APPLICATIONS / DATABASESSUPPLEMENTAL DATAFACULTYMIRROR SITESCOLLABORATIVE PROJECTSDEPARTMENTS

 


Section III
Genetic Subtype Discriminating Genes


The following tables contain a listing of the top 100 probe sets for each diagnostic subtypes ranked by their chi-square value (Tables S3-S8). Each table contains the Affymetrix U133 series probe set number, a gene description, gene symbol, chromosomal location, and primary GenBank reference. Chi-square values were calculated utilizing only the samples in the training set in a differential diagnosis decision tree format as discussed in the text and illustrated in Figure 2 (Tables S3-S8) or by a parallel approach (Tables S9-S14). The calculation of the fold change was done in a parallel format using the total data set and comparing the mean signal value in the class versus the mean signal value in the non-class. The last column indicates whether this gene had previously been identified as a class discriminator using the U95Av2 data (old) or identified as a class discriminator only using the U133 data (new) (Tables S3-S8).


Table S3.
Top 100 chi-square probe sets selected for BCR-ABL in decision tree format

 

U133
probe set

Gene description

Gene symbol

Location

GenBank Reference

Chi-square value

BCR-ABL above/below mean

Fold change

old or new

1

241812_at

EST FLJ39877

FLJ39877

2

AV648669

47.4

Above

5.2

new

2

201876_at

Paraoxonase 2

PON2

7q21.3

NM_000305.1

47.2

Above

18.7

old

3

201028_s_at

Antigen identified by monoclonal antibodies 12E7, F21 and O13

MIC2

Xp22.32

U82164.1

44.3

Above

2.6

old

4

200953_s_at

Cyclin D2

CCND2

12p13

NM_001759.1

42.3

Above

3.5

old

5

202947_s_at

glycophorin C (Gerbich blood group)

GYPC

2q14-q21

NM_002101.2

42.3

Above

3.1

old

6

223449_at

Semaphorin 6A

SEMA6A

5q23.1

AF225425.1

42.3

Above

4.3

new

7

201029_s_at

Antigen identified by monoclonal antibodies 12E7, F21 and O13

MIC2

Xp22.32

NM_002414.1

41.2

Above

2.4

old

8

204429_s_at

Solute carrier family 2 (facilitated glucose/fructose transporter), member 5

SLC2A5

1p36.2

BE560461

41.2

Above

5

old

9

210830_s_at

Paraoxonase 2

PON2

7q21.3

AF001602.1

41.2

Above

23.6

old

10

215028_at

Semaphorin 6A

SEMA6A

5

AB002438.1

41.2

Above

4.5

new

11

220024_s_at

Periaxin

PRX

19q13.13-q13.2

NM_020956.1

41.2

Above

8.2

new

12

201906_s_at

HYA22 protein

HYA22

3p21.3

NM_005808.1

41.1

Above

43.4

old

13

209365_s_at

Extracellular matrix protein 1

ECM1

1q21

U65932.1

41.1

Above

6

old

14

238689_at

GPR110 G protein-coupled receptor 110

GPR110

6

BG426455

41.1

Above

10.9

new

15

222154_s_at

DKFZP564A2416 unknown protein with a histone H5 signature.

DKFZP564A2416

2q33.1

AK002064.1

40.4

Above

12.4

new

16

218084_x_at

FXYD domain-containing ion transport regulator 5

FXYD5

19q12-q13.1

NM_014164.2

38

Above

1.5

new

17

212242_at

Tubulin, alpha 1 (testis specific)

TUBA1

2q36.2

AL565074

37

Above

3.2

old

18

201445_at

Calponin 3, acidic

CNN3

1p22-p21

NM_001839.1

36.3

Above

10.8

old

19

202771_at

KIAA0233 gene product

KIAA0233

16q24.3

NM_014745.1

36.3

Above

1.9

old

20

212298_at

Neuropilin 1

NRP1

10p12

BE620457

36.3

Above

13.8

new

21

212458_at

FLJ21897

FLJ21897

2

AW138902

36.3

Above

2.4

new

22

222488_s_at

Dynactin 4 (p62)

DCTN4

5q31-q32

BE218028

36.3

Above

3.6

new

23

222762_x_at

LIM domains containing 1

LIMD1

3p21.3

AU144259

36.3

Above

2.6

new

24

200951_s_at

Cyclin D2

CCND2

12p13

NM_001759.1

35.3

Above

12.7

old

25

204430_s_at

Solute carrier family 2 (facilitated glucose/fructose transporter), member 5

SLC2A5

1p36.2

NM_003039.1

35.3

Above

5.1

old

26

205467_at

Caspase 10, apoptosis related cysteine protease

CASP10

2q33-q34

NM_001230.1

35.3

Above

3.6

old

27

225660_at

Semaphorin 6A

SEMA6A

5q23.1

W92748

35.3

Above

3.3

new

28

225913_at

FLJ21140 (Ser/Thr protein kinase)

FLJ21140

15

AK025943.1

35.3

Above

2.9

new

29

236489_at

EST

 

6

AI282097

35.3

Above

16.7

new

30

240173_at

EST

 

4

AI732969

35.3

Above

10.3

new

31

240499_at

EST

 

10

AA482221

35.3

Above

1.3

new

32

201310_s_at

P311 protein. Similar to gastrin/cholecystokinin type B receptor.

P311

5q21.3

NM_004772.1

35.2

Below

2.2

new

33

215617_at

FLJ11754

FLJ11754

2

AU145711

35.2

Above

14.4

new

34

242579_at

EST

 

4

AA935461

35.2

Above

10.2

new

35

202717_s_at

CDC16 cell division cycle 16 homolog

CDC16

13q34

NM_003903.1

34.4

Above

1.1

new

36

205055_at

Integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1)

ITGAE

17p13

NM_002208.3

34.4

Below

2.1

new

37

217967_s_at

Chromosome 1 ORF 24

C1orf24

1q25

AF288391.1

34.4

Above

3.2

new

38

201656_at

Integrin, alpha 6

ITGA6

2q31.1

NM_000210.1

33.9

Above

2.8

new

39

207196_s_at

Nef-associated factor 1

NAF1

5q32-q33.1

NM_006058.1

32.2

Above

1.4

new

40

219315_s_at

hypothetical protein FLJ23058

FLJ20898

16p13.12

NM_024600.1

32.2

Above

5.3

new

41

202123_s_at

V-abl Abelson murine leukemia viral oncogene homolog 1

ABL1

9q34.1

NM_005157.2

31.4

Above

1.8

old

42

219938_s_at

proline-serine-threonine phosphatase interacting protein 2

PSTPIP2

18q12

NM_024430.1

31.2

Above

5

new

43

228046_at

EST;DKFZp434P0235

DKFZp4

34P0235

4

AA741243

31.2

Above

1.1

new

44

64064_at

Immune associated nucleotide 4 like 1

IAN4L1

7q36

AI435089

30.9

Above

3.3

new

45

222729_at

F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)

FBXW7

4q31.23

BE551877

30.5

Above

2.4

new

46

229975_at

EST

 

4

AI826437

30.5

Above

9.1

new

47

200864_s_at

RAB11A, member RAS oncogene family

RAB11A

15q21.3-q22.31

NM_004663.1

29.7

Above

1.4

old

48

203089_s_at

Protease, serine, 25

PRSS25

2p12

NM_013247.1

29.7

Above

1.7

new

49

205376_at

Inositol polyphosphate-4-phosphatase, type II

INPP4B

4q31.1

NM_003866.1

29.7

Above

12.4

new

50

209229_s_at

KIAA1115 protein

KIAA1115

19q13.42

BC002799.1

29.7

Above

1.3

new

51

219871_at

Hypothetical protein FLJ13197

FLJ13197

4p14

NM_024614.1

29.7

Above

14.5

new

52

222868_s_at

Interleukin 18 binding protein

IL18BP

11q13

AI521549

29.7

Above

7.1

new

53

235988_at

GPR110 G protein-coupled receptor 110

GPR110

6p12.3

AA746038

29.7

Above

15.8

new

54

239273_s_at

Matrix metalloproteinase 28

MMP28

17q11-q21.1

AI927208

29.7

Above

90.5

new

55

206150_at

Tumor necrosis factor receptor superfamily, member 7

TNFRSF7

12p13

NM_001242.1

29.5

Above

3.2

old

56

212203_x_at

Interferon induced transmembrane protein 3 (I-8U)

IFITM3

8q13.1

BF338947

29.5

Above

2.3

old

57

217110_s_at

Mucin 4

MUC4

3q29

AJ242547.1

29.5

Above

47.5

new

58

223075_s_at

hypothetical protein FLJ12783

FLJ12783

9q34.13-q34.3

AL136566.1

29.5

Above

3.9

new

59

229139_at

EST

 

8

AI202201

29.5

Above

10.8

new

60

229367_s_at

Hypothetical proteins FLJ22690.

FLJ22690

7

AW130536

29.5

Above

3.6

new

61

213093_at

FLJ30869

FLJ30869

Xq28

AI471375

29.1

Above

2.5

new

62

216033_s_at

FYN oncogene related to SRC

FYN

6

S74774.1

29.1

Above

2.7

new

63

202369_s_at

TRAM-like protein

KIAA0057

6p21.1-p12

NM_012288.1

28.7

Above

3.3

new

64

212592_at

immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides

IGJ

4q21

AV733266

28.7

Above

7.9

old

65

219218_at

hypothetical protein FLJ23058

FLJ23058

17q25.3

NM_024696.1

28.7

Below

6.2

new

66

242051_at

EST

 

Y

AI695695

28.7

Above

2.2

new

67

200655_s_at

Calmodulin 1 (phosphorylase kinase, delta)

CALM1

14q24-q31

NM_006888.1

28.5

Above

1.3

new

68

202794_at

Inositol polyphosphate-1-phosphatase

INPP1

2q32

NM_002194.2

28.4

Above

1.6

new

69

218348_s_at

HSPC055 protein

HSPC055

16p13.3

NM_014153.1

27.7

Below

1.1

new

70

205269_at

Lymphocyte cytosolic protein 2

LCP2

5q33.1-qter

AI123251

26.9

Above

1.6

new

71

238488_at

Ran binding protein 11

LOC51194

5q12.2

BF511602

26.9

Above

2.7

new

72

202242_at

Transmembrane 4 superfamily member 2

TM4SF2

Xq11.4

NM_004615.1

26.6

Above

1.7

new

73

218764_at

Hypothetical protein MGC5363

MGC5363

14q22.1-q22.3

NM_024064.1

26.6

Above

1.7

new

74