These data are a subset of subjects and CpG sites reported in the original paper where liver samples were assayed using the Illumina GoldenGate Methylation BeadArray Cancer Panel I. Technical replicate samples were removed to ensure all samples were independent. The matched cirrhotic samples from subjects with hepatocellular carcinoma (HCC, labeled Tumor) were also excluded. Therefore methylation levels in liver tissue are provided for independent subjects whose liver was Normal (N=20), cirrhotic but not having HCC (N=16, Cirrhosis non-HCC), and HCC (N=20, Tumor).
data(hccframe)A data frame with 56 observations on the following 46 variables.
groupan ordered factor with levels Normal < Cirrhosis non-HCC < Tumor
CDKN2B_seq_50_S294_Fa numeric vector representing a CpG site proportion methylation for CDKN2B
DDIT3_P1313_Ra numeric vector representing a CpG site proportion methylation for DDIT3
ERN1_P809_Ra numeric vector representing a CpG site proportion methylation for ERN1
GML_E144_Fa numeric vector representing a CpG site proportion methylation for GML
HDAC9_P137_Ra numeric vector representing a CpG site proportion methylation for HDAC9
HLA.DPA1_P205_Ra numeric vector representing a CpG site proportion methylation for HLA.DPA1
HOXB2_P488_Ra numeric vector representing a CpG site proportion methylation for HOXB2
IL16_P226_Fa numeric vector representing a CpG site proportion methylation for IL16
IL16_P93_Ra numeric vector representing a CpG site proportion methylation for IL16
IL8_P83_Fa numeric vector representing a CpG site proportion methylation for IL8
MPO_E302_Ra numeric vector representing a CpG site proportion methylation for MPO
MPO_P883_Ra numeric vector representing a CpG site proportion methylation for MPO
PADI4_P1158_Ra numeric vector representing a CpG site proportion methylation for PADI4
SOX17_P287_Ra numeric vector representing a CpG site proportion methylation for SOX17
TJP2_P518_Fa numeric vector representing a CpG site proportion methylation for TJP2
WRN_E57_Fa numeric vector representing a CpG site proportion methylation for WRN
CRIP1_P874_Ra numeric vector representing a CpG site proportion methylation for CRIP1
SLC22A3_P634_Fa numeric vector representing a CpG site proportion methylation for SLC22A3
CCNA1_P216_Fa numeric vector representing a CpG site proportion methylation for CCNA1
SEPT9_P374_Fa numeric vector representing a CpG site proportion methylation for SEPT9
ITGA2_E120_Fa numeric vector representing a CpG site proportion methylation for ITGA2
ITGA6_P718_Ra numeric vector representing a CpG site proportion methylation for ITGA6
HGF_P1293_Ra numeric vector representing a CpG site proportion methylation for HGF
DLG3_E340_Fa numeric vector representing a CpG site proportion methylation for DLG3
APP_E8_Fa numeric vector representing a CpG site proportion methylation for APP
SFTPB_P689_Ra numeric vector representing a CpG site proportion methylation for SFTPB
PENK_P447_Ra numeric vector representing a CpG site proportion methylation for PENK
COMT_E401_Fa numeric vector representing a CpG site proportion methylation for COMT
NOTCH1_E452_Ra numeric vector representing a CpG site proportion methylation for NOTCH1
EPHA8_P456_Ra numeric vector representing a CpG site proportion methylation for EPHA8
WT1_P853_Fa numeric vector representing a CpG site proportion methylation for WT1
KLK10_P268_Ra numeric vector representing a CpG site proportion methylation for KLK10
PCDH1_P264_Fa numeric vector representing a CpG site proportion methylation for PCDH1
TDGF1_P428_Ra numeric vector representing a CpG site proportion methylation for TDGF1
EFNB3_P442_Ra numeric vector representing a CpG site proportion methylation for EFNB3
MMP19_P306_Fa numeric vector representing a CpG site proportion methylation for MMP19
FGFR2_P460_Ra numeric vector representing a CpG site proportion methylation for FGFR2
RAF1_P330_Fa numeric vector representing a CpG site proportion methylation for RAF1
BMPR2_E435_Fa numeric vector representing a CpG site proportion methylation for BMPR2
GRB10_P496_Ra numeric vector representing a CpG site proportion methylation for GRB10
CTSH_P238_Fa numeric vector representing a CpG site proportion methylation for CTSH
SLC6A8_seq_28_S227_Fa numeric vector representing a CpG site proportion methylation for SLC6A8
PLXDC1_P236_Fa numeric vector representing a CpG site proportion methylation for PLXDC1
TFE3_P421_Fa numeric vector representing a CpG site proportion methylation for TFE3
TSG101_P139_Ra numeric vector representing a CpG site proportion methylation for TSG101
Archer KJ, Mas VR, Maluf DG, Fisher RA. High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. Molecular Genetics and Genomics, 283(4): 341-349, 2010.
See Also as ordinalgmifs