APPLICATIONS / DATABASESSUPPLEMENTAL DATAFACULTYMIRROR SITESCOLLABORATIVE PROJECTSDEPARTMENTS

 
 



Section III: Detailed Analysis (cont.)


SOM/DAV
The 10,991 probe sets that passed the variation filter were used for subsequent selection of discriminating genes using the self-organizing map (SOM) and discriminant analysis with variance (DAV) programs in the GeneMaths software package (version 1.5, Applied Maths, Belgium). The subgroups for which genes were selected included T-lineage ALL, TEL-AML1, E2A-PBX1, MLL rearrangement, BCR-ABL, hyperdiploid ALL (chromosomal number > 50) and the novel subgroup described in the text of the paper. The target number of total genes chosen by each algorithm was 500.
The SOM analysis was performed using 30 X 18 node format to enable an optimal number of genes per node (~20 genes per node). Nodes that contained genes whose expression varied more than 2-fold from the mean in more than 70% of the samples in a particular subgroup were chosen. A total of 451 genes were chosen using the SOM algorithm and 443 genes using the DAV algorithm. The combined gene sets contained 755 unique genes, of which 185 were present in both subsets. 2-D hierarchical clustering of the genes and samples were performed using Pearson's correlation coefficient as the metric and unweighted pair group method using arithmetic averages (UPGMA). Approximately 10% of the genes that were found to have correlation coefficients less than 0.7 in each branch of the dendrogram were removed and the process was repeated reiteratively until the correlation coefficient for all genes within a branch was > 0.7, or until the removal of additional gene resulted in a deterioration of the class distinction as indicated by inappropriate clustering of cases. Through this approach a subset of 215 genes were selected that optimally separated the 7 subgroups. These genes are listed in Table 15. The selection of genes by this approach does not provide for a ranking. For class prediction between 20 and 30 genes were used for each genetic subgroup, unless otherwise stated. The two-dimensional Hierarchical analysis of the cases using these selected genes are illustrated in Figure 18.

Table 15. Genes selected by DAV-SOM


 

     
 

Affymetrix number

Gene Name

GeneSymbol

Reference number

Above/Below Mean

BCR-ABL

       

1

39250_at

nephroblastoma overexpressed gene

NOV

X96584

Above

2

37600_at

extracellular matrix protein 1

ECM1

U68186

Above

3

38312_at

DKFZp564O222 from clone DKFZp564O222

 

AL050002

Above

4

38342_at

KIAA0239 protein

KIAA0239

D87076

Above

5

39712_at

S100 calcium-binding protein A13

S100A13

AI541308

Above

6

39730_at

v-abl Abelson murine leukemia viral oncogene homolog 1

ABL1

X16416

Above

7

39781_at

Insulin-like growth factor-binding protein
4

IGFBP4

U20982

Above

8

40051_at

TRAM-like protein

KIAA0057

D31762

Above

9

40504_at

paraoxonase 2

PON2

AF001601

Above

10

33362_at

Cdc42 effector protein 3

CEP3

AF094521

Above

11

33404_at

adenylyl cyclase-associated protein 2

CAP2

U02390

Above

12

34362_at

solute carrier family 2 facilitated glucose transporter member 5

SLC2A5

M55531

Above

13

36591_at

Tubulin alpha 1 testis specific

TUBA1

X06956

Above

14

38077_at

collagen type VI alpha 3

COL6A3

X52022

Above

15

40196_at

HYA22 protein

HYA22

D88153

Above

16

1911_s_at

Growth arrest and DNA-damage-inducible alpha

GADD45A

M60974

Above

17

1702_at

interleukin 2 receptor alpha

IL2RA

X01057

Above

18

1635_at

Human proto-oncogene tyrosine-protein kinase (ABL) gene, exon 1a and exons 2-10, complete cds.

ABL

U07563

Above

19

1636_g_at

Human proto-oncogene tyrosine-protein kinase (ABL) gene, exon 1a and exons 2-10, complete cds.

ABL

U07563

Above

20

1326_at

Caspase 10 apoptosis-related cysteine protease

CASP10

U60519

Above

21

330_s_at

Tubulin, alpha 1, isoform 44

TUBA1

HG2259-HT2348

Above

           

E2A-PBX1

       

1

33513_at

signaling lymphocytic activation molecule

SLAM

U33017

Above

2

37479_at

CD72 antigen

CD72

M54992

Above

3

37485_at

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

FACVL1

D88308

Above

4

39614_at

KIAA0802 protein

KIAA0802

AB018345

Above

5

39929_at

KIAA0922 protein

KIAA0922

AB023139

Above

6

40648_at

c-mer proto-oncogene tyrosine kinase

MERTK

U08023

Above

7

41017_at

Myosin-binding protein H

MYBPH

U27266

Above

8

41425_at

Friend leukemia virus integration 1

FLI1

M98833

Above

9

41862_at

KIAA0056 protein

KIAA0056

D29954

Above

10

32063_at

pre-B-cell leukemia transcription factor 1

PBX1

M86546

Above

11

37225_at

KIAA0172 protein

KIAA0172

D79994

Above

12

38285_at

mu-crystallin gene

 

AF039397

Above

13

38286_at

KIAA1071 protein

KIAA1071

AB028994

Above

14

38340_at

huntingtin interacting protein-1-related

KIAA0655

AB014555

Above

15

39379_at

cDNA DKFZp586C1019 from clone DKFZp586C1019

 

AL049397

Above

16

39402_at

interleukin 1 beta

IL1B

M15330

Above

17

40454_at

FAT tumor suppressor Drosophila
homolog

FAT

X87241

Above

18

41139_at

melanoma antigen family D 1

MAGED1

W26633

Above

19

41146_at

ADP-ribosyltransferase NAD poly ADP-ribose polymerase

ADPRT

J03473

Above

20

33355_at

Homo sapiens cDNA FLJ12900 fis clone NT2RP2004321

 

AL049381

Above

21

34783_s_at

BUB3 budding uninhibited by benzimidazoles 3 yeast homolog

BUB3

AF047473

Above

22

36179_at

mitogen-activated protein kinase-activated protein kinase 2

MAPKAPK2

U12779

Above

23

36589_at

aldo-keto reductase family 1 member B1 aldose reductase

AKR1B1

X15414

Above

24

38393_at

KIAA0247 gene product

KIAA0247

D87434

Above

25

38438_at

Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 p105

NFKB1

M58603

Above

26

1786_at

c-mer proto-oncogene tyrosine kinase

MERTK

U08023

Above

27

1520_s_at

interleukin 1 beta

IL1B

X04500

Above

28

1287_at

ADP-ribosyltransferase NAD poly ADP-ribose polymerase

ADPRT

J03473

Above

29

854_at

B lymphoid tyrosine kinase

BLK

S76617

Above

30

753_at

Nidogen 2

NID2

D86425

Above

31

430_at

nucleoside phosphorylase

NP

X00737

Above

32

362_at

Protein kinase C zeta

PRKCZ

Z15108

Above

     

 

   

Hyperdiploid >50

 

   

1

36795_at

prosaposin variant Gaucher disease and variant metachromatic leukodystrophy

PSAP

J03077

Above

2

38242_at

B cell linker protein

SLP65

AF068180

Above

3

38518_at

sex comb on midleg Drosophila like 2

SCML2

Y18004

Above

4

39628_at

RAB9 member RAS oncogene family

RAB9

U44103

Above

5

31863_at

KIAA0179 protein

KIAA0179

D80001

Above

6

33228_g_at

interleukin 10 receptor beta

IL10RB

AI984234

Above

7

33753_at

KIAA0666 protein

KIAA0666

AB014566

Above

8

37543_at

Rac/Cdc42 guanine exchange factor
GEF 6

ARHGEF6

D25304

Above

9

38968_at

SH3-domain binding protein 5 BTK-associated

SH3BP5

AB005047

Above

10

39039_s_at

CGI-76 protein

LOC51632

AI557497

Above

11

39329_at

Actinin alpha 1

ACTN1

X15804

Above

12

39389_at

CD9 antigen p24

CD9

M38690

Above

13

32207_at

membrane protein palmitoylated 1 55kD

MPP1

M64925

Above

14

32236_at

ubiquitin-conjugating enzyme E2G 2 homologous to yeast UBC7

UBE2G2

AF032456

Above

15

32251_at

hypothetical protein FLJ21174

FLJ21174

AA149307

Above

16

35764_at

chromosome X open reading frame 5

OFD1

Y15164

Above

17

36620_at

superoxide dismutase 1 soluble amyotrophic lateral sclerosis 1 adult

SOD1

X02317

Above

18

36937_s_at

PDZ and LIM domain 1 elfin

PDLIM1

U90878

Above

19

37326_at

proteolipid protein 2 colonic epithelium-enriched

PLP2

U93305

Above

20

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

21

38738_at

SMT3 suppressor of mif two 3 yeast homolog 1

SMT3H1

X99584

Above

22

39168_at

Ac-like transposable element

ALTE

AB018328

Above

23

40903_at

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

APT6M8-9

AL049929

Above

24

32572_at

ubiquitin specific protease 9 X chromosome Drosophila fat facets
related

USP9X

X98296

Above

25

1065_at

fms-related tyrosine kinase 3

FLT3

U02687

Above

26

306_s_at

high-mobility group nonhistone chromosomal protein 14

HMG14

J02621

Above

           

MLL

 

 

   

1

31492_at

Muscle specific gene

M9

AB019392

Above

2

36777_at

DNA segment on chromosome 12 unique 2489 expressed sequence

D12S2489E

AJ001687

Above

3

39301_at

Calpain 3 p94

CAPN3

X85030

Below

4

41448_at

Homeo box A4

HOXA4

AC004080

Above

5

39424_at

tumor necrosis factor receptor superfamily member 14 herpesvirus
entry mediator

TNFRSF14

U70321

Below

6

40076_at

Tumor protein D52-like 2

TPD52L2

AF004430

Above

7

40493_at

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

CD44

L05424

Above

8

40506_s_at

Homo sapiens polyadenylate binding protein mRNA, complete cds.

 

U75686

Above

9

40514_at

hypothetical 43.2 Kd protein

LOC51614

AF091085

Above

10

40763_at

Meis1 mouse homolog

MEIS1

U85707

Above

11

40797_at

a disintegrin and metalloproteinase domain 10

ADAM10

AF009615

Above

12

40798_s_at

a disintegrin and metalloproteinase domain 10

ADAM10

Z48579

Above

13

41747_s_at

myocyte-specific enhancer factor 2A (MEF2A) gene

MEF2A

U49020

Above

14

32193_at

Plexin C1

PLXNC1

AF030339

Above

15

32215_i_at

KIAA0878 protein

KIAA0878

AB020685

Above

16

33412_at

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

LGALS1

AI535946

Above

17

34306_at

muscleblind Drosophila like

MBNL

AB007888

Above

18

34785_at

KIAA1025 protein

KIAA1025

AB028948

Above

19

35298_at

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

EIF3S7

U54558

Above

20

36690_at

Nuclear receptor subfamily 3 group C member 1

NR3C1

M10901

Above

21

37675_at

solute carrier family 25 mitochondrial carrier phosphate carrier member 3

SLC25A3

X60036

Above

22

38391_at

capping protein actin filament
gelsolin-like

CAPG

M94345

Above

23

38413_at

defender against cell death 1

DAD1

D15057

Above

24

39110_at

eukaryotic translation initiation factor 4B

EIF4B

X55733

Above

25

39867_at

Tu translation elongation factor mitochondrial

TUFM

S75463

Above

26

2062_at

Insulin-like growth factor binding
protein 7

IGFBP7

L19182

Above

27

2036_s_at

CD44 antigen homing function and
Indian blood group system

CD44

M59040

Above

28

1914_at

Cyclin A1

CCNA1

U66838

Above

29

1327_s_at

mitogen-activated protein kinase kinase kinase 5

MAP3K5

U67156

Above

30

1126_s_at

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

CD44

L05424

Above

31

1102_s_at

Nuclear receptor subfamily 3 group C member 1

NR3C1

M10901

Above

32

873_at

homeo box A5

HOXA5

M26679

Above

33

706_at

Glucocorticoid receptor, beta

 

HG4582-HT4987

Above

34

657_at

protocadherin gamma subfamily C 3

PCDHGC3

L11373

Above

           

Novel

       

1

33137_at

latent transforming growth factor beta binding protein 4

LTBP4

Y13622

Above

2

38081_at

leukotriene A4 hydrolase

LTA4H

J03459

Above

3

38661_at

seb4D

HSRNASEB

X75314

Above

4

39878_at

protocadherin 9

PCDH9

AI524125

Above

5

35260_at

KIAA0867 protein

MONDOA

AB020674

Above

6

1373_at

transcription factor 3 E2A immunoglobulin enhancer binding factors E12/E47

TCF3

M31523

Above

7

35177_at

KIAA0725 protein

KIAA0725

AB018268

Above

8

38618_at

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

LIMK2

AC002073

Above

9

34947_at

phorbolin-like protein MDS019

MDS019

AA442560

Above

10

40692_at

transducin-like enhancer of split 4 homolog of Drosophila E sp1

TLE4

M99439

Above

11

38364_at

BCE-1 protein

BCE-1

AF068197

Above

12

37960_at

carbohydrate chondroitin 6/keratan sulfotransferase 2

CHST2

AB014679

Above

13

994_at

Protein tyrosine phosphatase receptor type M

PTPRM

X58288

Above

14

31892_at

Protein tyrosine phosphatase receptor type M

PTPRM

X58288

Above

15

995_g_at

Protein tyrosine phosphatase receptor type M

PTPRM

X58288

Above

16

41073_at

G protein-coupled receptor 49

GPR49

AI743745

Above

17

41708_at

KIAA1034 protein

KIAA1034

AB028957

Above

18

34376_at

protein kinase cAMP-dependent catalytic inhibitor gamma

PKIG

AB019517</