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 μ_i is the mean expression of that gene in the i^th class, σ_i² is the variance of that gene in the i^th class and n_i is the size of the i^th 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	409