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DMRforPairs: identifying differentially methylated regions between unique samples
using array based methylation profiles
#MMPMID24884391
Rijlaarsdam MA
; van der Zwan YG
; Dorssers LC
; Looijenga LH
BMC Bioinformatics
2014[May]; 15
(?): 141
PMID24884391
show ga
BACKGROUND: Array based methylation profiling is a cost-effective solution to
study the association between genome methylation and human disease & development.
Available tools to analyze the Illumina Infinium HumanMethylation450 BeadChip
focus on comparing methylation levels per locus. Other tools combine multiple
probes into a range, identifying differential methylated regions (DMRs). These
tools all require groups of samples to compare. However, comparison of unique,
individual samples is essential in situations where larger sample sizes are not
possible. RESULTS: DMRforPairs was designed to compare regional methylation
status between unique samples. It identifies probe dense genomic regions and
quantifies/tests their (difference in) methylation level between the samples. As
a proof of concept, DMRforPairs is applied to public data from four human cell
lines: two lymphoblastoid cell lines from healthy individuals and the cancer cell
lines A431 and MCF7 (including 2 technical replicates each). DMRforPairs
identified an increasing number of DMRs related to the sample phenotype when
biological similarity of the samples decreased. DMRs identified by DMRforPairs
were related to the biological origin of the cell lines. CONCLUSION: To our
knowledge, DMRforPairs is the first tool to identify and visualize relevant and
significant differentially methylated regions between unique samples.
free
free
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