Probe signal correction for differential methylation hybridization experiments

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Potter, Dustin P ^a,b   Yan, Pearlly ^a,b   Huang, Tim H M ^a,b   Lin, Shili ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SIGNIFICANCE; ESTIMATED PARAMETER; HYBRIDIZATION EFFECTS; MICROARRAY ANALYSIS; MICROARRAY EXPERIMENTS; MODEL SELECTION; PROBE SIGNALS; SIGNAL CORRECTION;

ALKYLATION; EXPERIMENTS; METHYLATION;

PROBES;

ANALYTIC METHOD; ARTICLE; BINDING AFFINITY; BREAST CANCER; CANCER CELL CULTURE; CONTROLLED STUDY; DIFFERENTIAL METHYLATION HYBRIDIZATION; DNA HYBRIDIZATION; DNA METHYLATION; DNA MICROARRAY; DNA PROBE; FULL MODEL; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; QUADRATIC MODEL; SIGNAL DETECTION; SIGNAL PROCESSING; BIOLOGICAL MODEL; BREAST TUMOR; DNA SEQUENCE; FEMALE; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METHODOLOGY; METHYLATION; NUCLEIC ACID HYBRIDIZATION; PATHOLOGY; SIGNAL TRANSDUCTION; STATISTICAL MODEL; TUMOR CELL LINE;

CARBOCYANINE; CYANINE DYE 3; FLUORESCENT DYE;

BASE SEQUENCE; BREAST NEOPLASMS; CARBOCYANINES; CELL LINE, TUMOR; DNA METHYLATION; DNA PROBES; FEMALE; FLUORESCENT DYES; GENE EXPRESSION PROFILING; HUMANS; METHYLATION; MODELS, GENETIC; MODELS, STATISTICAL; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION;

EID: 56449116884     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-453     Document Type: Article

References (20)

1. Carbone M Gruberb J Wong M Modern Criteria to Identify Human Carcinogens Seminars in Cancer Biology 2004, 14(6):427-432. 15489135
2. Jones PA Bayline SB The fundamental role of epigenetic events in cancer Nature Review Cancer 2002, 3. 12042769
3. Esteller M Epigenetics in Cancer N Engl J Med 2008, 358(11):1148-1159. 18337604
4. Jaenisch R Bird A Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals Nature Genetics 2003, 33(Suppl 245):54. 12610534
5. Herman JG Baylin SB Gene Silencing in Cancer in Association with Promoter Hypermethylation N Engl J Med 2003, 349(21):2042-2054. 14627790
6. Weber M Davies JJ Wittig D Oakeley EJ Haase M Lam WL Schubeler D Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells National Genetics 2005, 37:853-862. 16007088
7. Mukhopadhyay R Yu W Whitehead J Xu J Lezcano M Pack S Kanduri C Kanduri M Ginjala V Vostrov A Quitschke W Chernukhin I Klenova E Lobanenkov V Ohlsson R The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide Genome Research 2004, 14:1594-1602. 509268 15256511
8. Wei SH Yip TTC Chen CM Huang THM Identifying Clinicopathological Association of DNA Hypermethylation in Cancers Using CpG Island Microarrays DNA Methylation and Cancer Therapy Springer US 2005, 107:116.
9. Yan PS Potter D Deatherage D Lin S Huang THM Differential Methylation Hybridization: Profiling DNA methylation in a high-density CpG island microarray Methods in Mol Biol, DNA Methylation Protocols 2, 2008.
10. Smyth GK Speed TP Normalization of cDNA microarray data Methods 2003, 31:265-273. 14597310
11. Yang YH Dudoit S Luu P Lin DM Peng V Nga J Speed TP Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 2002, 30.
12. Mary-Huard T Daudin JJ Robin S Bitton F Cabannes E Hilson P Spotting effect in microarray experiments BMC Bioinformatics 2004, 5:63. 434492 15151695
13. Wu C Carta R Zhang L Sequence dependence of cross-hybridization on short oligo microarrays Nucleic Acids Res 2005, 33:9. 15914663
14. Wren J Kulkarni A Joslin J Butow RA Garner HR Cross-Hybridization on PCR-Spotted Microarrays IEEE Engineering in Medicine and Biology 2002, 2:71-75.
15. Wu Z Irizarry RA Gentleman R Martinez-Murillo F Spencer F A Model-Based Background Adjustment for Oligonucleotide Expression Arrays Journal of the American Statistical Association 2004, 99(468):909-917.
16. Johnson WE Li W Meyer CA Gottardo R Carroll JS Brown M Liu XS Model-based analysis of tiling-arrays for ChIP-chip PNAS 2006, 103(33):12457-12462. 1567901 16895995
17. Neve RM Chin K Yeh JFJ Baehner FL Fevr T Clark L Bayani N Coppe JP Tong F Speed T Spellman PT DeVries S Lapuk A Wang NJ Kuo WL Stilwell JL Pinkel D Albertson DG Waldman FM McCormick F Dickson RB Johnson MD Lippman M Ethier S Gazdar A Gray JW A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes Cancer Cell 2006, 10:515-527. 17157791
18. Yang YH Dudoit S Luu P Speed T Normalization for cDNA microarray data Microarrays: Optical Technologies and Informatics Proceedings of SPIE Bittner ML, Chen Y, Dorsel AN, Dougherty ER 2001, 4266. 11842121
19. Song J Johnson WE Zhu X Zhang X Li W Manrai A Liu J Chen R Liu XS Model-based analysis of two-color arrays (MA2C) Genome Biology 2007, 8(8):R178. 2375008 17727723
20. Huang THM Perry M Laux D Methylation profiling of CpG islands in human breast cancer cells Hum Mol Genet 1999, 8(3):459-470. 9949205