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. 2012 Apr 6;7(4):e34513. doi: 10.1371/journal.pone.0034513

Table 2. CpG sites with differential methylation between acute lymphoblastic leukemia cells and remission cells.

Median β-value (range)
Gene symbola CpG site locationb Distance from TSSc ALL diagnosis Remission Median Δβ-valued N Δβ-value>0.3e Adjusted P-valuef mRNA expressiong
ACCS 11p11 44,044,910 477 0.58 (0.03–0.92) 0.18 (0.09–0.49) 0.41 12 4.30E-04 nc
ACY3 11q13 67,174,534 172 0.04 (0.02–0.69) 0.41 (0.18–0.67) −0.37 12 1.94E-04 +[16]
AMICA1 11q23.3 117,602,131 1,204 0.80 (0.03–0.94) 0.35 (0.07–0.57) 0.45 15 6.53E-04 −[16] [17]
CD300LF 17q25.2 70,220,061 642 0.67 (0.35–0.85) 0.18 (0.04–0.44) 0.49 15 1.48E-04 −[16] [17]
COL6A2 21q22.3 46,343,270 800 0.44 (0.07–0.94) 0.03 (0.02–0.18) 0.41 14 1.48E-04 nc
COL6A2 21q22.3 46,342,715 245 0.34 (0.02–0.92) 0.03 (0.02–0.05) 0.32 10 1.94E-04 nc
CPNE7 16q24.3 88,170,539 862 0.86 (0.28–0.95) 0.25 (0.12–0.67) 0.61 15 1.94E-04 nc
CR1 1q32 205,736,601 476 0.46 (0.19–0.75) 0.04 (0.02–0.24) 0.41 13 1.48E-04 −[17]
DBC1 * 9q32-q33 121,170,638 884 0.61 (0.06–0.93) 0.05 (0.03–0.13) 0.56 15 1.48E-04 −[16]
EYA4 6q23 133,605,061 855 0.70 (0.32–0.84) 0.10 (0.04–0.20) 0.60 19 1.48E-04 nc
EYA4 6q23 133,603,412 −794 0.42 (0.03–0.87) 0.04 (0.04–0.09) 0.37 12 6.53E-04 nc
FAM83A 8q24.13 124,263,705 −228 0.66 (0.25–0.82) 0.36 (0.17–0.57) 0.31 11 5.36E-04 nc
FXYD2 11q23 117,203,859 158 0.22 (0.03–0.51) 0.67 (0.56–0.76) −0.45 14 1.48E-04 +[16] [17]
FXYD2 11q23 117,203,745 272 0.20 (0.02–0.81) 0.75 (0.59–0.86) −0.55 16 3.93E-04 +[16] [17]
LGALS8 1q43 234,751,397 −1,963 0.89 (0.35–0.94) 0.49 (0.19–0.85) 0.39 10 5.36E-04 nc
MYBPC2 19q13.33 55,628,143 139 0.06 (0.02–0.88) 0.67 (0.57–0.78) −0.61 15 6.53E-04 +[16]
MYO3A 10p11.1 26,263,054 148 0.57 (0.05–0.90) 0.07 (0.03–0.22) 0.51 14 1.48E-04 nc
MYO3A 10p11.1 26,262,977 −225 0.38 (0.02–0.83) 0.04 (0.03–0.09) 0.34 12 2.70E-04 nc
PI16 6p21.31 37,029,477 −710 0.14 (0.03–0.64) 0.44 (0.29–0.59) −0.31 9 4.30E-04 nc
RUNDC3B * 7q21.12 87,096,478 813 0.45 (0.04–0.80) 0.07 (0.03–0.15) 0.38 13 4.30E-04 nc
RYR3 15q14-q15 31,390,843 374 0.39 (0.06–0.89) 0.07 (0.03–0.18) 0.33 10 1.48E-04 nc
SEC14L4 22q12.1 29,231,446 236 0.44 (0.02–0.72) 0.05 (0.02–0.23) 0.40 12 8.11E-04 −[17]
THSD7A 7p21.3 11,840,245 −1,902 0.83 (0.42–0.93) 0.45 (0.19–0.69) 0.39 12 1.48E-04 nc
TMEM2 9q13-q21 73,572,286 942 0.77 (0.04–0.89) 0.22 (0.06–0.49) 0.54 13 4.30E-04 −[16]
UQCRFS1 19q12 34,395,007 −947 0.66 (0.02–0.95) 0.14 (0.02–0.35) 0.51 15 4.30E-04 nc
WDR35 2p24.3 20,052,748 −617 0.76 (0.27–0.91) 0.10 (0.03–0.24) 0.66 17 1.48E-04 nc
ZNF462 9q31.3 108,663,645 −1,554 0.66 (0.05–0.90) 0.06 (0.05–0.26) 0.60 16 4.30E-04 nc
ZNF502 3p21.32 44,729,363 221 0.62 (0.11–0.93) 0.03 (0.02–0.22) 0.59 15 1.48E-04 nc
a

Gene symbol according to the HUGO Gene Nomenclature Committee (http://www.genenames.org/);

*

indicates genes selected from the literature;DBC1 [24]; RUNDC3B [25].

b

Chromosome number and coordinate of the CpG site (Human genome build 36).

c

Distance from the transcription start site (TSS); −, upstream from the TSS; +, downstream from the TSS.

d

Median difference in beta-value between ALL patients at diagnosis and remission for paired samples (ALL-remission).

e

Number of ALL-remission pairs with Δβ-values larger than 0.30.

f

Adjusted Wilcoxon Signed-Rank P-values corrected for multiple testing with the Benjamini Hochberg approach.

g

Genes up (+) or down (−) regulated in ALL cells compared to controls according to published datasets [16], [17], n.c. = no change.