CL.methy: METHYLATION DATA OF 4 CELL LINES (CHR 7)

In DMRforPairs: DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

Description

This dataset provides the average methylation values on chromosomes 7 (33-35MG, 105-108MB) of two commercially available EBV transfected lymphoblastoid cell lines from healthy individuals (NA17105 (African American male) and NA17018 (Chinese female), Coriell Institute for Medical Research (NJ, USA)). The dataset also contains the breast cancer cell line MCF7 (Soule et al. 1973) and HPV negative squamous-cell vulva carcinoma cell line A431 (Giard et al. 1973 & Hietanen et al. 1995). Raw data is publically avaliable via the Illumina website and discussed in Bibikova et al. 2009 & 2011. Import and pre-processing was carried out using the LUMI package (Du et al. 2008) in R following the optimized "lumi: QN+BMIQ" pipeline (Marabita et al. 2013). This includes exclusion of poorly performing probes (p<0.01, n=713), color adjustment, quantile normalization and correction for probe type bias (Infinium I vs II) using the BMIQ algorithm (Teschendorf 2013).

Usage

CL.methy

Format

A data frame of 14 variables containing 711 observations. Variables: targetID (probe name), chromosome, position (bp), class.gene.related (functional class related to gene), class.island.related (functional class related to CpG island), gene.symbol, A431.M, MCF7.M, NA17105.M, NA17018.M, A431.beta, MCF7.beta, NA17105.beta, NA17018.beta

Source

Bibikova et al 2009 & 2011, download from Illumina website.

References

• Soule, H.D., et al., A human cell line from a pleural effusion derived from a breast carcinoma. J Natl Cancer Inst, 1973. 51(5): p. 1409-16.

• Giard, D.J., et al., In vitro cultivation of human tumors: establishment of cell lines derived from a series of solid tumors. J Natl Cancer Inst, 1973. 51(5): p. 1417-23.

• Hietanen, S., et al., Human papillomavirus in vulvar and vaginal carcinoma cell lines. Br J Cancer, 1995. 72(1): p. 134-9.

• Bibikova, M., et al., High density DNA methylation array with single CpG site resolution. Genomics, 2011. 98(4): p. 288-95.

• Bibikova, M., et al., Genome-wide DNA methylation profiling using Infinium(R) assay. Epigenomics, 2009. 1(1): p. 177-200.

• Du, P., W.A. Kibbe, and S.M. Lin, lumi: a pipeline for processing Illumina microarray. Bioinformatics, 2008. 24(13): p. 1547-8.

• Marabita, F., et al., An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform. Epigenetics, 2013. 8(3): p. 333-46.

• Teschendorff, A.E., et al., A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450k DNA methylation data. Bioinformatics, 2013. 29(2): p. 189-96.

DMRforPairs documentation built on Nov. 8, 2020, 4:52 p.m.