On the analysis of the illumina 450k array data: Probes ambiguously mapped to the human genome

Frontiers in Genetics

Volumn 3, Issue MAY, 2012, Pages

  Zhang, Xu ^a   Mu, Wenbo ^b   Zhang, Wei ^c  

^a UNIVERSITY OF CHICAGO   (United States)

^b University of Illinois at Chicago   (United States)

^c UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84875491176     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00073     Document Type: Note

References (10)

1. Bell, J. T., Pai, A. A., Pickrell, J. K., Gaffney, D. J., Pique-Regi, R., Degner, J. F., Gilad, Y., and Pritchard, J. K. (2011). DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 12, R10.
2. Fraser, H. B., Lam, L. L., Neumann, S. M., and Kobor, M. S. (2012). Population-specificity of human DNA methylation. Genome Biol. 13, R8.
3. Kent, W. J. (2002). BLAT - the BLAST-like alignment tool. Genome Res. 12, 656-664.
4. Laird, P. W. (2010). Principles and challenges of genom-ewide DNA methylation analysis. Nat. Rev. Genet. 11, 191-203.
5. Langmead, B., and Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359.
6. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25.
7. Li, H., Ruan, J., and Durbin, R. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858.
8. Moen, L. E., Mu, W., Delaney, S., Wing, C., McQuade, J., Godley, L. A., Dolan, M. E., and Zhang, W. (2012). Differences in DNA methylation between the African and European HapMap populations. Proc. Am. Assoc. Cancer Res. 5010. [Abstract]
9. Philibert, R. A., Plume, J. M., Gibbons, E X., Brody, G. H., and Beach, S. R. (2012). The impact of recent alcohol use on genome wide DNA methylation signatures. Front. Genet. 3:54. doi: 10.3389/fgene.2012.00054
10. Sandoval, J., Heyn, H., Moran, S., Serra-Musach, J., Pujana, M. A., Bibikova, M., and Esteller, M. (2011). Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6, 692-70