hccframe: Liver Cancer Methylation Data

In ordinalgmifs: Ordinal Regression for High-Dimensional Data

Liver Cancer Methylation Data

Description

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).

Usage

data(hccframe)

Format

A data frame with 56 observations on the following 46 variables.

group

an ordered factor with levels Normal < Cirrhosis non-HCC < Tumor

CDKN2B_seq_50_S294_F

a numeric vector representing a CpG site proportion methylation for CDKN2B

DDIT3_P1313_R

a numeric vector representing a CpG site proportion methylation for DDIT3

ERN1_P809_R

a numeric vector representing a CpG site proportion methylation for ERN1

GML_E144_F

a numeric vector representing a CpG site proportion methylation for GML

HDAC9_P137_R

a numeric vector representing a CpG site proportion methylation for HDAC9

HLA.DPA1_P205_R

a numeric vector representing a CpG site proportion methylation for HLA.DPA1

HOXB2_P488_R

a numeric vector representing a CpG site proportion methylation for HOXB2

IL16_P226_F

a numeric vector representing a CpG site proportion methylation for IL16

IL16_P93_R

a numeric vector representing a CpG site proportion methylation for IL16

IL8_P83_F

a numeric vector representing a CpG site proportion methylation for IL8

MPO_E302_R

a numeric vector representing a CpG site proportion methylation for MPO

MPO_P883_R

a numeric vector representing a CpG site proportion methylation for MPO

PADI4_P1158_R

a numeric vector representing a CpG site proportion methylation for PADI4

SOX17_P287_R

a numeric vector representing a CpG site proportion methylation for SOX17

TJP2_P518_F

a numeric vector representing a CpG site proportion methylation for TJP2

WRN_E57_F

a numeric vector representing a CpG site proportion methylation for WRN

CRIP1_P874_R

a numeric vector representing a CpG site proportion methylation for CRIP1

SLC22A3_P634_F

a numeric vector representing a CpG site proportion methylation for SLC22A3

CCNA1_P216_F

a numeric vector representing a CpG site proportion methylation for CCNA1

SEPT9_P374_F

a numeric vector representing a CpG site proportion methylation for SEPT9

ITGA2_E120_F

a numeric vector representing a CpG site proportion methylation for ITGA2

ITGA6_P718_R

a numeric vector representing a CpG site proportion methylation for ITGA6

HGF_P1293_R

a numeric vector representing a CpG site proportion methylation for HGF

DLG3_E340_F

a numeric vector representing a CpG site proportion methylation for DLG3

APP_E8_F

a numeric vector representing a CpG site proportion methylation for APP

SFTPB_P689_R

a numeric vector representing a CpG site proportion methylation for SFTPB

PENK_P447_R

a numeric vector representing a CpG site proportion methylation for PENK

COMT_E401_F

a numeric vector representing a CpG site proportion methylation for COMT

NOTCH1_E452_R

a numeric vector representing a CpG site proportion methylation for NOTCH1

EPHA8_P456_R

a numeric vector representing a CpG site proportion methylation for EPHA8

WT1_P853_F

a numeric vector representing a CpG site proportion methylation for WT1

KLK10_P268_R

a numeric vector representing a CpG site proportion methylation for KLK10

PCDH1_P264_F

a numeric vector representing a CpG site proportion methylation for PCDH1

TDGF1_P428_R

a numeric vector representing a CpG site proportion methylation for TDGF1

EFNB3_P442_R

a numeric vector representing a CpG site proportion methylation for EFNB3

MMP19_P306_F

a numeric vector representing a CpG site proportion methylation for MMP19

FGFR2_P460_R

a numeric vector representing a CpG site proportion methylation for FGFR2

RAF1_P330_F

a numeric vector representing a CpG site proportion methylation for RAF1

BMPR2_E435_F

a numeric vector representing a CpG site proportion methylation for BMPR2

GRB10_P496_R

a numeric vector representing a CpG site proportion methylation for GRB10

CTSH_P238_F

a numeric vector representing a CpG site proportion methylation for CTSH

SLC6A8_seq_28_S227_F

a numeric vector representing a CpG site proportion methylation for SLC6A8

PLXDC1_P236_F

a numeric vector representing a CpG site proportion methylation for PLXDC1

TFE3_P421_F

a numeric vector representing a CpG site proportion methylation for TFE3

TSG101_P139_R

a numeric vector representing a CpG site proportion methylation for TSG101

Source

The full dataset is available as GSE18081 from Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18081

References

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

See Also as ordinalgmifs

Examples

data(hccframe)

ordinalgmifs documentation built on May 31, 2023, 6:31 p.m.