Table 2.

Genes corresponding to cluster A–E in Fig. 4A showing hyper- (A, B, D) or hypomethylation (C, E) in relation to AR activity in bone metastases, and functionally enriched pathways according to MetaCore analysis of genes with inverse correlation between CpG methylation and gene expression

Cluster	Genes	Enriched pathways
A	ABCB9, ACOT11, ADAM28, ATHL1, AVIL, B3GNT5, BAALC, BATF, C14ORF173, C20ORF118, CCDC109B, CD300LF, CD38, CD5, CDC25B, CNPY4, CTLA4, E2F2, ENTPD3, FAM110B, GPR68, HCST, HEY1, HOXB4, HOXB5, HOXB6, INF2, KCNJ5, KIAA1274, KLHL2, KLK12, LIMS1, MAP1LC3A, MARCH3, MCOLN3, MDC1, MST1R, MXI1, NHS, NME2, NNT, NPL, OAS2, PARVB, PARVG, PAX6, PHF11, PIK3CD, PKM2, PLEKHO1, PPAP2C, PTGER1, RALA, RBM38, RBP1, ROD1, RPH3AL, RUNX2, SCNN1A, SCRN1, SDPR, SH2B3, SKA2, SLC43A3, SPC25, SPOCK2, SYK, TCF4, TCP11, TMEM105, TMEM176A, TNS3, TOX3, TRIM9, TYMS, UCHL1, WASPIP, VDR, VIM, YWHAH, ZBP1	Development: TGF-beta-dependent induction of EMT via RhoA, PI3K and ILK Cytoskeleton remodeling: Reverse signaling by Ephrin-B, Integrin outside-in signaling Immune response: IL-15 signaling via JAK-STAT cascade, KLRK1 (NKG2D) signaling pathway, IL-2 signaling via JAK/ STAT, Role of DAP12 receptors in NK cells CHDI_Correlations from discovery data causal network SHH signaling in colorectal cancer
B	ABP1, ACOT11, ACTB, ARHGEF2, BATF, C6ORF115, CCDC28B, CCR1, CD300LF, CD34, COL4A6, CX3CL1, ELF4, EMP1, EPHA2, FBXL10, FGR, FOXM1, GADD45A, GALE, GIMAP8, GMFG, HES6, HMGB3, HOXB3, HOXB4, HOXB6, IFI27, IL23A, IL2RB, IVNS1ABP, KLF13, KLHL6, LBX2, LRRN2, MAL, NCKAP1L, NDUFA4L2, NPAS2, NRM, NT5DC2, PAM, PARVG, PCK2, PIGR, PITX1, PPT2, RFXDC2, RNF34, SARDH, SDC1, SEL1L3, SERPINB1, SHANK3, SLC15A3, SLC35D3, SOX2, SPOCK2, STAT5A, SULT1A1, TAGLN2, TCF4, TIMP1, TMEM105, TMEM173, TOX3, TYROBP
D	AGPS, BTG1, CD93, CENPV, GNAI2, LRFN4, NCAPG, NCF4, PRR7, PTK6, SC65, SDC1, SGOL1, TAGLN2, TGIF2, TMEM37, TNFAIP8L1, TSPAN4, UCP2
C	ACSL3, BBS4, C10ORF81, CANT1, CREB3L4, CTDSP1, EHF, GREB1, MLPH, NDRG3, NEDD4L, NPAL3, NUP93, RPL37, SGMS1, STEAP2, SVIL	Recurrent gene fusions in prostate cancer Transcription targets of androgen receptor involved in prostate cancer Androgen receptor activation and downstream signaling in prostate cancer TMPRSS2-ERG fusion in prostate cancer G-protein signaling_G-protein alpha-i signaling cascades Signal transduction_mTORC1 downstream signaling
E	ATP6A, C19ORF48, CANT1, CLIP1, EHF, ELK4, GNL3, KIAA1244, NEDD4L, PEX11A, RAP1GAP, RGS10, SLC45A3, SPDF, STX19, SVIL, TMPRSS2, TRIM36, XPO6, ZNF280D