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ALL Methylation Supplementary Table 4-12

List of highly correlated Refseq genes with upregulated FDR<0.05 and hypomethylated FDR<0.05 in BCRABL1

RefSeq Genes Annotation Cytoband Max Pearson Corr Estimate P Max Pearson Corr Max Pearson Corr Affy Probe GEP FC GEP FDR GEP Common Rank Max Pearson Corr HELP Probe MET Delta MET FDR
NM_007161 LST1 leukocyte specific transcript 1 chr6p21.3 0.693576754 0 214181_x_at -2.452891041 0.02281842 712 / 12428 MSPI0406S00315957 -0.887726022 0.034708524
NM_014957 DENND3 DENN/MADD domain containing 3 chr8q24.3 0.574958436 1.56E-12 212975_at -1.985001164 0.008496879 399 / 12428 MSPI0406S00447241 -0.719279426 0.001546857
NM_001135585 SLC2A5 solute carrier family 2 (facilitated glucose/fructose transporter), member 5 chr1p36.2 0.547707365 2.66E-11 204430_s_at -3.479277511 2.62E-05 56 / 12428 MSPI0406S00008592 -0.828694892 0.005085113
NM_002039 GAB1 GRB2-associated binding protein 1 chr4q31.21 0.523017676 2.82E-10 207112_s_at -1.659369786 0.048616857 1115 / 12428 MSPI0406S00245299 -1.666173045 0.002892065
NM_001003799 TARP TCR gamma alternate reading frame protein chr7p15-p14 0.510410371 8.78E-10 216920_s_at -1.889565251 0.002678373 246 / 12428 MSPI0406S00366420 -0.468422963 0.004963779
NM_003659 AGPS alkylglycerone phosphate synthase chr2q31.2 0.50199314 1.82E-09 205401_at -1.953559161 0.002272693 232 / 12428 MSPI0406S00141266 -0.845507626 0.001005789
NM_020404 CD248 CD248 molecule, endosialin chr11q13 0.457175711 6.55E-08 219025_at -1.460842593 0.005644502 339 / 12428 MSPI0406S00571642 -0.508044042 0.010064896
NM_002101 GYPC glycophorin C (Gerbich blood group) chr2q14-q21 0.439256083 2.39E-07 202947_s_at -2.227473339 2.10E-05 49 / 12428 MSPI0406S00129703 -0.766018407 0.035788866
NM_006000 TUBA4A tubulin, alpha 4a chr2q35 0.419159503 9.35E-07 212242_at -2.59067051 3.01E-07 19 / 12428 MSPI0406S00150109 -1.263160911 0.000214148
NM_018384 GIMAP5 GTPase, IMAP family member 5 chr7q36.1 0.411618951 1.53E-06 64064_at -1.702972357 0.000900182 160 / 12428 MSPI0406S00402531 -1.608957454 6.33E-06
NM_001025160 CD97 CD97 molecule chr19p13 0.407183077 2.03E-06 202910_s_at -2.393425549 2.71E-05 59 / 12428 MSPI0406S00875954 -0.407907074 0.033117577
NM_001215 CA6 carbonic anhydrase VI chr1p36.2 0.406278373 2.14E-06 206873_at -2.741231532 9.85E-07 24 / 12428 MSPI0406S00008461 -1.053345182 0.000494224
NM_024711 GIMAP6 GTPase, IMAP family member 6 --- 0.406185455 2.16E-06 219777_at -5.366338926 1.75E-07 17 / 12428 MSPI0406S00402513 -0.518435188 0.016591587
NM_019029 CPVL carboxypeptidase, vitellogenic-like chr7p15-p14 0.401384584 2.91E-06 208146_s_at -3.411081466 1.08E-05 38 / 12428 MSPI0406S00363814 -1.161411914 0.022240916
NM_001013415 FBXW7 F-box and WD repeat domain containing 7 chr4q31.3 0.367109551 2.18E-05 218751_s_at -1.803801871 0.03874079 940 / 12428 MSPI0406S00246966 -1.049142559 9.24E-08
NM_001032278 MMP28 matrix metallopeptidase 28 chr17q11-q21.1 0.353574666 4.55E-05 219909_at -1.914146803 0.000602971 135 / 12428 MSPI0406S00802461 -0.612602859 0.03725776
NM_002514 NOV nephroblastoma overexpressed gene chr8q24.1 0.352408342 4.84E-05 214321_at -1.808278162 0.021514518 686 / 12428 MSPI0406S00440752 -0.898229399 0.001564684
NM_024701 ASB13 ankyrin repeat and SOCS box-containing 13 chr10p15.1 0.345592007 6.91E-05 218862_at -2.580162927 5.72E-05 68 / 12428 MSPI0406S00500267 -0.614981574 0.011399959
NM_020742 NLGN4X neuroligin 4, X-linked chrXp22.32-p22.31 0.32172095 0.000225739 221933_at -3.836289002 2.71E-05 58 / 12428 MSPI0406S00985875 -1.010239447 0.001334634
NM_001203 BMPR1B bone morphogenetic protein receptor, type IB chr4q22-q24 0.308962307 0.000408888 210523_at -1.987960788 0.000785167 150 / 12428 MSPI0406S00238219 -0.184433061 0.039744765
NM_001025105 CSNK1A1 casein kinase 1, alpha 1 chr5q32 0.306153225 0.000464382 213086_s_at -1.31851961 0.007839232 388 / 12428 MSPI0406S00289714 -0.493073976 0.002020533
NM_001077447 PPCS phosphopantothenoylcysteine synthetase chr1p34.2 0.303412334 0.000525146 218341_at -1.37687988 0.008569442 402 / 12428 MSPI0406S00033095 -0.672452644 9.22E-05
NM_004832 GSTO1 glutathione S-transferase omega 1 chr10q25.1 0.299837443 0.000615401 201470_at -1.493141591 0.001208781 183 / 12428 MSPI0406S00534528 -0.508309444 0.029237701
NM_001947 DUSP7 dual specificity phosphatase 7 chr3p21 0.298715367 0.000646544 213848_at -1.815948621 0.01143718 477 / 12428 MSPI0406S00179450 -0.615453337 5.12E-05
NM_005157 ABL1 c-abl oncogene 1, receptor tyrosine kinase chr9q34.1 0.295998329 0.000728045 202123_s_at -1.751913944 1.46E-07 16 / 12428 MSPI0406S00488377 -0.552701507 3.22E-07
NM_018364 RSBN1 round spermatid basic protein 1 chr1p13.2 0.289345322 0.000968966 213694_at -1.596901248 0.012179218 495 / 12428 MSPI0406S00050810 -0.611802655 0.000261687
NM_001127207 SMARCAL1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1 chr2q34-q35 0.287757913 0.001036319 218452_at -1.724748288 0.015306346 565 / 12428 MSPI0406S00148581 -0.609074727 0.00112886
NM_001031804 MAF v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) chr16q22-q23 0.284041354 0.001211072 206363_at -1.481120286 0.013957393 531 / 12428 MSPI0406S00771527 -0.318047374 0.004400327
NM_001082618 CD33 CD33 molecule chr19q13.3 0.277167256 0.001606757 206120_at -1.516465838 0.008353042 395 / 12428 MSPI0406S00903676 -0.895048195 0.008911455
NM_001025070 RPS14 ribosomal protein S14 chr5q31-q33 0.272778126 0.00191751 208645_s_at -1.37777176 0.005952432 349 / 12428 MSPI0406S00290374 -0.573089629 7.74E-05
NM_005668 ST8SIA4 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4 chr5q21 0.270917985 0.002064932 206925_at -1.608352531 0.028421665 806 / 12428 MSPI0406S00278455 -0.312806135 0.01429502
NM_006597 HSPA8 heat shock 70kDa protein 8 chr11q24.1 0.269370291 0.00219534 221891_x_at -1.393314189 0.013003379 508 / 12428 MSPI0406S00591443 -0.509074017 0.000935853
NM_019055 ROBO4 roundabout homolog 4, magic roundabout (Drosophila) chr11q24.2 0.267988407 0.00231803 220758_s_at -1.34587037 0.029129278 817 / 12428 MSPI0406S00592126 -1.103255279 0.000576909
NM_016141 DYNC1LI1 dynein, cytoplasmic 1, light intermediate chain 1 chr3p22.3 0.261164735 0.00301969 217976_s_at -1.345161549 0.006348723 356 / 12428 MSPI0406S00171248 -0.559936353 3.73E-05
NM_014905 GLS glutaminase chr2q32-q34 0.252200376 0.004230514 203158_s_at -1.694851704 0.005731421 343 / 12428 MSPI0406S00143021 -0.281813759 0.03214956
NM_001000 RPL39 ribosomal protein L39 chrXq22-q24 0.248317746 0.004878323 208695_s_at -1.320856182 0.010905444 455 / 12428 MSPI0406S01011445 -0.368060572 0.003350526
NM_002624 PFDN5 prefoldin subunit 5 chr12q12 0.244004809 0.005700642 207132_x_at -1.291845418 0.047474641 1099 / 12428 MSPI0406S00613833 -0.533019262 0.000488576
NM_000118 ENG endoglin chr9q33-q34.1 0.242933403 0.005923173 201808_s_at -1.858268027 0.039330301 960 / 12428 MSPI0406S00484934 -0.321539887 0.002240309
NM_001002030 ECHDC1 enoyl Coenzyme A hydratase domain containing 1 chr6q22.33 0.240767222 0.006396851 219974_x_at -1.266053997 0.044264706 1043 / 12428 MSPI0406S00337228 -1.510526772 7.90E-09
NM_006354 TADA3L transcriptional adaptor 3 (NGG1 homolog, yeast)-like chr3p25.3 0.23928975 0.006738957 215273_s_at -1.859147364 0.022642547 706 / 12428 MSPI0406S00164511 -0.488951908 0.007195122
NM_002961 S100A4 S100 calcium binding protein A4 chr1q21 0.235565688 0.007674362 203186_s_at -2.818347306 0.000408059 119 / 12428 MSPI0406S00056069 -0.610563916 0.000155242
NM_019094 NUDT4 /// NUDT4P1 nudix (nucleoside diphosphate linked moiety X)-type motif 4 /// nudix (nucleoside diphosphate linked moiety X)-type motif 4 pseudogene 1 chr12q21 /// chr1q21.1 0.235494506 0.007693309 212183_at -1.639240502 0.049945829 1143 / 12428 MSPI0406S00621954 -0.995405959 0.006698153
NM_006098 GNB2L1 guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 chr5q35.3 0.23014606 0.009240919 200651_at -1.323209017 0.04445142 1050 / 12428 MSPI0406S00303209 -0.288657878 0.005673837
NR_002212 NUDT4 /// NUDT4P1 nudix (nucleoside diphosphate linked moiety X)-type motif 4 /// nudix (nucleoside diphosphate linked moiety X)-type motif 4 pseudogene 1 chr12q21 /// chr1q21.1 0.224201274 0.011277417 212181_s_at -1.491584497 0.009756183 428 / 12428 MSPI0406S00621954 -0.995405959 0.006698153
NM_015550 OSBPL3 oxysterol binding protein-like 3 chr7p15 0.223157048 0.011673172 209627_s_at -1.833232331 0.001132207 177 / 12428 MSPI0406S00362414 -0.493288218 0.002992169
NM_001060 TBXA2R thromboxane A2 receptor chr19p13.3 0.213873947 0.015760617 336_at -2.000324591 2.10E-05 50 / 12428 MSPI0406S00863537 -0.226339922 0.028627389
NM_000901 NR3C2 nuclear receptor subfamily 3, group C, member 2 chr4q31.1 0.207038942 0.019517 205259_at -1.868819118 0.04973409 1140 / 12428 MSPI0406S00246208 -0.459957734 0.000810295
NM_004663 RAB11A RAB11A, member RAS oncogene family chr15q21.3-q22.31 0.194053224 0.028810421 200864_s_at -1.492532527 2.62E-05 55 / 12428 MSPI0406S00715744 -0.361483413 0.002744501
NM_001024 LOC100291837 /// RPS21 similar to ribosomal protein S21 /// ribosomal protein S21 chr20q13.3 0.193459747 0.029312677 200834_s_at -1.332193741 0.041256382 986 / 12428 MSPI0406S00937681 -0.449998124 0.003821809
NM_170672 RASGRP3 RAS guanyl releasing protein 3 (calcium and DAG-regulated) chr2p25.1-p24.1 0.19252598 0.030117979 205801_s_at -1.331870668 0.005034294 320 / 12428 MSPI0406S00102376 -0.214235194 0.000392282
NM_015041 CLUAP1 clusterin associated protein 1 chr16p13.3 0.189729255 0.032643183 204576_s_at -1.328754385 0.02281842 713 / 12428 MSPI0406S00737981 -0.553848045 0.000541729
NM_001127453 DFNA5 deafness, autosomal dominant 5 chr7p15 0.188815346 0.033506261 203695_s_at -2.696871245 0.000577921 132 / 12428 MSPI0406S00362336 -0.592198185 7.26E-05
NM_014240 LIMD1 LIM domains containing 1 chr3p21.3 0.183718675 0.038680813 218850_s_at -1.704365745 0.012628833 499 / 12428 MSPI0406S00175023 -1.089685446 0.004567718
NM_022551 RPS18 ribosomal protein S18 chr6p21.3 0.183285919 0.039149519 201049_s_at -1.335922108 0.010404819 448 / 12428 MSPI0406S00317147 -0.949755567 0.001390267
NM_001104586 ALS2CR8 amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8 chr2q33.2 0.182944439 0.039522723 219834_at -1.319547766 0.045878911 1067 / 12428 MSPI0406S00145619 -0.364033099 0.019013273
NM_001142401 CD164 CD164 molecule, sialomucin chr6q21 0.178022802 0.045241326 208405_s_at -1.378414172 0.0213837 678 / 12428 MSPI0406S00334219 -0.873485828 0.037566803