Supplementary Information

Treatment Specific Changes in Gene Expression Discriminate in vivo Drug Response
in Human Leukemia Cells

C. Selection of Discriminating Genes

Figure 3: Discriminating genes by different gene selection methods.

The overlap among the 500 top-ranked probe sets identified by linear discriminant analysis (LDA), the 500 top-ranked probe sets identified by ANOVA and the 4x100 top-ranked probe sets (359 and 352 unique probe sets) identified by distinction calculation (one-versus-all) are shown as percentage overlap. The circle indicates the overlap among all three methods. (a) Probe sets for post-treatment expression and (b) probe sets for fold-change in expression.

Table 2: Discriminating genes by fold-change and post-treatment expression.

Shown in the following table are the 27 probe sets (26 genes, 18%) that were present in both sets of genes discriminating among the four treatments (the 150 probe sets based on fold-change and the 150 probe sets based on post-treatment expression), as determined by LDA

probe set ID	accession number	gene name
34967_at	AF001549	RNA polymerase I transcription factor RRN3
34577_at	U10694	melanoma antigen, family A, 9
41415_at	L36720	bystin-like
37781_at	AB023138	neurexin 2
1916_s_at	V01512	c-fos
39286_at	D64109	transducer of ERBB2, 2
37662_at	AI701164	ubiquitin-conjugating enzyme E2G 1
38082_at	AB014550	KIAA0650 protein
31872_at	X79201	synovial sarcoma translocation, chromosome 18
37244_at	AA746355	ubiquitin carboxyl-terminal esterase L3
2065_s_at	L22473	BCL2-associated X protein
38386_r_at	U34683	glutathione synthetase
2000_at	U26455	ataxia telangiectasia mutated
38615_at	AF097021	differentially expressed in hematopoietic lineages
37105_at	M16117	cathepsin G
36710_at	Z38026	cathelicidin antimicrobial peptide
37096_at	M34379	elastase 2, neutrophil
33963_at	M96326	azurocidin 1 (cationic antimicrobial protein 37)
38879_at	D83664	S100 calcium binding protein A12 (calgranulin C)
41471_at	W72424	S100 calcium binding protein A9 (calgranulin B)
41096_at	AI126134	S100 calcium binding protein A8 (calgranulin A)
32821_at	AI762213	lipocalin 2 (oncogene 24p3)
31506_s_at	L12691	defensin, alpha 3, neutrophil-specific
31793_at	AL036554	defensin, alpha 3, neutrophil-specific
37864_s_at	Y14737	immunoglobulin heavy constant gamma 3
37391_at	X12451	cathepsin L
2081_s_at	L07032	protein kinase C, theta

Fig. 4: Hierarchical clustering of changes in expression for selected genes.

Hierarchical clustering of fold-change in gene expression after treatment, using the 150 most discriminating probe sets (124 genes and 23 ESTs; P=0.017) selected by LDA. Each column represents a patient (n=60) labeled according to the treatment given (color legend at the bottom) and each row represents a gene probe set. Hierarchical clustering (top dendrogram) correctly grouped each patient into the four treatments, with one exception. Red indicates up-regulation and green indicates down-regulation in gene expression (fold-change) after treatment, according to the fold-change scale in the upper right. Solid lines enclose groups of genes showing greatest difference for the treatment indicated. These are the same data as shown in Fig. 4 of the primary manuscript, but with gene names provided. Hierarchical clustering performed after removing either one of two replicate probe sets for three genes did not cause a difference in clustering (data not shown).

Table 3: Discriminating genes by one-versus-all distinction calculation.

To distinguish one treatment from all other treatments, we also computed distinction values for each probe set. The 353 gene probe sets are rank-ordered according to the distinction value (DC) for each treatment [HDMTX (HD), HDMTX+MP (HDMP), LDMTX+MP (LDMP), MP], (-) indicates genes down-regulated and (+) genes up-regulated. Additionally, we performed one thousand permutations with random class labels to obtain the P values for each probe set. The P value was defined as the probability of obtaining by random assignment distinction values less than or equal to the observed. Among a large number of probe sets with P values <0.01, 50 probe sets with the largest distinction values were selected, listed here are the top 50 probe sets for each treatment.

probe set ID	accession number	gene name	>HD DC	HDMP DC	LDMP DC	MP DC	HD P val.	HDMP P val.	LDMP P val.	MP P val.	rank
41471_at	W72424	S100 calcium binding protein A9 (calgranulin B)	0.9	-0.3	-0.5	-0.4	0.000	0.139	0.001	0.017	HD+01
35926_s_at	AF004230	leukocyte immunoglobulin-like receptor, subfamily B	0.8	-0.4	-0.4	-0.3	0.000	0.017	0.011	0.088	HD+02
31793_at	AL036554	defensin, alpha 3, neutrophil-specific	0.8	-0.3	-0.4	-0.3	0.000	0.060	0.008	0.122	HD+03
41096_at	AI126134	S100 calcium binding protein A8 (calgranulin A)	0.7	-0.4	-0.4	-0.3	0.000	0.057	0.010	0.077	HD+04
34703_f_at	AA151971	clone=IMAGE-588365	0.6	-0.1	-0.4	-0.4	0.000	0.660	0.014	0.029	HD+05
41126_at	AA978353	phosphoserine aminotransferase	0.6	-0.2	-0.3	-0.3	0.000	0.218	0.057	0.133	HD+06
37105_at	M16117	cathepsin G	0.6	-0.2	-0.4	-0.2	0.000	0.206	0.006	0.229	HD+07
38087_s_at	W72186	S100 calcium binding protein A4	0.6	-0.5	0.0	-0.3	0.000	0.008	0.712	0.059	HD+08
39119_s_at	AA631972	natural killer cell transcript 4	0.6	-0.1	-0.4	-0.2	0.000	0.737	0.012	0.133	HD+09
32793_at	X00437	T cell receptor beta locus	0.6	0.0	-0.4	-0.4	0.000	0.964	0.012	0.035	HD+10
33963_at	M96326	azurocidin 1 (cationic antimicrobial protein 37)	0.6	-0.3	-0.4	-0.2	0.001	0.095	0.008	0.430	HD+11
34702_f_at	M27826	endogenous retroviral protease	0.6	-0.1	-0.4	-0.2	0.000	0.404	0.010	0.266	HD+12
38363_at	W60864	TYRO protein tyrosine kinase binding protein	0.5	-0.2	-0.2	-0.3	0.000	0.172	0.140	0.108	HD+13
2000_at	U26455	ataxia telangiectasia mutated	0.5	-0.3	-0.4	0.0	0.000	0.071	0.038	0.570	HD+14
38615_at	AF097021	differentially expressed in hematopoietic lineages	0.5	-0.2	-0.4	0.0	0.000	0.281	0.010	0.712	HD+15
32749_s_at	AL050396	filamin A, alpha (actin binding protein 280)	0.5	-0.3	-0.2	-0.2	0.000	0.125	0.260	0.225	HD+16
2065_s_at	L22473	BCL2-associated X protein	0.5	-0.5	-0.1	-0.1	0.000	0.007	0.688	0.436	HD+17
32847_at	U48959	myosin, light polypeptide kinase	0.5	0.0	-0.3	-0.2	0.000	0.926	0.028	0.402	HD+18
39829_at	AB016811	ADP-ribosylation factor-like 7	0.5	0.1	-0.4	-0.3	0.002	0.457	0.035	0.049	HD+19
757_at	D28364	annexin II, 5 UTR	0.5	-0.2	-0.2	-0.4	0.000	0.313	0.367	0.007	HD+20
40362_at	X61498	nuclear factor of light polypeptide gene enhancer	0.5	-0.3	-0.2	-0.2	0.000	0.096	0.476	0.125	HD+21
33501_r_at	S71043	Ig alpha 2=immunoglobulin A heavy chain allotype 2	0.5	-0.1	-0.3	-0.2	0.000	0.512	0.022	0.211	HD+22
33284_at	M19507	myeloperoxidase	0.5	-0.3	-0.4	0.0	0.001	0.069	0.006	0.697	HD+23
34546_at	AI250799	defensin, alpha 4, corticostatin	0.5	-0.1	-0.3	-0.2	0.000	0.406	0.052	0.205	HD+24
40155_at	D31883	actin binding LIM protein 1	0.5	0.0	-0.3	-0.3	0.000	0.895	0.027	0.087	HD+25
38805_at	X89750	TGFB-induced factor (TALE family homeobox)	-0.8	0.2	0.3	0.3	0.000	0.395	0.003	0.402	HD-01
39286_at	D64109	transducer of ERBB2, 2	-0.6	0.2	0.2	0.5	0.000	0.218	0.154	0.021	HD-02
36628_at	L42542	ralA binding protein 1	-0.6	0.2	0.2	0.4	0.001	0.312	0.166	0.031	HD-03
34402_at	AB024327	unr-interacting protein	-0.6	0.2	0.2	0.3	0.000	0.213	0.044	0.247	HD-04
33893_r_at	AB007939	KIAA0470 gene product	-0.6	-0.1	0.4	0.3	0.000	0.569	0.004	0.117	HD-05
39024_at	AF042357	nucleoporin 98kD	-0.5	0.1	0.3	0.3	0.001	0.713	0.095	0.063	HD-06
41549_s_at	AF091077	adaptor-related protein complex 1, sigma 2 subunit	-0.5	0.6	0.2	-0.1	0.000	0.000	0.356	0.498	HD-07
41360_at	AA044787	CCR4-NOT transcription complex, subunit 8	-0.5	0.1	0.1	0.4	0.000	0.584	0.290	0.035	HD-08
37781_at	AB023138	neurexin 2	-0.5	0.6	0.1	0.2	0.000	0.002	0.528	0.243	HD-09
37642_at	D63877	KIAA0157 protein	-0.5	-0.1	0.3	0.4	0.000	0.514	0.034	0.017	HD-10
41598_at	AA890010	clone=IMAGE-1403679	-0.5	0.3	0.3	0.1	0.001	0.109	0.013	0.894	HD-11
38270_at	AF005043	poly (ADP-ribose) glycohydrolase	-0.5	0.2	0.3	0.2	0.001	0.364	0.014	0.719	HD-12
41597_s_at	AF047442	SEC22 vesicle trafficking protein-like 1	-0.5	0.3	0.3	0.2	0.000	0.180	0.079	0.427	HD-13
34751_at	AI970189	KIAA0997 protein	-0.5	0.5	0.2	0.0	0.002	0.008	0.100	0.747	HD-14
37902_at	L13278	crystallin, zeta (quinone reductase)	-0.5	0.1	0.4	0.1	0.000	0.474	0.015	0.785	HD-15
36585_at	M36341	ADP-ribosylation factor 4	-0.5	0.0	0.3	0.2	0.000	0.784	0.051	0.151	HD-16
38973_at	AB028943	HIC1-related gene on chromosome 22	-0.5	0.2	0.1	0.3	0.000	0.277	0.129	0.173	HD-17
38093_at	U90909	clone 23722 mRNA	-0.5	0.1	0.4	0.1	0.000	0.712	0.027	0.249	HD-18
31510_s_at	Z48950	H3 histone, family 3B (H3.3B)	-0.5	0.2	0.2	0.3	0.000	0.149	0.131	0.148	HD-19
40976_at	AF052432	katanin p80 (WD40-containing) subunit B 1	-0.5	0.1	0.1	0.3	0.000	0.595	0.247	0.076	HD-20
37984_s_at	M57763	ADP-ribosylation factor 6	-0.5	0.2	0.2	0.3	0.000	0.200	0.186	0.137	HD-21
39436_at	AF079221	BCL2/adenovirus E1B 19kD interacting protein	-0.5	0.5	0.1	0.2	0.000	0.012	0.753	0.148	HD-22
1512_at	D86550	tyrosine-(Y)-phosphorylation regulated kinase	-0.5	0.0	0.4	0.1	0.001	0.965	0.002	0.654	HD-23
38994_at	AF037989	STAT induced STAT inhibitor-2	-0.5	0.3	0.3	0.0	0.000	0.098	0.093	0.732	HD-24
41790_at	AL031230	glycosylphosphatidylinositol specific phospholipase	-0.5	0.2	0.3	0.0	0.001	0.213	0.005	0.829	HD-25
322_at	D88532	phosphoinositide-3-kinase, regulatory subunit	-0.3	0.8	-0.1	0.0	0.050	0.000	0.359	0.897	HDMP+01
39951_at	L20826	plastin 1 (I isoform)	-0.2	0.8	0.0	-0.2	0.112	0.000	0.878	0.173	HDMP+02
32257_f_at	AF003001	telomeric repeat binding factor (NIMA-interacting) 1	-0.2	0.7	0.0	-0.1	0.188	0.000	0.652	0.522	HDMP+03
782_at	U93867	polymerase (RNA) III (DNA directed) (62kD)	-0.1	0.7	-0.1	-0.4	0.492	0.000	0.436	0.060	HDMP+04
491_at	U46116	protein tyrosine phosphatase, receptor type, G	0.0	0.6	-0.2	-0.4	0.914	0.001	0.181	0.080	HDMP+05
37563_at	AB007871	KIAA0411 gene product	-0.1	0.6	-0.1	-0.2	0.641	0.001	0.757	0.086	HDMP+06
40478_at	AL021396	hypothetical protein	-0.1	0.6	-0.1	-0.2	0.462	0.000	0.311	0.380	HDMP+07
39489_g_at	W27720	protocadherin 9	-0.2	0.6	-0.1	0.0	0.082	0.001	0.588	0.825	HDMP+08
39008_at	M13699	ceruloplasmin (ferroxidase)	-0.1	0.6	-0.3	0.1	0.586	0.001	0.028	0.603	HDMP+09
36729_g_at	M76446	adrenergic, alpha-1D-, receptor	-0.1	0.6	-0.1	-0.2	0.614	0.002	0.607	0.182	HDMP+10
40383_at	AB023200	gene from NF2/meningioma region of 22q12	0.0	0.6	-0.2	-0.2	0.895	0.002	0.083	0.404	HDMP+11
1368_at	M27492	interleukin 1 receptor, type I	-0.1	0.6	-0.1	-0.2	0.529	0.001	0.298	0.449	HDMP+12
33353_at	W26466	32f11 Homo sapiens cDNA	0.1	0.6	-0.4	-0.1	0.330	0.002	0.005	0.573	HDMP+13
35002_g_at	Z85986	serine/threonine kinase 38	-0.4	0.6	-0.1	0.3	0.002	0.002	0.652	0.194	HDMP+14
34102_at	M90424	lipocalin 1	-0.1	0.6	-0.3	0.1	0.336	0.001	0.036	0.531	HDMP+15
36435_at	AF070670	protein phosphatase 1A	-0.1	0.6	-0.2	0.0	0.370	0.006	0.286	0.806	HDMP+16
39943_at	U27459	origin recognition complex, subunit 2-like	-0.3	0.6	-0.2	0.2	0.013	0.001	0.202	0.267	HDMP+17
39544_at	AB002351	desmuslin	-0.3	0.6	-0.1	0.2	0.030	0.001	0.255	0.089	HDMP+18
33432_at	AI547308	similar to hypothetical protein MNCb-2386	-0.1	0.6	-0.3	0.0	0.511	0.006	0.028	0.856	HDMP+19
37583_at	U52191	Smcy homolog, Y chromosome (mouse)	-0.2	0.5	0.1	-0.3	0.172	0.001	0.377	0.050	HDMP+20
33427_s_at	AF106861	attractin	-0.1	0.5	-0.1	-0.1	0.276	0.002	0.610	0.600	HDMP+21
32443_at	U28687	zinc finger protein 157 (HZF22)	-0.3	0.5	-0.1	0.0	0.062	0.007	0.493	0.981	HDMP+22
31896_at	AL050281	neuroblastoma-amplified protein	-0.2	0.5	-0.1	0.0	0.146	0.007	0.366	0.984	HDMP+23
34594_at	D13644	related to the N terminus of tre	-0.4	0.5	0.2	-0.1	0.005	0.002	0.643	0.872	HDMP+24
35308_at	D83200	hypothetical protein MGC2668	-0.4	0.5	-0.1	0.1	0.009	0.003	0.341	0.327	HDMP+25
41667_s_at	AJ006068	dTDP-D-glucose 4,6-dehydratase	-0.1	-0.7	0.2	0.3	0.313	0.000	0.063	0.137	HDMP-01
37662_at	AI701164	ubiquitin-conjugating enzyme E2G 1	-0.1	-0.6	0.3	0.2	0.281	0.000	0.058	0.135	HDMP-02
38713_at	Z99716	septin 3	0.5	-0.6	0.0	-0.1	0.000	0.002	0.714	0.786	HDMP-03
32117_at	U51698	apoptosis antagonizing transcription factor	0.0	-0.6	0.3	0.1	0.823	0.004	0.070	0.378	HDMP-04
36514_at	U66469	cell growth regulatory with ring finger domain	0.3	-0.6	-0.1	0.1	0.026	0.002	0.572	0.614	HDMP-05
38313_at	AB028985	ATP-binding cassette, sub-family A (ABC1)	0.2	-0.6	0.3	-0.2	0.121	0.003	0.084	0.272	HDMP-06
39307_s_at	X81637	clathrin light chain b gene	0.0	-0.6	0.3	0.1	0.781	0.002	0.029	0.906	HDMP-07
41826_at	W28287	KIAA1467 protein	0.1	-0.6	0.2	0.1	0.592	0.001	0.345	0.360	HDMP-08
37130_g_at	AI936758	neuropeptide FF-amide peptide precursor	0.2	-0.5	0.3	-0.1	0.208	0.006	0.247	0.901	HDMP-09
38082_at	AB014550	KIAA0650 protein	-0.1	-0.5	0.2	0.4	0.377	0.000	0.161	0.010	HDMP-10
34960_g_at	M15059	Fc fragment of IgE, low affinity II	0.1	-0.5	0.1	0.1	0.299	0.002	0.500	0.458	HDMP-11
37121_at	S69115	natural killer cell group 7 sequence	0.3	-0.5	0.1	-0.2	0.018	0.005	0.571	0.389	HDMP-12
37244_at	AA746355	ubiquitin carboxyl-terminal esterase L3	0.2	-0.5	-0.2	0.4	0.112	0.004	0.502	0.056	HDMP-13
1814_at	D50683	transforming growth factor, beta receptor II	-0.1	-0.5	0.1	0.4	0.351	0.003	0.211	0.160	HDMP-14
579_at	M95724	centromere protein C 1	0.3	-0.5	-0.1	0.1	0.035	0.007	0.671	0.670	HDMP-15
35969_at	N23137	M-phase phosphoprotein 9	0.0	-0.5	0.2	0.2	0.954	0.002	0.226	0.213	HDMP-16
33706_at	AB006198	squamous cell carcinoma antigen	0.1	-0.5	0.1	0.2	0.656	0.005	0.261	0.245	HDMP-17
41246_at	AI743134	trinucleotide repeat containing 3	0.1	-0.5	0.0	0.3	0.357	0.003	0.956	0.099	HDMP-18
31838_at	U79274	protein predicted by clone 23733	0.2	-0.5	0.1	0.0	0.196	0.004	0.583	0.854	HDMP-19
35963_at	AI201243	HLA class II region expressed gene KE2	0.2	-0.5	-0.1	0.2	0.071	0.004	0.982	0.717	HDMP-20
41398_at	AL049305	hypothetical protein FLJ21940	0.1	-0.5	0.1	0.0	0.301	0.003	0.510	0.940	HDMP-21
40821_at	M61832	S-adenosylhomocysteine hydrolase	0.1	-0.5	0.0	0.2	0.392	0.002	0.499	0.670	HDMP-22
41277_at	AW021542	sin3-associated polypeptide, 18kD	0.0	-0.5	0.3	0.0	0.862	0.004	0.103	0.716	HDMP-23
33870_at	AB029005	chromosome 5 open reading frame 7	-0.1	-0.5	0.3	0.3	0.324	0.005	0.053	0.155	HDMP-24
32102_at	AB018273	spastic ataxia of Charlevoix-Saguenay (sacsin)	-0.1	-0.5	0.3	0.2	0.635	0.005	0.021	0.538	HDMP-25
38041_at	U41514	UDP-N-acetyl-alpha-D-galactosamine	-0.2	-0.2	0.5	-0.2	0.167	0.241	0.002	0.246	LDMP+01
32695_at	Z97632	bombesin-like receptor 3	-0.1	-0.3	0.5	-0.1	0.502	0.058	0.001	0.340	LDMP+02
40377_at	AB014582	KIAA0682 gene product	-0.3	-0.1	0.5	-0.1	0.044	0.720	0.000	0.270	LDMP+03
37036_at	AB002299	KIAA0301 protein	-0.2	-0.3	0.5	-0.1	0.246	0.102	0.012	0.899	LDMP+04
39717_g_at	AI597616	mitochondrial ribosomal protein L33	-0.4	-0.1	0.5	0.1	0.001	0.429	0.005	0.428	LDMP+05
33773_at	U13948	myeloid/lymphoid or mixed-lineage leukemia	-0.2	0.0	0.5	-0.3	0.087	0.881	0.007	0.127	LDMP+06
40030_at	Y15801	protein kinase, Y-linked	-0.1	-0.4	0.5	-0.1	0.541	0.022	0.000	0.169	LDMP+07
891_at	M77698	YY1 transcription factor	-0.5	-0.1	0.5	0.1	0.002	0.532	0.000	0.738	LDMP+08
34307_at	U81006	transmembrane 9 superfamily member 2	-0.2	-0.3	0.5	-0.1	0.120	0.136	0.000	0.568	LDMP+09
32643_at	L07956	glucan (1,4-alpha-), branching enzyme 1	-0.1	-0.2	0.5	-0.2	0.412	0.227	0.025	0.539	LDMP+10
40473_at	AF024636	serine/threonine kinase 24 (STE20 homolog, yeast)	-0.5	-0.1	0.5	0.1	0.000	0.770	0.002	0.431	LDMP+11
39490_f_at	W26381	ADP-ribosylation factor GTPase activating protein 1	-0.3	0.0	0.5	-0.1	0.030	0.961	0.002	0.414	LDMP+12
38472_at	D63477	KIAA0143 protein	0.0	-0.2	0.5	-0.3	0.815	0.332	0.003	0.064	LDMP+13
1914_at	U66838	cyclin A1	-0.1	0.0	0.5	-0.3	0.560	0.793	0.074	0.323	LDMP+14
38042_at	X03674	glucose-6-phosphate dehydrogenase	-0.1	0.1	0.5	-0.5	0.617	0.524	0.001	0.002	LDMP+15
34891_at	AI540958	dynein, cytoplasmic, light polypeptide	-0.4	0.1	0.5	0.0	0.004	0.715	0.000	0.693	LDMP+16
33457_at	AB029028	KIAA1105 protein	-0.1	-0.3	0.5	-0.2	0.551	0.125	0.003	0.169	LDMP+17
37497_at	L16499	hematopoietically expressed homeobox	-0.4	0.2	0.5	0.0	0.000	0.339	0.026	0.685	LDMP+18
41750_at	D49489	protein disulfide isomerase-related protein	-0.2	-0.2	0.4	-0.1	0.221	0.245	0.001	0.316	LDMP+19
37735_at	U31383	guanine nucleotide binding protein 10	-0.2	-0.3	0.4	0.1	0.081	0.058	0.000	0.597	LDMP+20
316_g_at	D45132	PR domain containing 2, with ZNF domain	-0.1	-0.2	0.4	-0.3	0.468	0.347	0.011	0.211	LDMP+21
2044_s_at	M15400	retinoblastoma 1 (including osteosarcoma)	-0.2	-0.3	0.4	0.0	0.162	0.082	0.012	0.697	LDMP+22
41562_at	L13689	murine leukemia viral (bmi-1) oncogene homolog	-0.3	-0.1	0.4	0.0	0.071	0.430	0.000	0.160	LDMP+23
40167_s_at	AF038187	CS box-containing WD protein	-0.1	-0.3	0.4	-0.1	0.626	0.055	0.002	0.568	LDMP+24
40607_at	U97105	dihydropyrimidinase-like 2	-0.1	-0.2	0.4	-0.2	0.564	0.304	0.005	0.179	LDMP+25
37096_at	M34379	elastase 2, neutrophil	0.6	0.0	-0.5	-0.2	0.000	0.811	0.000	0.279	LDMP-01
37391_at	X12451	cathepsin L	0.1	0.2	-0.5	0.2	0.396	0.164	0.000	0.320	LDMP-02
31914_at	AF054177	chromodomain helicase DNA binding protein 1-like	0.3	0.4	-0.5	-0.2	0.063	0.015	0.001	0.274	LDMP-03
1186_at	D49493	growth differentiation factor 10	0.1	0.2	-0.5	0.2	0.284	0.306	0.006	0.436	LDMP-04
34967_at	AF001549	RNA polymerase I transcription factor RRN3	0.0	0.2	-0.5	0.4	0.966	0.328	0.004	0.052	LDMP-05
34243_i_at	U89358	lethal (3) malignant brain tumor l(3)mbt protein	0.4	0.1	-0.5	0.0	0.009	0.696	0.003	0.846	LDMP-06
39948_at	AI693307	MAX protein	0.3	0.0	-0.5	0.1	0.029	0.824	0.010	0.998	LDMP-07
41218_at	AB018272	KIAA0729 protein	-0.1	0.3	-0.5	0.4	0.385	0.111	0.002	0.009	LDMP-08
2081_s_at	L07032	protein kinase C, theta	0.1	0.3	-0.5	0.2	0.377	0.122	0.002	0.398	LDMP-09
34472_at	AB012911	frizzled homolog 6 (Drosophila)	0.5	-0.2	-0.5	0.0	0.000	0.302	0.001	0.877	LDMP-10
38879_at	D83664	S100 calcium binding protein A12 (calgranulin C)	0.5	0.0	-0.5	-0.2	0.000	0.936	0.008	0.145	LDMP-11
39369_at	AB023152	KIAA0935 protein	0.3	0.0	-0.4	0.0	0.025	0.835	0.007	0.742	LDMP-12
32821_at	AI762213	lipocalin 2 (oncogene 24p3)	0.6	-0.1	-0.4	-0.2	0.000	0.579	0.002	0.296	LDMP-13
35023_at	U00803	fyn-related kinase	0.0	0.3	-0.4	0.1	0.846	0.077	0.012	0.471	LDMP-14
37927_at	X12654	chromosome condensation 1	0.3	-0.3	-0.4	0.3	0.069	0.105	0.006	0.048	LDMP-15
39993_at	D11466	phosphatidylinositol glycan, class A	0.2	0.1	-0.4	0.2	0.131	0.729	0.002	0.326	LDMP-16
795_s_at	X66358	cyclin-dependent kinase-like 1 (CDC2-related kinase)	0.1	0.2	-0.4	0.2	0.460	0.244	0.000	0.162	LDMP-17
40684_at	U78190	GTP cyclohydrolase I feedback regulatory protein	0.3	0.1	-0.4	0.0	0.040	0.548	0.003	0.920	LDMP-18
39919_at	AI423340	C1q-related factor	-0.1	0.4	-0.4	0.4	0.417	0.056	0.022	0.044	LDMP-19
39956_at	AF041853	kinesin family member 3A	0.1	0.0	-0.4	0.4	0.340	0.966	0.007	0.042	LDMP-20
41232_at	AL050022	DKFZP564D116 protein	0.2	0.0	-0.4	0.3	0.210	0.993	0.005	0.117	LDMP-21
32869_at	AF073362	MRE11 meiotic recombination 11 homolog A	-0.1	0.4	-0.4	0.3	0.414	0.035	0.007	0.041	LDMP-22
39201_r_at	W28760	51c8 Homo sapiens cDNA	0.2	0.3	-0.4	-0.1	0.115	0.146	0.001	0.910	LDMP-23
39527_at	AF090102	KIAA1155 protein	0.3	0.0	-0.4	0.1	0.037	0.879	0.004	0.706	LDMP-24
36105_at	M18728	carcinoembryonic antigen-related cell adhesion	0.4	0.0	-0.4	-0.2	0.002	0.897	0.003	0.538	LDMP-25
41415_at	L36720	bystin-like	-0.3	-0.2	0.0	0.6	0.020	0.242	0.973	0.000	Mp+01
36225_s_at	W27611	splicing factor proline/glutamine rich	-0.4	0.1	0.0	0.6	0.005	0.495	0.751	0.003	Mp+02
35005_at	AF051941	nucleoside diphosphate kinase type 6	-0.2	-0.2	-0.2	0.6	0.100	0.354	0.205	0.000	Mp+03
40690_at	X54942	CDC28 protein kinase 2	-0.3	-0.2	0.1	0.6	0.014	0.296	0.274	0.003	Mp+04
39643_at	U94703	polymerase (DNA directed), gamma 2	-0.1	-0.1	-0.2	0.6	0.346	0.683	0.241	0.001	Mp+05
35943_s_at	D13317	GA binding protein transcription factor	-0.1	-0.1	-0.2	0.5	0.416	0.522	0.242	0.000	Mp+06
39637_at	U14528	solute carrier family 26 (sulfate transporter)	-0.2	-0.2	-0.1	0.5	0.155	0.277	0.721	0.000	Mp+07
41462_at	AF065482	sorting nexin 2	-0.2	-0.4	0.1	0.5	0.063	0.028	0.171	0.008	Mp+08
1199_at	D13748	eukaryotic translation initiation factor 4A, isoform 1	-0.2	-0.1	-0.1	0.5	0.279	0.635	0.587	0.006	Mp+09
39368_at	AL031668	eukaryotic translation initiation factor 2	-0.3	-0.1	0.1	0.5	0.022	0.448	0.265	0.017	Mp+10
40349_at	AL049442	clone DKFZp586N1720	-0.3	-0.1	-0.1	0.5	0.039	0.581	0.657	0.000	Mp+11
32251_at	AA149307	hypothetical protein FLJ21174	-0.4	0.0	-0.1	0.5	0.003	0.793	0.287	0.000	Mp+12
40191_s_at	AI761647	clone=IMAGE-2370113	-0.5	0.3	-0.3	0.5	0.000	0.084	0.262	0.007	Mp+13
1939_at	M22898	tumor protein p53 (Li-Fraumeni syndrome)	-0.2	-0.2	-0.1	0.5	0.093	0.262	0.936	0.008	Mp+14
35432_at	AF074723	RNA polymerase II transcriptional regulation mediator	-0.1	-0.3	0.0	0.5	0.333	0.103	0.636	0.011	Mp+15
2025_s_at	M80261	APEX nuclease (multifunctional DNA repair enzyme)	-0.1	-0.1	-0.1	0.5	0.331	0.531	0.649	0.010	Mp+16
37535_at	M27691	cAMP responsive element binding protein 1	-0.3	0.1	-0.1	0.5	0.062	0.490	0.515	0.006	Mp+17
37722_s_at	U26266	deoxyhypusine synthase	-0.3	-0.1	0.0	0.5	0.013	0.718	0.835	0.004	Mp+18
40122_at	AF037448	NS1-associated protein 1	-0.2	-0.1	-0.1	0.5	0.124	0.551	0.979	0.011	Mp+19
1936_s_at	M13930	v-myc myelocytomatosis viral oncogene homolog	-0.5	0.2	0.0	0.5	0.001	0.292	0.827	0.001	Mp+20
1944_f_at	AF001359	mutL homolog 1, colon cancer, nonpolyposis type 2	0.0	-0.4	-0.1	0.5	0.980	0.013	0.789	0.012	Mp+21
628_at	L37882	frizzled homolog 2 (Drosophila)	-0.1	-0.3	0.0	0.5	0.449	0.077	0.979	0.003	Mp+22
38414_at	U05340	CDC20 cell division cycle 20 homolog	-0.1	-0.3	0.0	0.5	0.635	0.087	0.895	0.007	Mp+23
39731_at	Z23064	RNA binding motif protein, X chromosome	-0.4	-0.1	0.2	0.5	0.003	0.626	0.123	0.011	Mp+24
32129_at	AL079314	hypothetical protein, similar to PRAJA1	-0.1	-0.1	-0.2	0.5	0.459	0.505	0.354	0.008	Mp+25
35227_at	U72066	retinoblastoma binding protein 8	0.1	0.1	0.4	-0.8	0.370	0.659	0.063	0.001	MP-01
39775_at	X54486	serine (or cysteine) proteinase inhibitor, clade G	0.2	0.0	0.4	-0.7	0.184	0.796	0.021	0.000	MP-02
38386_r_at	U34683	glutathione synthetase	0.4	0.1	0.0	-0.7	0.001	0.684	0.820	0.000	MP-03
39957_at	AF150247	hypothetical protein	0.2	-0.2	0.3	-0.6	0.103	0.293	0.108	0.000	MP-04
1106_s_at	M12959	T cell receptor alpha locus	0.4	-0.1	0.1	-0.6	0.014	0.703	0.535	0.000	MP-05
39230_at	AL022318	similar to APOBEC1	0.3	0.0	0.2	-0.6	0.053	0.999	0.436	0.001	MP-06
40755_at	X92841	MHC class I polypeptide-related sequence A	0.4	-0.2	0.1	-0.6	0.003	0.238	0.517	0.001	MP-07
32904_at	M28393	perforin 1 (pore forming protein)	0.2	0.1	0.2	-0.6	0.217	0.634	0.177	0.002	MP-08
34660_at	AI142565	ribonuclease, RNase A family, k6	0.3	0.2	-0.1	-0.6	0.029	0.319	0.382	0.004	MP-09
41188_at	W28186	putative integral membrane transporter	0.1	0.0	0.3	-0.6	0.588	0.807	0.038	0.003	MP-10
35621_at	L77213	phosphomevalonate kinase	0.6	-0.2	0.0	-0.6	0.000	0.158	0.810	0.004	MP-11
37980_at	U03644	CBF1 interacting corepressor	0.1	0.1	0.2	-0.5	0.378	0.572	0.374	0.002	MP-12
41855_at	AF030424	histone acetyltransferase 1	0.1	-0.1	0.4	-0.5	0.559	0.638	0.018	0.000	MP-13
35109_at	AB018299	KIAA0756 protein	0.2	-0.1	0.2	-0.5	0.106	0.745	0.289	0.008	MP-14
37624_at	M29458	carbonic anhydrase III, muscle specific	0.2	0.2	0.0	-0.5	0.231	0.329	0.864	0.001	MP-15
40942_g_at	W27026	VAMP (vesicle-associated membrane protein)	0.0	0.3	0.2	-0.5	0.869	0.059	0.494	0.009	MP-16
37967_at	AF000424	lymphocyte antigen 117	0.3	-0.1	0.1	-0.5	0.040	0.477	0.780	0.003	MP-17
36155_at	D87465	KIAA0275 gene product	0.3	0.3	-0.2	-0.5	0.022	0.164	0.185	0.001	MP-18
31556_at	X61072	T cell receptor, clone IGRA17	0.3	0.0	0.1	-0.5	0.078	0.799	0.612	0.014	MP-19
32140_at	Y08110	sortilin-related receptor	0.4	0.2	0.0	-0.5	0.006	0.345	0.723	0.003	MP-20
36710_at	Z38026	cathelicidin antimicrobial peptide	0.5	-0.1	-0.2	-0.5	0.001	0.622	0.076	0.031	MP-21
41400_at	K02581	thymidine kinase 1, soluble	0.2	0.1	0.1	-0.5	0.150	0.777	0.632	0.005	MP-22
40141_at	AB014595	cullin 4B	0.0	0.4	0.1	-0.5	0.931	0.019	0.653	0.003	MP-23
38968_at	AB005047	SH3-domain binding protein 5	0.1	0.1	0.2	-0.5	0.591	0.523	0.200	0.004	MP-24
34965_at	AF031824	cystatin F (leukocystatin)	0.4	-0.1	0.0	-0.5	0.003	0.462	0.605	0.018	MP-25

Figure 5: Treatment-induced changes in percentage of ALL cells in S-phase.

Treatment-induced changes in percentage of ALL cells in S-phase of the cell cycle. Percentages of bone marrow leukemia cells in S-phase from bone marrow leukemia blast at diagnosis and post-treatment were available for 23 of the 60 patients analyzed in this study. Propidium-iodide stained DNA content was measured by flow cytometry with the Coulter EPICS-V flow cytometer (Coulter Electronics. Inc., Hialeah, Florida). The computer program PEAK was used to calculate the percentages of cells in the G0/G1, S, G2+M phase. (a) The median fold-change of ATM expression in the four treatment groups: HDMTX, n=7, median= +2.3, range (-1.2 to 3.2); MP, n=6, median= +1.3, range (-3.0 to 2.6); HDMTX+MP, n=5, median= -1.1, range (-2.3 to 1.3); LDMTX+MP, n=5, median= -1.1, range (-2.0 to 1.3). ATM induction was significantly greater after HDMTX as compared to the other three treatments (P=0.007, Wilcoxon). (b) The median change in %S-phase of ALL cells from pre- to post-treatment in the four treatment groups: HDMTX, median= -35, range (-67 to102); MP, median= +13.6, range (-27 to 95); HDMTX+MP, median= +87, range (-88 to 386); LDMTX+MP, median= +105, range (-38 to187). The difference in change of %S-phase was statistically significant when the HDMTX group was compared to the other three treatments combined (P=0.033, Wilcoxon).