Table 5.

Genomic classifiers (45 selected from 116) that distinguish IF patients with T-ALL

Rank order	Affymetrix identifier	Common name	GenBank accession	Gene description	Centroid score*
1†	211005_at	LAT	AF036906	Linker for activation of T cells‡	−0.6998
2†	215772_x_at	SUCLG2	AL050226	Succinate-CoA ligase, GDP-forming, beta§	−0.6042
3†	212459_x_at	SUCLG2	BF593940	Succinate-CoA ligase, GDP-forming, beta§	−0.5550
4†	205590_at	RASGRP1	NM_005739	RAS guanyl releasing protein 1§	−0.5363
5†	205831_at	CD2	NM_001767	CD2 antigen (p50)§	−0.5248
6	235824_at	—	BF238392	Homo sapiens transcribed sequences‡¶	0.5199
7†	209881_s_at	LAT	AF036905	Linker for activation of T cells‡	−0.4970
8	225386_s_at	LOC92906	AI559701	Hypothetical protein BC008217§	−0.4181
9†	221526_x_at	PARD3	AW452651	Par-3 partitioning defective 3 homolog§	−0.3911
10†	201518_at	CBX1	NM_006807	Chromobox homolog 1 (Drosophila)§	−0.3727
11	224428_s_at	CDCA7	AY029179	Cell division cycle associated 7§	−0.3614
12†	205449_at	HSU79266	NM_013299	Protein predicted by clone 23627§	−0.3532
13†	221521_s_at	Pfs2	BC003186	DNA replication complex GINS protein PSF2§	−0.3339
14†	203085_s_at	TGFB1	BC000125	Transforming growth factor, beta 1¶	0.3322
15†	215447_at	TFPI	AL080215	Homo sapiens mRNA; cDNA DKFZp586J0323 (from clone)¶	0.3006
16†	221558_s_at	LEF1	AF288571	Lymphoid enhancer-binding factor 1§	−0.2902
17	224553_s_at	TNFRSF18	AF117297	Tumor necrosis factor receptor, member 18¶	0.2890
18†	214835_s_at	SUCLG2	AF131748	Succinate-CoA ligase, GDP-forming, beta§	−0.2870
19†	211031_s_at	CYLN2	BC006259	Cytoplasmic linker 2¶	0.2776
20	1555758_a_at	CDKN3	AF213040	Cyclin-dependent kinase inhibitor 3 (CDK2)§	−0.2737
21†	209773_s_at	RRM2	BC001886	Ribonucleotide reductase M2 polypeptide§	−0.2559
22†	212372_at	MYH10	AK026977	Myosin, heavy polypeptide 10, nonmuscle§	−0.2492
23†	201719_s_at	EPB41L2	NM_001431	Erythrocyte membrane protein band 4.1-like 2§	−0.2465
24†	208749_x_at	FLOT1	AF085357	Flotillin 1§	−0.2428
25†	202705_at	CCNB2	NM_004701	Cyclin B2§	−0.2362
26	238732_at	COL24A1	AI631241	Collagen, type XXIV, alpha 1¶	0.2356
27†	209714_s_at	CDKN3	AF213033	Cyclin-dependent kinase inhibitor 3 (CDK2)§	−0.2201
28	1552623_at	HSH2	BC025237	Hematopoietic SH2 protein¶	0.2121
29†	218477_at	TMEM14A	NM_014051	Transmembrane protein 14A§	−0.2103
30†	206674_at	FLT3	NM_004119	fms-related tyrosine kinase 3¶	0.2045
31†	207016_s_at	ALDH1A2	AB015228	Aldehyde dehydrogenase 1 family, A2§	−0.2013
32	244033_at	C14orf145	AI937080	Chromosome 14 open reading frame 145§	−0.1972
33†	210115_at	RPL39L	L05096	Ribosomal protein L39-like§	−0.1940
Shared fold-dynamic classifiers between IF patients and drug-resistant cell lines
43	223380_s_at	LATS2	AF207547	LATS, large tumor suppressor, homolog 2‡¶	0.1590
46	210427_x_at	ANXA2	BC001388	Annexin A2‡	−0.1556
52	218847_at	IMP-2	NM_006548	IGF-II mRNA-binding protein 2‡¶	0.1437
65	207761_s_at	DKFZP586A0522	NM_014033	DKFZP586A0522 protein‡¶	0.0865
66	213060_s_at	CHI3L2	U58515	Chitinase 3–like 2‡	−0.0846
73	201590_x_at	ANXA2	NM_004039	Annexin A2‡	−0.0714
81	227013_at	LATS2	AI535735	LATS, large tumor suppressor, homolog 2 (Drosophila)‡¶	0.0634
88	226550_at	—	AI672159	Homo sapiens cDNA FLJ39602 fis, clone SKNSH2005061‡¶	0.0458
90	216203_at	SPTLC2	U15555	Serine palmitoyltransferase, long chain base subunit 2‡¶	0.0413
93	218618_s_at	FAD104	NM_022763	FAD104‡¶	0.0358
103	202954_at	UBE2C	NM_007019	Ubiquitin-conjugating enzyme E2C‡	−0.0207
109	230493_at	—	AW664964	Homo sapiens transcribed sequence ref:NP_060312.1; ∼FLJ20489‡	−0.0080

— indicates not applicable.

^*Rank order was determined by the absolute value (x) for each gene.

^†Top 25 rank-ordered genomic classifiers common to the U133 Plus 2.0 and U133Achips.

^‡Genes shared with drug-resistant cell lines having 1.5-fold up- or down-regulation (see Table S1 for complete list).

^§Genomic classifiers down-regulated (n = 79) in IF patients.

^¶Genomic classifiers up-regulated (n = 37) in IF patients.