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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

From: A novel DNA methylation signature is associated with androgen receptor activity and patient prognosis in bone metastatic prostate cancer

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