069_at

AE-binding protein 1

AEBP1

AF053944

0.5423

Below

4

1520_s_at

interleukin 1 beta

IL1B

X04500

0.5399

Above

5

578_at

Human recombination acitivating protein (RAG2) gene, last exon

RAG2

M94633

0.5208

Below

6

32251_at

hypothetical protein FLJ21174

FLJ21174

AA149307

0.5164

Above

7

40480_s_at

FYN oncogene related to SRC FGR YES

FYN

M14333

0.5090

Above

8

38604_at

neuropeptide Y

NPY

AI198311

0.5083

Above

9

40903_at

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

APT6M8-9

AL049929

0.5080

Above

10

38968_at

SH3-domain binding protein 5 BTK-associated

SH3BP5

AB005047

0.5057

Above

11

37272_at

inositol 1 4 5-trisphosphate 3-kinase B

ITPKB

X57206

0.5025

Below

12

35688_g_at

mature T-cell proliferation 1

MTCP1

Z24459

0.5018

Above

13

1488_at

protein tyrosine phosphatase receptor type K

PTPRK

L77886

0.4977

Below

14

36885_at

spleen tyrosine kinase

SYK

L28824

0.4964

Below

15

1630_s_at

tyrosine kinase syk

syk

HG3730-HT4000

0.4913

Below

16

38317_at

transcription elongation factor A SII like 1

TCEAL1

M99701

0.4901

Above

17

38649_at

KIAA0970 protein

KIAA0970

AB023187

0.4898

Below

18

39721_at

ephrin-B1

EFNB1

U09303

0.4895

Above

19

33307_at

kraken-like

BK126B4.1

AL022316

0.4880

Below

20

38518_at

sex comb on midleg Drosophila like 2

SCML2

Y18004

0.4879

Above

21

39402_at

interleukin 1 beta

IL1B

M15330

0.4750

Above

22

36489_at

phosphoribosyl pyrophosphate synthetase 1

PRPS1

D00860

0.4718

Above

23

37747_at

Human annexin V (ANX5) gene, exon 13.

(ANX5

U05770

0.4717

Above

24

40200_at

heat shock transcription factor 1

HSF1

M64673

0.4689

Below

25

35940_at

POU domain class 4 transcription factor 1

POU4F1

X64624

0.4685

Above

26

35727_at

hypothetical protein FLJ20517

FLJ20517

AI249721

0.4675

Below

27

1357_at

ubiquitin specific protease 4 proto-oncogene

USP4

U20657

0.4670

Below

28

36592_at

prohibitin

PHB

S85655

0.4668

Above

29

37014_at

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

MX1

M33882

0.4635

Above

30

40891_f_at

DNA segment on chromosome X unique 9879 expressed sequence

DXS9879E

X92896

0.4608

Above

31

40846_g_at

interleukin enhancer binding factor 3 90kD

ILF3

U10324

0.4605

Below

32

41132_r_at

heterogeneous nuclear ribonucleoprotein H2 H

HNRPH2

U01923

0.4605

Above

33

37280_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59912

0.4595

Below

34

35939_s_at

POU domain class 4 transcription factor 1

POU4F1

L20433

0.4594

Above

35

890_at

ubiquitin-conjugating enzyme E2A RAD6 homolog

UBE2A

M74524

0.4570

Above

36

38738_at

SMT3 suppressor of mif two 3 yeast homolog 1

SMT3H1

X99584

0.4568

Above

37

38458_at

Human cytochrome b5 (CYB5) gene, exon 6 and complete cds.

CYB5

L39945

0.4552

Above

38

38869_at

KIAA1069 protein

KIAA1069

AB028992

0.4549

Above

39

915_at

interferon-induced protein with tetratricopeptide repeats 1

IFIT1

M24594

0.4544

Above

40

38408_at

transmembrane 4 superfamily member 2

TM4SF2

L10373

0.4535

Above

41

39301_at

calpain 3 p94

CAPN3

X85030

0.4533

Below

42

41425_at

Friend leukemia virus integration 1

FLI1

M98833

0.4519

Below

43

2094_s_at

v-fos FBJ murine osteosarcoma viral oncogene homolog

FOS

K00650

0.4514

Above

44

36605_at

transcription factor 4

TCF4

M74719

0.4497

Above

45

37709_at

DNA segment numerous copies expressed probes GS1 gene

DXF68S1E

M86934

0.4493

Above

46

36128_at

transmembrane trafficking protein

TMP21

L40397

0.4488

Above

47

171_at

von Hippel-Lindau binding protein 1

VBP1

U56833

0.4473

Above

48

41490_at

phosphoribosyl pyrophosphate synthetase 2

PRPS2

Y00971

0.4466

Above

49

36536_at

schwannomin interacting protein 1

SCHIP-1

AF070614

0.4448

Above

50

35843_at

Homo sapiens mRNA cDNA

DKFZp434D0935

L40402

0.4443

Above

             

MLL

       

1

39402_at

interleukin 1 beta

IL1B

M15330

0.7355

Below

2

307_at

arachidonate 5-lipoxygenase

ALOX5

J03600

0.7221

Below

3

1389_at

membrane metallo-endopeptidase neutral endopeptidase enkephalinase CALLA CD10

MME

J03779

0.7178

Below

4

37280_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59912

0.7021

Below

5

36650_at

cyclin D2

CCND2

D13639

0.6759

Below

6

37043_at

inhibitor of DNA binding 3 dominant negative helix-loop-helix protein

ID3

AL021154

0.6743

Below

7

1520_s_at

interleukin 1 beta

IL1B

X04500

0.6689

Below

8

40913_at

ATPase Ca transporting plasma membrane 4

ATP2B4

W28589

0.6684

Below

9

36536_at

schwannomin interacting protein 1

SCHIP-1

AF070614

0.6554

Below

10

37398_at

platelet/endothelial cell adhesion molecule CD31 antigen

PECAM1

AA100961

0.6548

Below

11

39114_at

decidual protein induced by progesterone

DEPP

AB022718

0.6478

Below

12

37967_at

lymphocyte antigen 117

LY117

AF000424

0.6432

Below

13

1325_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59423

0.6421

Below

14

38336_at

KIAA1013 protein

KIAA1013

AB023230

0.6395

Below

15

577_at

midkine neurite growth-promoting factor 2

MDK

M94250

0.6363

Below

16

38671_at

KIAA0620 protein

KIAA0620

AB014520

0.6353

Below

17

33412_at

LGALS1 Lectin, galactoside-binding, soluble, 1

LGALS1

AI535946

0.6351

Above

18

40451_at

hypothetical protein FLJ21434

FLJ21434

AL080203

0.6350

Below

19

36908_at

Human macrophage mannose receptor (MRC1) gene, exon 30.

MRC1

M93221

0.6290

Below

20

963_at

ligase IV DNA ATP-dependent

LIG4

X83441

0.6282

Below

21

41346_at

like-glycosyltransferase

LARGE

AJ007583

0.6214

Below

22

32207_at

membrane protein palmitoylated 1 55kD

MPP1

M64925

0.6155

Below

23

2062_at

insulin-like growth factor binding protein 7

IGFBP7

L19182

0.6145

Above

24

38408_at

transmembrane 4 superfamily member 2

TM4SF2

L10373

0.6137

Below

25

854_at

B lymphoid tyrosine kinase

BLK

S76617

0.6075

Above

26

32193_at

plexin C1

PLXNC1

AF030339

0.6065

Above

27

35939_s_at

POU domain class 4 transcription factor 1

POU4F1

L20433

0.6046

Below

28

33705_at

phosphodiesterase 4B cAMP-specific dunce Drosophila homolog phosphodiesterase E4

PDE4B

L20971

0.5991

Below

29

34168_at

deoxynucleotidyltransferase terminal

DNTT

M11722

0.5979

Below

30

36383_at

v-ets avian erythroblastosis virus E26 oncogene related

ERG

M17254

0.5976

Below

31

38968_at

SH3-domain binding protein 5 BTK-associated

SH3BP5

AB005047

0.5976

Below

32

39263_at

2 5 oligoadenylate synthetase 2

OAS2

M87434

0.5967

Below

33

39329_at

actinin alpha 1

ACTN1

X15804

0.5953

Below

34

34699_at

CD2-associated protein

CD2AP

AL050105

0.5945

Below

35

1267_at

protein kinase C eta

PRKCH

M55284

0.5941

Below

36

35172_at

tyrosylprotein sulfotransferase 2

TPST2

AF049891

0.5937

Below

37

38124_at

midkine neurite growth-promoting factor 2

MDK

X55110

0.5936

Below

38

33813_at

tumor necrosis factor receptor superfamily member 1B

TNFRSF1B

AI813532

0.5934

Below

39

34176_at

hypothetical protein from clone 643

LOC57228

AF091087

0.5930

Below

40

39424_at

tumor necrosis factor receptor superfamily member 14 herpesvirus entry mediator

TNFRSF14

U70321

0.5930

Below

41

40729_s_at

nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1

NFKBIL1

Y14768

0.5905

Below

42

32607_at

brain acid-soluble protein 1

BASP1

AF039656

0.5905

Above

43

38342_at

KIAA0239 protein

KIAA0239

D87076

0.5896

Below

44

32533_s_at

vesicle-associated membrane protein 5 myobrevin

VAMP5

AF054825

0.5880

Below

45

39330_s_at

actinin alpha 1

ACTN1

M95178

0.5867

Below

46

40519_at

protein tyrosine phosphatase receptor type C

PTPRC

Y00638

0.5848

Above

47

39338_at

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

S100A10

AI201310

0.5844

Above

48

35940_at

POU domain class 4 transcription factor 1

POU4F1

X64624

0.5824

Below

49

39712_at

S100 calcium-binding protein A13

S100A13

AI541308

0.5818

Below

50

39379_at

Homo sapiens mRNA cDNA DKFZp586C1019 from clone DKFZp586C1019

 

AL049397

0.5811

Above

             

Novel

         

1

31892_at

protein tyrosine phosphatase receptor type M

PTPRM

X58288

0.8668

Above

2

41734_at

KIAA0870 protein

KIAA0870

AB020677

0.8614

Below

3

995_g_at

protein tyrosine phosphatase receptor type M

PTPRM

X58288

0.8505

Above

4

994_at

protein tyrosine phosphatase receptor type M

PTPRM

X58288

0.7694

Above

5

37967_at

lymphocyte antigen 117

LY117

AF000424

0.7399

Below

6

34676_at

KIAA1099 protein

KIAA1099

AB029022

0.7298

Above

7

41159_at

clathrin heavy polypeptide Hc

CLTC

D21260

0.7283

Above

8

39728_at

interferon gamma-inducible protein 30

IFI30

J03909

0.7138

Below

9

37542_at

lipoma HMGIC fusion partner-like 2

LHFPL2

D86961

0.7069

Above

10

35350_at

B cell RAG associated protein

BRAG

AB011170

0.7049

Below

11

41438_at

KIAA1451 protein

KIAA1451

AL049923

0.6999

Below

12

34370_at

archain 1

ARCN1

X81198

0.6999

Below

13

36029_at

chromosome 11 open reading frame 8

C11ORF8

U57911

0.6964

Above

14

37960_at

carbohydrate chondroitin 6/keratan sulfotransferase 2

CHST2

AB014679

0.6947

Above

15

35869_at

MD-1 RP105-associated

MD-1

AB020499

0.6908

Below

16

36601_at

vinculin

VCL

M33308

0.6908

Below

17

40775_at

integral membrane protein 2A

ITM2A

AL021786

0.6879

Above

18

37281_at

KIAA0233 gene product

KIAA0233

D87071

0.6837

Below

19

957_at

arrestin, beta 2

ARRB2

HG2059-HT2114

0.6744

Below

20

33284_at

myeloperoxidase

MPO

M19507

0.6712

Below

21

40585_at

adenylate cyclase 7

ADCY7

D25538

0.6712

Below

22

37908_at

guanine nucleotide binding protein 11

GNG11

U31384

0.6656

Above

23

40167_s_at

CS box-containing WD protein

LOC55884

AF038187

0.6581

Below

24

38576_at

H2B histone family member B

H2BFB

AJ223353

0.6576

Below

25

36591_at

tubulin alpha 1 testis specific

TUBA1

X06956

0.6576

Below

26

37712_g_at

MADS box transcription enhancer factor 2 polypeptide C myocyte enhancer factor 2C

MEF2C

S57212

0.6576

Below

27

33924_at

KIAA1091 protein

KIAA1091

AB029014

0.6484

Below

28

32724_at

phytanoyl-CoA hydroxylase Refsum disease

PHYH

AF023462

0.6466

Above

29

33358_at

EST (retina)

 

W29087

0.6457

Above

30

33740_at

chromosome 1 open reading frame 2

C1ORF2

AF023268

0.6441

Below

31

36588_at

KIAA0810 protein

KIAA0810

AB018353

0.6441

Below

32

38802_at

progesterone binding protein

HPR6.6

Y12711

0.6441

Below

33

38408_at

transmembrane 4 superfamily member 2

TM4SF2

L10373

0.6440

Below

34

32227_at

proteoglycan 1 secretory granule

PRG1

X17042

0.6409

Below

35

34840_at

Homo sapiens cDNA FLJ22642 fis clone HSI06970

 

AI700633

0.6409

Below

36

1131_at

mitogen-activated protein kinase kinase 2

MAP2K2

L11285

0.6409

Below

37

33410_at

integrin alpha 6

ITGA6

S66213

0.6391

Above

38

38006_at

CD48 antigen B-cell membrane protein

CD48

M37766

0.6342

Below

39

33907_at

eukaryotic translation initiation factor 4 gamma 3

EIF4G3

AF012072

0.6304

Below

40

41273_at

FK506 binding protein 12-rapamycin associated protein 1

FRAP1

AL046940

0.6304

Below

41

39781_at

insulin-like growth factor-binding protein 4

IGFBP4

U20982

0.6301

Below

42

39893_at

guanine nucleotide binding protein G protein gamma 7

GNG7

AB010414

0.6301

Below

43

37326_at

proteolipid protein 2 colonic epithelium-enriched

PLP2

U93305

0.6267

Below

44

36687_at

cytochrome c oxidase subunit VIIb

COX7B

N50520

0.6266

Below

45

40423_at

KIAA0903 protein

KIAA0903

AB020710

0.6254

Above

46

32542_at

four and a half LIM domains 1

FHL1

AF063002

0.6236

Below

47

33232_at

cysteine-rich protein 1 intestinal

CRIP1

AI017574

0.6211

Below

48

37280_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59912

0.6208

Above

49

1325_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59423

0.6208

Above

50

40729_s_at

nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1

NFKBIL1

Y14768

0.6199

Below

             

T-ALL

         

1

38242_at

B cell linker protein

SLP65

AF068180

0.8683

Below

2

37988_at

CD79B antigen immunoglobulin-associated beta

CD79B

M89957

0.8422

Below

3

1096_g_at

CD19 antigen

CD19

M28170

0.8181

Below

4

39318_at

T-cell leukemia/lymphoma 1A

TCL1A

X82240

0.8128

Below

5

38018_g_at

CD79A antigen immunoglobulin-associated alpha

CD79A

U05259

0.8127

Below

6

36878_f_at

major histocompatibility complex class II DQ beta 1

HLA-DQB1

M60028

0.8053

Below

7

38147_at

SH2 domain protein 1A Duncan s disease lymphoproliferative syndrome

SH2D1A

AL023657

0.8016

Above

8

35350_at

B cell RAG associated protein

BRAG

AB011170

0.7914

Below

9

38051_at

mal T-cell differentiation protein

MAL

X76220

0.7900

Above

10

266_s_at

CD24 antigen small cell lung carcinoma cluster 4 antigen

CD24

L33930

0.7867

Below

11

38521_at

CD22 antigen

CD22

X59350

0.7856

Below

12

37344_at

major histocompatibility complex class II DM alpha

HLA-DMA

X62744

0.7835

Below

13

34033_s_at

leukocyte immunoglobulin-like receptor subfamily A with TM domain member 2

LILRA2

AF025531

0.7761

Below

14

36638_at

connective tissue growth factor

CTGF

X78947

0.7755

Below

15

38213_at

galactosidase alpha

GLA

U78027

0.7701

Below

16

41734_at

KIAA0870 protein

KIAA0870

AB020677

0.7693

Below

17

37711_at

MADS box transcription enhancer factor 2 polypeptide C myocyte enhancer factor 2C

MEF2C

S57212

0.7560

Below

18

36239_at

POU domain class 2 associating factor 1

POU2AF1

Z49194

0.7440

Below

19

38319_at

CD3D antigen delta polypeptide TiT3 complex

CD3D

AA919102

0.7426

Above

20

38894_g_at

neutrophil cytosolic factor 4 40kD

NCF4

AL008637

0.7422

Below

21

33705_at

phosphodiesterase 4B cAMP-specific dunce Drosophila homolog phosphodiesterase E4

PDE4B

L20971

0.7414

Below

22

38017_at

CD79A antigen immunoglobulin-associated alpha

CD79A

U05259

0.7360

Below

23

41156_g_at

catenin cadherin-associated protein alpha 1 102kD

CTNNA1

U03100

0.7315

Below

24

38994_at

STAT induced STAT inhibitor-2

STATI2

AF037989

0.7292

Below

25

37710_at

MADS box transcription enhancer factor 2 polypeptide C myocyte enhancer factor 2C

MEF2C

L08895

0.7283

Below

26

41155_at

catenin cadherin-associated protein alpha 1 102kD

CTNNA1

U03100

0.7278

Below

27

40570_at

forkhead box O1A rhabdomyosarcoma

FOXO1A

AF032885

0.7258

Below

28

34224_at

fatty acid desaturase 3

FADS3

AC004770

0.7254

Below

29

38604_at

neuropeptide Y

NPY

AI198311

0.7212

Below

30

36773_f_at

major histocompatibility complex class II DQ beta 1

HLA-DQB1

M81141

0.7197

Below

31

32562_at

endoglin Osler-Rendu-Weber syndrome 1

ENG

X72012

0.7180

Below

32

36502_at

PFTAIRE protein kinase 1

PFTK1

AB020641

0.7179

Below

33

37180_at

phospholipase C gamma 2 phosphatidylinositol-specific

PLCG2

X14034

0.7114

Below

34

38893_at

neutrophil cytosolic factor 4 40kD

NCF4

AL008637

0.7100

Below

35

387_at

cyclin-dependent kinase 9 CDC2-related kinase

CDK9

X80230

0.7024

Below

36

32035_at

Human MHC class II HLA-DRw53-associated glycoprotein beta- chain mRNA complete cds

 

M16942

0.6992

Below

37

41153_f_at

Homo sapiens alphaE-catenin (CTNNA1) gene

CTNNA1

AF102803

0.6976

Below

38

40780_at

C-terminal binding protein 2

CTBP2

AF016507

0.6976

Below

39

40775_at

integral membrane protein 2A

ITM2A

AL021786

0.6952

Above

40

39402_at

interleukin 1 beta

IL1B

M15330

0.6945

Below

41

38522_s_at

CD22 antigen

CD22

X52785

0.6945

Below

42

41166_at

immunoglobulin heavy constant mu

IGHM

X58529

0.6941

Below

43

36937_s_at

PDZ and LIM domain 1 elfin

PDLIM1

U90878

0.6937

Below

44

38833_at

Human mRNA for SB classII histocompatibility antigen alpha-chain

 

X00457

0.6925

Below

45

2047_s_at

junction plakoglobin

JUP

M23410

0.6920

Below

46

36277_at

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

CD3E

M23323

0.6899

Above

47

40688_at

linker for activation of T cells

LAT

AJ223280

0.6898

Above

48

39389_at

CD9 antigen p24

CD9

M38690

0.6879

Below

49

33162_at

insulin receptor

INSR

X02160

0.6879

Below

50

31891_at

chitinase 3-like 2

CHI3L2

U58515

0.6872

Above

             

TEL-AML1

         

1

37780_at

piccolo presynaptic cytomatrix protein

PCLO

AB011131

0.7121

Above

2

38203_at

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

KCNN1

U69883

0.7086

Above

3

36524_at

Rho guanine nucleotide exchange factor GEF 4

ARHGEF4

AB029035

0.6782

Above

4

38578_at

tumor necrosis factor receptor superfamily member 7

TNFRSF7

M63928

0.6718

Above

5

32730_at

Homo sapiens mRNA for KIAA1750 protein partial cds

 

AL080059

0.6616

Above

6

34194_at

Homo sapiens cDNA FLJ21697 fis clone COL09740

 

AL049313

0.6518

Above

7

40272_at

collapsin response mediator protein 1

CRMP1

D78012

0.6160

Above

8

41819_at

FYN-binding protein FYB-120/130

FYB

U93049

0.6058

Above

9

1488_at

protein tyrosine phosphatase receptor type K

PTPRK

L77886

0.6056

Above

10

35665_at

phosphoinositide-3-kinase class 3

PIK3C3

Z46973

0.6022

Above

11

35614_at

transcription factor-like 5 basic helix-loop-helix

TCFL5

AB012124

0.5983

Above

12

36008_at

protein tyrosine phosphatase type IVA member 3

PTP4A3

AF041434

0.5976

Above

13

35362_at

myosin X

MYO10

AB018342

0.5964

Above

14

37908_at

guanine nucleotide binding protein 11

GNG11

U31384

0.5888

Above

15

39329_at

actinin alpha 1

ACTN1

X15804

0.5840

Below

16

1936_s_at

proto-oncogene c-myc, alt. transcript 3, ORF 114

 

HG3523-HT4899

0.5761

Below

17

33690_at

Homo sapiens mRNA cDNA DKFZp434A202

DKFZp434A202

AL080190

0.5725

Above

18

39389_at

CD9 antigen p24

CD9

M38690

0.5684

Below

19

37343_at

inositol 1 4 5-triphosphate receptor type 3

ITPR3

U01062

0.5642

Above

20

1299_at

telomeric repeat binding factor 2

TERF2

X93512

0.5585

Above

21

38652_at

hypothetical protein FLJ20154

FLJ20154

AF070644

0.5563

Above

22

38763_at

(clone D21-1) L-iditol-2 dehydrogenase gene

 

L29254

0.5535

Below

23

37724_at

v-myc avian myelocytomatosis viral oncogene homolog

MYC

V00568

0.5506

Below

24

36937_s_at

PDZ and LIM domain 1 elfin

PDLIM1

U90878

0.5506

Below

25

1325_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59423

0.5482

Above

26

41549_s_at

adaptor-related protein complex 1 sigma 2 subunit

AP1S2

AF091077

0.5474

Below

27

39827_at

hypothetical protein

FLJ20500

AA522530

0.5471

Below

28

32724_at

phytanoyl-CoA hydroxylase Refsum disease

PHYH

AF023462

0.5459

Above

29

31786_at

Sam68-like phosphotyrosine protein T-STAR

T-STAR

AF051321

0.5403

Above

30

38570_at

major histocompatibility complex class II DO beta

HLA-DOB

X03066

0.5384

Above

31

39330_s_at

actinin alpha 1

ACTN1

M95178

0.5375

Below

32

36493_at

lymphocyte-specific protein 1

LSP1

M33552

0.5356

Below

33

574_s_at

caspase 1 apoptosis-related cysteine protease interleukin 1 beta convertase

CASP1

M87507

0.5336

Below

34

32224_at

KIAA0769 gene product

KIAA0769

AB018312

0.5326

Above

35

1077_at

recombination activating gene 1

RAG1

M29474

0.5302

Above

36

37280_at

MAD mothers against decapentaplegic Drosophila homolog 1

MADH1

U59912

0.5283

Above

37

41200_at

CD36 antigen collagen type I receptor thrombospondin receptor like 1

CD36L1

Z22555

0.5261

Above

38

36009_at

hypothetical protein

CL683

AF091092

0.5259

Below

39

36933_at

N-myc downstream regulated

NDRG1

D87953

0.5254

Below

40

1126_s_at

Human cell surface glycoprotein CD44 (CD44) gene, 3' end of long tailed isoform.

CD44

L05424

0.5232

Below

41

39824_at

ESTs

 

AI391564

0.5231

Above

42

38078_at

filamin B beta actin-binding protein-278

FLNB

AF042166

0.5208

Below

43

38127_at

syndecan 1

SDC1

Z48199

0.5199

Above

44

32941_at

interferon consensus sequence binding protein 1

ICSBP1

M91196

0.5195

Below

45

37276_at

IQ motif containing GTPase activating protein 2

IQGAP2

U51903

0.5191

Below

46

34768_at

DKFZP564E1962 protein

DKFZP564E1962

AL080080

0.5184

Below

47

39781_at

insulin-like growth factor-binding protein 4

IGFBP4

U20982

0.5173

Below

48

37918_at

integrin beta 2 antigen CD18 p95 lymphocyte function-associated antigen 1 macrophage antigen 1 mac-1 beta subunit

ITGB2

M15395

0.5162

Below

49

41490_at

phosphoribosyl pyrophosphate synthetase 2

PRPS2

Y00971

0.5155

Below

50

41814_at

fucosidase alpha-L- 1 tissue

FUCA1

M29877

0.5101

Above

 

Illustrated below are the results of a two-dimensional hierarchical clustering algorithm of the 327 diagnostic ALL cases using the top 50 probe sets for each of the 7 groups chosen by the Wilkins' metric. As some genes are chosen for more than one group, there are 304 unique probe sets represented in Figure 17.

Figure 17. Heirarchical cluster of 327 Diagnostic ALL samples using genes selected by Wilkins' metric

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