Table 5

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

Rank orderAffymetrix identifierCommon nameGenBank accessionGene descriptionCentroid 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 
Rank orderAffymetrix identifierCommon nameGenBank accessionGene descriptionCentroid 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.

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