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Supplementary Information

Gene Expression Profiling of Pediatric Acute Myelogenous Leukemia

Section IV: MLL in combined ALL and AML dataset

Table S13. Top 100 probe sets selected by SAM for MLL chimeric fusions irrespective of blast lineage (whole dataset)

  U133 probe set Gene description Symbol Location GenBank reference UniGene reference SAM d-score MLL Above/ Below mean 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.