DNA methylation microarray data analysis software tools

DNA methylation is involved in numerous physiological processes and also disease states, such as cancer (Jones, 2012). This has raised wide interest in developing large-scale DNA methylation profiling technologies to improve our molecular understanding of diseases. The recently released Infinium HumanMethylation450 (Bibikova et al., 2011; Dedeurwaerder et al., 2011) is a preferred technology for studying the DNA methylomes of various cell types in large-scale studies, and there is a current explosion of data generated with this technology (Rakyan et al., 2011). Sequencing-based methods, although offering much higher genome coverage, are still not affordable by all laboratories, notably those with moderate budgets. Another reason for the success of DNA methylation arrays is the ease of reading and understanding the data generated, notably because microarrays have been widely used over the past decades, particularly for gene expression profiling.

References:
(Jones, 2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet.
(Bibikova et al., 2011) High density DNA methylation array with single CpG site resolution. Genomics.
(Dedeurwaerder et al., 2011) Evaluation of the Infinium Methylation 450K technology. Epigenomics.
(Rakyan et al., 2011) Epigenome-wide association studies for common human diseases. Nat Rev Genet.

Source text:
(Dedeurwaerder et al., 2014) A comprehensive overview of Infinium HumanMethylation450 data processing. Brief Bioinform.

Data preprocessing

Data processing

Genome variant analysis

Data visualization

Enrichment analysis

Integrative analysis

Utilities