St. Jude Research/Supplemental Data/AML1/section 4

Section IV

Table of Contents

Section IV. MLL in combined ALL and AML datasets

Table S13. Top 100 probe sets selected by SAM for MLL chimeric fusion gene irrespective of blast lineage

	U133 probe set	Gene description	Symbol	Location	GenBank reference	UniGene reference	SAM d-score	MLL Above/ Below	Fold change
1	204069_at	Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)	MEIS1	Chr:2p14-p13	NM_002398	Hs.170177	14.6	Above	6.0
2	201153_s_at	muscleblind-like (Drosophila)	MBNL1	Chr:3q25	NM_021038	Hs.28578	12.7	Above	1.9
3	201152_s_at	muscleblind-like (Drosophila)	MBNL1	Chr:3q25	N31913	Hs.28578	12.6	Above	1.9
4	214651_s_at	homeo box A9	HOXA9	Chr:7p15-p14	U41813	Hs.127428	11.5	Above	6.6
5	219463_at	chromosome 20 open reading frame 103	C20orf103	Chr:20p12	NM_012261	Hs.22920	11.3	Above	11.3
6	209905_at	homeo box A9	HOXA9	Chr:7p15-p14	AI246769	Hs.127428	10.2	Above	6.8
7	201850_at	capping protein (actin filament), gelsolin-like	CAPG	Chr:2cen-q24	NM_001747	Hs.82422	9.9	Above	3.1
8	204082_at	pre-B-cell leukemia transcription factor 3	PBX3	Chr:9q33-q34	NM_006195	Hs.294101	9.9	Above	3.0
9	201151_s_at	muscleblind-like (Drosophila)	MBNL1	Chr:3q25	BF512200	Hs.28578	9.6	Above	2.2
10	213147_at	homeo box A10	HOXA10	Chr:7p15-p14	AI375919	Hs.110637	9.4	Above	4.9
11	206847_s_at	homeo box A7	HOXA7	Chr:7p15-p14	AF026397	Hs.446318	9.2	Above	3.6
12	213150_at	homeo box A10	HOXA10	Chr:7p15-p14	BF792917	Hs.110637	8.9	Above	5.7
13	218217_at	likely homolog of rat and mouse retinoid-inducible serine carboxypeptidase	RISC	Chr:17q23.2	NM_021626	Hs.431107	8.8	Above	3.2
14	204497_at	adenylate cyclase 9	ADCY9	Chr:16p13.3	AB011092	Hs.20196	8.7	Above	5.8
15	218376_s_at	NEDD9 interacting protein with calponin homology and LIM domains	NICAL	Chr:6q21	NM_022765	Hs.33476	8.7	Above	2.1
16	213844_at	homeo box A5	HOXA5	Chr:7p15-p14	NM_019102	Hs.37034	8.5	Above	5.5
17	211733_x_at	sterol carrier protein 2	SCP2	Chr:1p32	BC005911	Hs.75760	8.4	Above	1.4
18	201105_at	lectin, galactoside-binding, soluble, 1 (galectin 1)	LGALS1	Chr:22q13.1	NM_002305	Hs.407909	8.2	Above	3.3
19	204824_at	endonuclease G	ENDOG	Chr:9q34.1	NM_004435	Hs.420106	8.2	Above	2.5
20	212174_at	adenylate kinase 2	AK2	Chr:1p34	W02312	Hs.294008	8.1	Above	2.1
21	219099_at	chromosome 12 open reading frame 5	C12orf5	Chr:12p13.3	NM_020375	Hs.24792	8.0	Above	1.9
22	218312_s_at	hypothetical protein FLJ12895	FLJ12895	Chr:19q13.43	NM_023926	Hs.235390	-8.0	Below	2.3
23	205472_s_at	dachshund homolog (Drosophila)	DACH	Chr:13q22	NM_004392	Hs.63931	8.0	Above	6.1
24	214297_at	chondroitin sulfate proteoglycan 4 (melanoma-associated)	CSPG4	Chr:15q23	BE857703	Hs.436301	7.9	Above	5.2
25	203733_at	dexamethasone-induced transcript	DEXI	Chr:16p13.2	NM_014015	Hs.157925	7.9	Above	2.6
26	202603_at	a disintegrin and metalloproteinase domain 10	ADAM10	Chr:15q2	N51370	Hs.172028	7.8	Above	1.7
27	205471_s_at	dachshund homolog (Drosophila)	DACH	Chr:13q22	AW772082	Hs.63931	7.8	Above	5.4
28	209167_at	glycoprotein M6B	GPM6B	Chr:Xp22.2	AI419030	Hs.5422	7.6	Above	4.7
29	205821_at	DNA segment on chromosome 12 (unique) 2489 expressed sequence	D12S2489E	Chr:12p13.2-p12.3	NM_007360	Hs.387787	7.6	Above	3.0
30	203781_at	mitochondrial ribosomal protein L33	MRPL33	Chr:2p21	NM_004891	Hs.14454	7.6	Above	2.4
31	218966_at	myosin VC	MYO5C	Chr:15q21	NM_018728	Hs.111782	-7.5	Below	2.8
32	201163_s_at	insulin-like growth factor binding protein 7	IGFBP7	Chr:4q12	NM_001553	Hs.435795	7.5	Above	2.5
33	212175_s_at	adenylate kinase 2	AK2	Chr:1p34	AL513611	Hs.294008	7.5	Above	1.8
34	211066_x_at	protocadherin gamma subfamily C, 3	PCDHGC3	Chr:5q31	BC006439	Hs.283794	7.4	Above	2.6
35	204839_at	RNase MRP/RNase P protein-like	POP5	Chr:12q24.31	NM_015918	Hs.279913	7.4	Above	1.3
36	219577_s_at	ATP-binding cassette, sub-family A (ABC1), member 7	ABCA7	Chr:19p13.3	NM_019112	Hs.134514	7.4	Above	1.7
37	212173_at	adenylate kinase 2	AK2	Chr:1p34	AU154985	Hs.294008	7.4	Above	2.1
38	204937_s_at	zinc finger protein 274	ZNF274	Chr:19qter	NM_016325	Hs.83761	-7.3	Below	1.7
39	219033_at	hypothetical protein FLJ21308	FLJ21308	Chr:5q11.2	NM_024615	Hs.310185	7.3	Above	2.4
40	212306_at	cytoplasmic linker associated protein 2	CLASP2	Chr:3p22.3	AI741784	Hs.108614	7.3	Above	1.4
41	206289_at	homeo box A4	HOXA4	Chr:7p15-p14	NM_002141	Hs.147747	7.2	Above	2.1
42	201944_at	hexosaminidase B (beta polypeptide)	HEXB	Chr:5q13	NM_000521	Hs.69293	7.1	Above	1.8
43	214259_s_at	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	AKR7A2	Chr:1p35.1-p36.23	AI144075	Hs.512807	7.1	Above	1.7
44	215836_s_at	protocadherin gamma subfamily C, 3	PCDHGC3	Chr:5q31	AK026188	Hs.283794	7.1	Above	2.3
45	52164_at	chromosome 11 open reading frame 24	C11orf24	Chr:11q13	AA065185	Hs.303025	7.0	Above	1.6
46	217520_x_at	similar to HP95	na	Chr:15q12	BG396614	Hs.374397	7.0	Above	2.9
47	202976_s_at	Rho-related BTB domain containing 3	RHOBTB3	Chr:5q15	NM_014899	Hs.31653	7.0	Above	2.5
48	211926_s_at	myosin, heavy polypeptide 9, non-muscle	MYH9	Chr:22q13.1	AI827941	Hs.146550	7.0	Above	1.5
49	215204_at	Homo sapiens cDNA FLJ14090 fis, clone MAMMA1000264.	---	---	AU147295	Hs.288575	7.0	Above	1.9
50	205996_s_at	adenylate kinase 2	AK2	Chr:1p34	NM_013411	Hs.294008	7.0	Above	2.0
51	221763_at	thyroid hormone receptor interactor 8	TRIP8	Chr:10q22.1	AI694023	Hs.442675	7.0	Above	1.8
52	200897_s_at	palladin	KIAA0992	Chr:4q32.3	NM_016081	Hs.194431	6.9	Above	4.2
53	213915_at	natural killer cell group 7 sequence	NKG7	Chr:19q13.41	NM_005601	Hs.10306	6.9	Above	2.2
54	210549_s_at	chemokine (C-C motif) ligand 23	CCL23	Chr:17q21.1	U58913	Hs.169191	6.8	Above	11.8
55	209079_x_at	protocadherin gamma subfamily C, 3	PCDHGC3	Chr:5q31	AF152318	Hs.283794	6.8	Above	2.3
56	209616_s_at	carboxylesterase 1 (monocyte/macrophage serine esterase 1)	CES1	Chr:16q13-q22.1	S73751	Hs.278997	6.8	Above	9.0
57	209822_s_at	very low density lipoprotein receptor	VLDLR	Chr:9p24	L22431	Hs.370422	6.8	Above	2.6
58	214790_at	SUMO-1-specific protease	SUSP1	Chr:6q13-q14.3	AK001406	Hs.435628	6.7	Above	3.0
59	201050_at	phospholipase D3	PLD3	Chr:19q13.2	NM_012268	Hs.257008	6.7	Above	5.6
60	221458_at	5-hydroxytryptamine (serotonin) receptor 1F	HTR1F	Chr:3p12	NM_000866	Hs.248136	6.7	Above	1.8
61	203836_s_at	mitogen-activated protein kinase kinase kinase 5	MAP3K5	Chr:6q22.33	D84476	Hs.151988	6.7	Above	1.7
62	210660_at	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	LILRB1	Chr:19q13.4	AF025529	Hs.149924	6.7	Above	2.8
63	200953_s_at	cyclin D2	CCND2	Chr:12p13	NM_001759	Hs.376071	-6.7	Below	3.7
64	213908_at	Homo sapiens hypothetical protein LOC339005, mRNA (cDNA clone IMAGE:4837016), partial cds	---	---	AI824078	Hs.212670	6.6	Above	3.3
65	218824_at	hypothetical protein FLJ10781	FLJ10781	Chr:19q13.33	NM_018215	Hs.8395	6.6	Above	2.7
66	204304_s_at	prominin 1	PROM1	Chr:4p15.33	NM_006017	Hs.370052	6.6	Above	3.6
67	208679_s_at	actin related protein 2/3 complex, subunit 2, 34kDa	ARPC2	Chr:2q36.1	AF279893	Hs.83583	6.6	Above	1.3
68	200046_at	defender against cell death 1	DAD1	Chr:14q11-q12	NM_001344	Hs.82890	6.5	Above	1.6
69	212588_at	protein tyrosine phosphatase, receptor type, C	PTPRC	Chr:1q31-q32	Y00062	Hs.444324	6.5	Above	1.6
70	206851_at	ribonuclease, RNase A family, 3 (eosinophil cationic protein)	RNASE3	Chr:14q24-q31	NM_002935	Hs.73839	6.5	Above	6.1
71	203603_s_at	zinc finger homeobox 1b	ZFHX1B	Chr:2q22	NM_014795	Hs.34871	6.5	Above	1.6
72	202139_at	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	AKR7A2	Chr:1p35.1-p36.23	NM_003689	Hs.512807	6.5	Above	1.8
73	202957_at	hematopoietic cell-specific Lyn substrate 1	HCLS1	Chr:3q13	NM_005335	Hs.14601	6.5	Above	1.4
74	204736_s_at	chondroitin sulfate proteoglycan 4 (melanoma-associated)	CSPG4	Chr:15q23	NM_001897	Hs.436301	6.5	Above	3.2
75	200989_at	hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	HIF1A	Chr:14q21-q24	NM_001530	Hs.412416	-6.5	Below	1.9
76	202054_s_at	aldehyde dehydrogenase 3 family, member A2	ALDH3A2	Chr:17p11.2	NM_000382	Hs.440662	6.5	Above	2.1
77	201818_at	hypothetical protein FLJ12443	FLJ12443	Chr:5p15.33	NM_024830	Hs.179882	6.5	Above	1.5
78	56256_at	transgelin	TAGLN	Chr:11q23.2	AA150165	Hs.410977	6.5	Above	1.7
79	200760_s_at	cytoskeleton related vitamin A responsive protein	JWA	Chr:3p14	N92494	Hs.92384	6.4	Above	1.4
80	218147_s_at	glycosyltransferase AD-017	AD-017	Chr:3p21.31	NM_018446	Hs.297304	6.4	Above	1.5
81	210548_at	chemokine (C-C motif) ligand 23	CCL23	Chr:17q21.1	U58913	Hs.169191	6.4	Above	6.3
82	212587_s_at	protein tyrosine phosphatase, receptor type, C	PTPRC	Chr:1q31-q32	AI809341	Hs.444324	6.4	Above	1.8
83	206606_at	lipase, hepatic	LIPC	Chr:15q21-q23	NM_000236	Hs.9994	6.4	Above	3.6
84	220643_s_at	Fas apoptotic inhibitory molecule	FAIM	Chr:3q22.3	NM_018147	Hs.173438	6.4	Above	1.9
85	208967_s_at	adenylate kinase 2	AK2	Chr:1p34	U39945	Hs.294008	6.3	Above	1.6
86	203562_at	fasciculation and elongation protein zeta 1 (zygin I)	FEZ1	Chr:11q24.2	NM_005103	Hs.79226	6.3	Above	2.7
87	200782_at	annexin A5	ANXA5	Chr:4q26-q28	NM_001154	Hs.145741	6.3	Above	2.3
88	57540_at	ribokinase	RBSK	Chr:2p23.3	AI823980	Hs.11916	6.2	Above	2.1
89	209170_s_at	glycoprotein M6B	GPM6B	Chr:Xp22.2	AF016004	Hs.5422	6.2	Above	3.3
90	1405_i_at	chemokine (C-C motif) ligand 5	CCL5	Chr:17q11.2-q12	M21121	Hs.489044	6.2	Above	4.7
91	205717_x_at	protocadherin gamma subfamily C, 3	PCDHGC3	Chr:5q31	NM_002588	Hs.283794	6.2	Above	1.8
92	201705_at	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 (Mov34 homolog)	PSMD7	Chr:16q23-q24	NM_002811	Hs.440604	6.2	Above	1.2
93	221676_s_at	coronin, actin binding protein, 1C	CORO1C	Chr:12q24.1	BC002342	Hs.17377	6.2	Above	1.6
94	202265_at	B lymphoma Mo-MLV insertion region (mouse)	BMI1	Chr:10p11.23	NM_005180	Hs.380403	6.1	Above	2.1
95	201278_at	Homo sapiens cDNA FLJ35517 fis, clone SPLEN2000698.	---	---	N21202	Hs.519270	-6.1	Below	1.8
96	203216_s_at	myosin VI	MYO6	Chr:6q13	NM_004999	Hs.118483	6.1	Above	5.2
97	201280_s_at	disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)	DAB2	Chr:5p13	NM_001343	Hs.81988	-6.1	Below	3.3
98	207419_s_at	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)	RAC2	Chr:22q13.1	NM_002872	Hs.301175	6.1	Above	1.6
99	216331_at	integrin, alpha 7	ITGA7	Chr:12q13	AK022548	Hs.74369	6.1	Above	7.1
100	209168_at	glycoprotein M6B	GPM6B	Chr:Xp22.2	AW148844	Hs.5422	6.1	Above	2.1

In the analysis below, genes were selected that showed high expression across the majority of MLL chimeric fusion gene containing cases, irrespective of their lineage. This was accomplished by selecting those genes from Table S13, for which ≥60% of MLL containing cases in each lineage expressed the gene at a level greater than the mean expression in non-MLL cases. Twenty-one genes were identified that met these criteria are listed below.