Celiac_data: NFkB-related genes in celiac disease

In lb664/MethylCal: MethylCal: Bayesian Calibration of Methylation Levels

Description

Dataset containing human genomic control DNA measured at eight distinct actual methylation percentages (0%, 12.5%, 25%, 37.5%, 50%, 62.5%, 87.5% and 100%) obtained by mixing different ratios of unmethylated and fully methylated human control DNA, 13 controls (C), 17 celiac patients at the time of diagnosis (D) and the same patients after two years of treatment with a gluten-free diet (T). The patient data was pyrosequenced in three runs.

Usage

data(Celiac_data)

Format

A data frame consisting of eight NFkB-related genes (MAP3K7, TNFAIP3, RELA, NFKBIA, TRADD, MAP3K14, MALT1 and MAP3K7IP1/TAB1) containing 35 CpG positions and 58 variables:

Target

character: DMR/CpG island name

Chrom

integer: Chromosome

CpG_pos

integer: CpG position

0.0%, 12.5%, 25.0%, 37.5%, 50.0%, 62.5%, 87.5%, 100.0%

numeric: Actual Methylation Percentages (AMPs)

10C, 11C, 12C, 13C, 01C, 02C, 03C, 04C, 05C, 06C, 07C, 08C, 09C

numeric: Healthy controls

10D, 11D, 12D, 13D, 14D, 15D, 16D, 17D, 01D, 02D, 03D, 04D, 05D, 06D, 07D, 08D, 09D

numeric: Celiac patients at the time of diagnosis

10T, 11T, 12T, 13T, 14T, 15T, 16T, 17T, 01T, 02T, 03T, 04T, 05T, 06T, 07T, 08T, 09T

numeric: Same patients after two years of treatment with a gluten-free diet

References

Fernandez-Jimenez N, Castellanos-Rubio A, Plaza-Izurieta L, Irastorza I, Elcoroaristizabal X, Jauregi-Miguel A, Jauregi-Miguel A, Lopez-Euba T, Tutau C, de Pancorbo MM, Vitoria JC, Ramon Bilbao J. Coregulation and modulation of NFkB-related genes in celiac disease: uncovered aspects of gut mucosal inflammation. Hum Mol Genet. 2014; 23(5):1298-1310. (PMC)

Fernandez-Jimenez N, Plaza-Izurieta L, Lopez-Euba T, Jauregi-Miguel A, Ramon Bilbao J. Cubic regression-based degree of correction predicts the performance of whole bisulfitome amplified DNA methylation analysis. Epigenetics. 2012; 7(12):1349-54. (PubMed)

Examples

data(Celiac_data)
head(Celiac_data)

lb664/MethylCal documentation built on May 23, 2019, 4:02 a.m.