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Table 1 GO function analysis of the DMGs in plasma cf-DNA in different stage of HCC development

From: Genome-wide methylation profiling of the different stages of hepatitis B virus-related hepatocellular carcinoma development in plasma cell-free DNA reveals potential biomarkers for early detection and high-risk monitoring of hepatocellular carcinoma

Stage Term Count % PValue Genes
Early GO:0007156 ~ homophilic cell adhesion 15 7.85 6.63E-11 PCDHGA1,PCDHGA2,PCDHA3,PCDHB5,PCDHA4,PCDHGA3,PCDHGA5,PCDHB12,PCDHB4,PCDHGB2,PCDHGA4,PCDHGB1,PCDH17,PCDHA5,PCDHA2
GO:0016337 ~ cell-cell adhesion 16 8.38 1.53E-07 PCDH17,PCDHA2,PCDHA3,PCDHA4,PCDHA5,PCDHB5,ICAM4,PCDHB4,PCDHB12,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1,PCDHGB1,PCDHGB2
GO:0007155 ~ cell adhesion 19 9.95 2.94E-04 PCDH17,PCDHA2,PCDHA3,PCDHA4,BCAR1,PCDHA5,PCDHB5,ICAM4,PCDHB4,PCDHB12,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1,PCDHGB1,LOXL2,PCDHGB2,TNXB
GO:0022610 ~ biological adhesion 19 9.95 2.99E-04 PCDH17,PCDHA2,PCDHA3,PCDHA4,BCAR1,PCDHA5,PCDHB5,ICAM4,PCDHB4,PCDHB12,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1,PCDHGB1,LOXL2,PCDHGB2,TNXB
GO:0007010 ~ cytoskeleton organization 14 7.33 5.53E-04 MACF1,CDC42BPG,PYY,BCAR1,TCHH,ACTA1,STMN1,GRID2IP,FSCN2,PRKCZ,CYTH2,NEFH,TNXB,SYNM
GO:0045761 ~ regulation of adenylate cyclase activity 6 3.14 3.08E-03 HTR1A,HTR7,GNAZ,GIPR,GABBR1,ADRB1
GO:0031279 ~ regulation of cyclase activity 6 3.14 3.52E-03 HTR1A,HTR7,GNAZ,GIPR,GABBR1,ADRB1
GO:0007268 ~ synaptic transmission 10 5.24 3.65E-03 HTR7,PCDHB5,PCDHB4,DLGAP2,KCNC4,GRIK4,LIN7B,MTNR1B,SLC1A6,KCNN3
GO:0030817 ~ regulation of cAMP biosynthetic process 6 3.14 3.84E-03 HTR1A,HTR7,GNAZ,GIPR,GABBR1,ADRB1
GO:0051339 ~ regulation of lyase activity 6 3.14 3.84E-03 HTR1A,HTR7,GNAZ,GIPR,GABBR1,ADRB1
Middle GO:0007156 ~ homophilic cell adhesion 7 3.35 2.95E-03 PCDH17,DCHS1,PKD1,PCDHGA3,PCDHGA2,PCDHGA1,PCDHGB1
GO:0019226 ~ transmission of nerve impulse 10 4.78 1.37E-02 KCNMB3,NPBWR1,OXT,VIPR1,CHAT,SPTBN4,EGR3,SLC12A5,SLC17A7
GO:0030574 ~ collagen catabolic process 3 1.44 1.94E-02 MMP11,MMP9,PRTN3
GO:0007628 ~ adult walking behavior 3 1.44 2.32E-02 TRH,SPTBN4,CHAT
GO:0010817 ~ regulation of hormone levels 6 2.87 2.39E-02 SHH,RBP1,DUOX1,FOXE1,SMPD3,ECE2
GO:0030900 ~ forebrain development 6 2.87 2.45E-02 ID4,LHX6,SHH,ZIC5,AVPR1A,FOXG1
GO:0042445 ~ hormone metabolic process 5 2.39 2.77E-02 SHH,RBP1,DUOX1,FOXE1,ECE2
GO:0007267 ~ cell-cell signaling 13 6.22 2.91E-02 Sep5,SLC17A7,SHH,TRH,EGR3,SMPD3,ECE2,SLC12A5,OXT,NPBWR1,VIPR1,TNFSF9,CHAT
GO:0016337 ~ cell-cell adhesion 8 3.83 3.01E-02 PCDHGA1,SCARF2,PKD1,PCDHGA3,DCHS1,PCDH17,PCDHGA2,PCDHGB1
GO:0051047 ~ positive regulation of secretion 5 2.39 3.03E-02 Sep5,TRH,OXT,SCAMP5,AVPR1A
Late GO:0007156 ~ homophilic cell adhesion 34 14.72 1.99E-33 PCDHGA5,PCDHGA12,PCDHA9,PCDHA10,PCDHA13,PCDHAC1,RET,PCDHGA6,PCDHGB7,PCDHGB6,PCDHA7,PCDHGB5,PCDHA5,PCDHGA1,PCDHGB2,PCDHA1,PCDHA4,PCDHB11,PCDH7,PCDHGA3,PCDHGA8,PCDHGA4,PCDHGA2,PCDHGB4,PCDHGA9,PCDHB16,PCDHGA10,PCDHA3,PCDHGA11,PCDHA11,PCDHGA7,PCDHGB1,PCDHA2,PCDHGB3,PCDHA6,PCDHA8,PCDH8,PCDHA12
GO:0016337 ~ cell-cell adhesion 37 16.02 9.80E-26 PCDHGA5,PCDHGA12,SCARF2,PCDHA9,PCDHA10,PCDHA13,PCDHAC1,RET,PCDHGA6,PCDHGB7,PCDHGB6,PCDHA7,PCDHGB5,PCDHA5,PCDHGA1,PCDHGB2,PCDHA1,PCDHA4,PCDHB11,PCDH7,PCDHGA3,PCDHGA8,PCDHGA4,PCDHGA2,PCDHGA9,PCDHGB4,PCDHB16,PCDHGA10,PCDHA3,PCDHGA11,PCDHA11,PCDHGA7,PCDHGB1,PCDHA2,PCDHGB3,CALCA,PCDHA6,PCDHA8,PCDH8,CLDN11,PCDHA12
GO:0007155 ~ cell adhesion 46 19.91 2.45E-19 PCDHGA5,ITGBL1,PCDHGA12,SCARF2,PCDHA9,PCDHA10,PCDHA13,PCDHAC1,RET,PCDHGA6,PCDHGB7,PCDHGB6,COL5A3,PCDHA7,PCDHGB5,PCDHA5,PCDHGA1,PCDHA1,PCDHA4,PCDHGB2,NLGN4X,PCDHB11,PCDH7,PCDHGA3,PODXL2,PCDHGA8,MAGI1,PCDHGA4,PCDHGA2,PCDHGA9,PCDHGB4,COL16A1,PCDHB16,ACHE,PCDHGA10,PCDHA3,GP5,PCDHGA11,PCDHA11,PCDHGA7,PCDHGB1,PCDHA2,PCDHGB3,COL18A1,CALCA,PCDHA6,PCDHA8,PCDH8,CLDN11,PCDHA12
GO:0022610 ~ biological adhesion 46 19.91 2.59E-19 PCDHGA5,ITGBL1,PCDHGA12,SCARF2,PCDHA9,PCDHA10,PCDHA13,PCDHAC1,RET,PCDHGA6,PCDHGB7,PCDHGB6,COL5A3,PCDHA7,PCDHGB5,PCDHA5,PCDHGA1,PCDHA1,PCDHA4,PCDHGB2,NLGN4X,PCDHB11,PCDH7,PCDHGA3,PODXL2,PCDHGA8,MAGI1,PCDHGA4,PCDHGA2,PCDHGA9,PCDHGB4,COL16A1,PCDHB16,ACHE,PCDHGA10,PCDHA3,GP5,PCDHGA11,PCDHA11,PCDHGA7,PCDHGB1,PCDHA2,PCDHGB3,COL18A1,CALCA,PCDHA6,PCDHA8,PCDH8,CLDN11,PCDHA12
GO:0003002 ~ regionalization 13 5.63 1.28E-05 PAX1,LHX1,TCF15,GATA4,TBX20,HOXC4,CYP26B1,TBX3,GBX2,PCDH8,MYF6,CYP26C1,HOXD4
GO:0007389 ~ pattern specification process 15 6.49 1.34E-05 PAX1,LHX1,TCF15,ZIC1,GATA4,TBX20,BCOR,HOXC4,CYP26B1,TBX3,GBX2,PCDH8,MYF6,CYP26C1,HOXD4
GO:0009952 ~ anterior/posterior pattern formation 11 4.76 1.75E-05 PAX1,HOXC4,LHX1,GBX2,TBX3,PCDH8,TCF15,MYF6,CYP26C1,HOXD4,GATA4
GO:0006355 ~ regulation of transcription, DNA-dependent 44 19.05 5.34E-05 PATZ1,PRDM16,PAX1,LHX1,SIM1,IRX2,ZNF148,TBX2,PHOX2B,FOXP4,TWIST2,CDKN2A,EVX2,ZNF808,LHX9,TLX1,FOXO3,FOXO3B,ELAVL2,VSX1,TBX3,GBX2,SPI1,BMP2,ISL2,IRX5,HOXD4,MEIS1,EBF3,TCF15,ZNF619,DMRT1,KCNH6,SOX1,TBX20,SOX7,ZNF560,GATA4,L3MBTL4,HOXC4,BCOR,RFX1,MYF6,TBX4,NPAS4
GO:0051252 ~ regulation of RNA metabolic process 44 19.05 9.00E-05 PATZ1,PRDM16,PAX1,LHX1,SIM1,IRX2,ZNF148,TBX2,PHOX2B,FOXP4,TWIST2,CDKN2A,EVX2,ZNF808,LHX9,TLX1,FOXO3,FOXO3B,ELAVL2,VSX1,TBX3,GBX2,SPI1,BMP2,ISL2,IRX5,HOXD4,MEIS1,EBF3,TCF15,ZNF619,DMRT1,KCNH6,SOX1,TBX20,SOX7,ZNF560,GATA4,L3MBTL4,HOXC4,BCOR,RFX1,MYF6,TBX4,NPAS4
GO:0045449 ~ regulation of transcription 55 23.81 3.16E-04 PRDM16,PAX1,SIM1,IRX2,TBX2,PHOX2B,FOXP4,ZNF808,TBX3,GBX2,SPI1,HOXD4,MEIS1,APBB2,PPP1R13L,TCF15,ARID3C,NRK,SOX1,TBX20,SOX7,CALCA,HIVEP3,TBX4,PATZ1,LHX1,ZNF148,ZNF703,TWIST2,CDKN2A,EVX2,FOXO3,FOXO3B,TLX1,LHX9,ELAVL2,VSX1,BMP2,ISL2,IRX5,EBF3,FERD3L,ZNF619,DMRT1,KCNH6,SCRT2,GATA4,ZNF560,L3MBTL4,BCOR,HOXC4,AMH,RFX1,INSM2,MYF6,NPAS4