St. Jude Research/Supplemental Data/ALL2/section c

C. SELECTION OF DISCRIMINATING GENES

Fig. 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)