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Table 1 Significant overlap and preserved modules in WGCNA of 3′UTR methylation and expression

From: Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia

Methylation module (size)

Expression module (size)

Overlap count (p value)

Z summary

Median rank

Functional annotation

Gene symbols

Magenta (79)

Turquoise (181)

20 (6.17E-05)

28

6

Regulation of Ras protein signal transduction

ABCC3,ALS2CL,ATG16L2,COG8,DNASE1,DOCK9,ESPL1,PDE4D,TMEM63C,TNFAIP2,TNFRSF4,TTLL1,UQCC1,ZNF385A

Red (101)

Grey60 (52)

9 (2.04E-03)

13

19

Cell division and chromosome partitioning/cytoskeleton

CHID1,FDXR,HERC2,HERC6,MYO9B,SEPT5,UBXN7

Yellow (165)

Turquoise (181)

28 (3.18E-03)

28

6

Kinases

ATG16L2,BMP1,C1orf159,CLUH,COL6A2,CRTC1,DAGLA,DNAH3,ENTHD2,EPHA10,FAM101B,FAM53A,GPR56,IGF1R,LAMC3,NLRP2,NR3C2,OPLAH,PITPNM2,PPP2R2B,PRKCA,PTPRK,RASGRF1,STK32C,THNSL2

Turquoise (284)

Blue (176)

41 (4.83E-03)

13

18

Signaling and apoptosis, cell cycle checkpoint

ACOXL,ANKH,ARHGEF18,B3GAT3,CCAR1,CCDC137,CKB,CREM,DDX39A,DFFB,DNAJB12,FAIM3,HUS1,ITPK1,KIAA0930,LRPAP1,MGRN1,MRPS24,NADK,NRARP,NUBPL,NUP155,OSBPL7,PHF14,PIP5K1A,PPFIA3,PSTPIP1,PTMA,RALBP1,RIN3,RPS6KB2,SH3BP2,SH3TC1,TP53I3,TRAF4,TRIB2,TSSC1,USP42

Brown (197)

Light green (49)

12 (5.48E-03)

9.8

9

Apoptosis/cell death

UEVLD,UNC13B,DTNB,BANP,IRF7,CCNL2,INTS9,FNTA,RBM19,DNASE1,GRB7

Midnightblue (45)

Turquoise (181)

10 (1.24E-02)

28

6

Ion binding

ABLIM2,ACE,COMMD1,ELFN2,GLT1D1,HAUS7,TOM1

Turquoise (284)

Midnight blue (55)

15 (2.11E-02)

12

2

Nucleotide binding

ADCY9,AGTRAP,BSDC1,INO80E,MCHR1,MTHFSD,NADK,P4HB,PDE8A,POR,RAB3A,RPS19BP1,SMUG1,SOX12,STX8