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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(A_ij - E_ij)²/E_ij, summing over intervals i = 1..m and classes j = 1..k. A_ij is the number of samples in the i^thinterval that are of the j^th class. E_ij is the expected frequency of A_ij and is calculated as E_ij = R_i * C_i/N, where R_i is the number of samples in the i^th interval, C_j is the number of samples in the j^th 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 Merit_s to a subset S containing k genes, defined as Merit_s = (k* r_cf)/sqrt(k + k * (k - 1) * r_ff), where r_cf is the average gene-class correlation and r_ff 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 r_xy = 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