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

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