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PMID: 18947421 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Probe signal correction for differential methylation hybridization experiments.

BMC bioinformatics ·Vol. 9 ·2008-10-23 ·Pages 453

Potter DP, Yan P, Huang TH, Lin S

Abstract

Non-biological signal (or noise) has been the bane of microarray analysis. Hybridization effects related to probe-sequence composition and DNA dye-probe interactions have been observed in differential methylation hybridization (DMH) microarray experiments as well as other effects inherent to the DMH protocol. We suggest two models to correct for non-biologically relevant probe signal with an overarching focus on probe-sequence composition. The estimated effects are evaluated and the strengths of the models are considered in the context of DMH analyses. The majority of estimated parameters were statistically significant in all considered models. Model selection for signal correction is based on interpretation of the estimated values and their biological significance.

MeSH Terms
Base Sequence Breast Neoplasms/genetics,metabolism,pathology Carbocyanines/metabolism Cell Line, Tumor DNA Methylation DNA Probes Female Fluorescent Dyes/metabolism Gene Expression Profiling/methods Humans Methylation Models, Genetic Models, Statistical Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Sequence Analysis, DNA Signal Transduction
Chemicals
Carbocyanines DNA Probes Fluorescent Dyes cyanine dye 3
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Potter Dustin P
Human Cancer Genetics Program, OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA. potterdp@gmail.com
Yan Pearlly
Huang Tim H M
Lin Shili
References (16)
16 references, click to expand
  1. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.
    Nucleic Acids Res. 2002 Feb 15;30(4):e15 PMID: 11842121
  2. Cross-hybridization on PCR-spotted microarrays.
    IEEE Eng Med Biol Mag. 2002 Mar-Apr;21(2):71-5 PMID: 12012609
  3. The fundamental role of epigenetic events in cancer.
    Nat Rev Genet. 2002 Jun;3(6):415-28 PMID: 12042769
  4. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals.
    Nat Genet. 2003 Mar;33 Suppl:245-54 PMID: 12610534
  5. Normalization of cDNA microarray data.
    Methods. 2003 Dec;31(4):265-73 PMID: 14597310
  6. Gene silencing in cancer in association with promoter hypermethylation.
    N Engl J Med. 2003 Nov 20;349(21):2042-54 PMID: 14627790
  7. Spotting effect in microarray experiments.
    BMC Bioinformatics. 2004 May 19;5:63 PMID: 15151695
  8. The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide.
    Genome Res. 2004 Aug;14(8):1594-602 PMID: 15256511
  9. Sequence dependence of cross-hybridization on short oligo microarrays.
    Nucleic Acids Res. 2005 May 24;33(9):e84 PMID: 15914663
  10. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells.
    Nat Genet. 2005 Aug;37(8):853-62 PMID: 16007088
  11. Model-based analysis of tiling-arrays for ChIP-chip.
    Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12457-62 PMID: 16895995
  12. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.
    Cancer Cell. 2006 Dec;10(6):515-27 PMID: 17157791
  13. Model-based analysis of two-color arrays (MA2C).
    Genome Biol. 2007;8(8):R178 PMID: 17727723
  14. Epigenetics in cancer.
    N Engl J Med. 2008 Mar 13;358(11):1148-59 PMID: 18337604
  15. Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.
    Methods Mol Biol. 2009;507:89-106 PMID: 18987809
  16. Methylation profiling of CpG islands in human breast cancer cells.
    Hum Mol Genet. 1999 Mar;8(3):459-70 PMID: 9949205
Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-9-453
Email
potterdp@gmail.com
Published
2008-10-23
Epub
2008-00-23
Pages
453
Language
English
Region
England
NLM ID
100965194
PMCID
PMC2603337
Subset
IM
Grants
NCI NIH HHS · T32-CA106196-03 · United States
NCI NIH HHS · U54 CA113001-02 · United States
NCI NIH HHS · U54CA113001 · United States
NCI NIH HHS · T32 CA106196 · United States
NCI NIH HHS · U54 CA113001 · United States
External Links
PubMed source DOI: 10.1186/1471-2105-9-453 PMC Full Text View journal details
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