A Beta-mixture model for dimensionality reduction, sample classification and analysis

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Laurila, Kirsti ^a,b   Oster, Bodil ^c   Andersen, Claus L ^c   Lamy, Philippe ^b,c   Orntoft, Torben ^c   Yli Harja, Olli ^a   Wiuf, Carsten ^b  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^b AARHUS UNIVERSITY   (Denmark)

^c AARHUS UNIVERSITY HOSPITAL   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER TISSUES; COLON CANCER; DIMENSIONALITY REDUCTION; MICROARRAY DATA; NORMAL TISSUE; POSTERIOR PROBABILITY; SAMPLE CLASSIFICATION; TISSUE TYPES;

DISEASES; GENES; METHYLATION; MICROARRAYS; MIXTURES; PROBES; TISSUE;

ALKYLATION;

ALGORITHM; ARTICLE; COLON TUMOR; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; GENETIC ASSOCIATION; GENETICS; HUMAN; HUMAN GENOME; PRINCIPAL COMPONENT ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; COLONIC NEOPLASMS; CPG ISLANDS; DNA METHYLATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS;

EID: 79957516210     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-215     Document Type: Article

References (21)

1. Movassagh M, Choy MK, Goddard M, Bennett MR, Down TA, Foo RS. Differential DNA methylation correlates with differential expression of angiogenic factor in human heart failure. PLoS ONE 2010, 5:e8564. 10.1371/journal.pone.0008564, 2797324, 20084101.
2. Iwamoto K, Kato T. Epigenetic profiling in schizophrenia and major mental disorders. Neuropsychobiology 2009, 60:5-11. 10.1159/000234811, 19684418.
3. Menigatti M, Cattaneo E, Sabates-Bellver J, Ilinsky W, Went P, Buffoli F, Marquez VE, Jiricny J, Marra G. The protein tyrosine phosphatase receptor type R gene is an early and frequent target of silencing in human colorectal tumorigenesis. Mol Cancer 2009, 8:124. 10.1186/1476-4598-8-124, 2801661, 20015382.
4. Seidel C, Schagdarsurengin U, Blümke K, Würl P, Pfeifer GP, Hauptmann S, Taubert H, Dammann R. Frequent hypermethylation of MST1 and MST2 in soft tissue sarcoma. Mol Carcinog 2007, 46(10):865-871. 10.1002/mc.20317, 17538946.
5. Ibanez de Caceres I, Battagli C, Esteller M, Herman JG, Edelson MI, D E, Bergman C, Ehya H, Eisenberg BL, Cairns P. Tumor cell-specific BRCA1 and RASSF1A hypermethylation in serum, plasma, and peritoneal fluid from ovarian cancer patients. Cancer Res 2004, 64(18):6476-6481. 10.1158/0008-5472.CAN-04-1529, 15374957.
6. Kanai Y. Genome-wide DNA methylation profiles in precancerous conditions and cancers. Cancer Sci 2010, 101:36-45. 10.1111/j.1349-7006.2009.01383.x, 19891661.
7. Yang HJ, Liu VW, Wang Y, Tsang PC, Ngan HY. Differential DNA methylation profiles in gynecological cancers and correlation with clinico-pathological data. BMC Cancer 2006, 6:212. 10.1186/1471-2407-6-212, 1560388, 16928264.
8. Watts GS, Futscher BW, Holtan N, Degeest K, Domann FE, Rose SL. DNA methylation changes in ovarian cancer are cumulative with disease progression and identify tumor stage. BMC Med Genomics 2008, 1:47. 10.1186/1755-8794-1-47, 2566571, 18826610.
9. Meng H, Murrelle EL, Li G. Identification of a small optimal subset of CpG sites as bio-markes from high-throughput DNA methylation profiles. BMC Bioinformatics 2008, 9:457. 10.1186/1471-2105-9-457, 2613930, 18954440.
10. Sun S, Yan PS, Huang TH, Lin S. Identifying differentially methylated genes using mixed effect and generalized least square models. BMC Bioinformatics 2009, 10:404. 10.1186/1471-2105-10-404, 2800121, 20003206.
11. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Gayther SA, Apostolidou S, Jones A, Lechner M, Beck S, Jacobs IJ, Widschwendter M. An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One 2009, 4(12):e8274. 10.1371/journal.pone.0008274, 2793425, 20019873.
12. Houseman EA, Christensen BC, Yeh RF, Marsit CJ, Karagas MR, Wrensch M, Nelson HH, Wiemels J, Zheng S, Wiencke JK, Kelsey KT. Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. BMC Bioinformatics 2008, 9:365. 10.1186/1471-2105-9-365, 2553421, 18782434.
13. Lacey MR, Ehrlich M. Modeling dependence in methylation patterns with application to ovarian carcinomas. Stat Appl Genet Mol Biol 2009, 8:40.
14. Heijmans BT, Kremer D, Tobi EW, Boomsma DI, Slagboom PE. Heritable rather than age-related environmental and stochastic factors dominate variation in DNA methylation of the human IGF2/H19 locus. Human mol Genet 2007, 16(5):547-554.
15. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP. The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009, 41(2):178-186. 10.1038/ng.298, 2729128, 19151715.
16. Houshdaran S, Hawley S, Palmer C, Campan M, Olsen MN, Ventura AP, Knudsen BS, Drescher CW, Urban ND, Brown PO, Laird PW. DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines. PLoS One 2010, 5:e9359. 10.1371/journal.pone.0009359, 2825254, 20179752.
17. Rashid A, Shen L, Morris JS, Issa JP, Hamilton SR. CpG island methylation in colorectal adenomas. Am J Pathol 2001, 159(3):1129-1135. 10.1016/S0002-9440(10)61789-0, 1850474, 11549606.
18. Kim HC, Roh SA, Ga IH, Kim JS, Yu CS, Kim JC. CpG island methylation as an early event during adenoma progression in carcinogenesis of sporadic colorectal cancer. J Gastroenterol Hepatol 2005, 20(12):1920-1926. 10.1111/j.1440-1746.2005.03943.x, 16336454.
19. Dyrskjøt L, Thykjaer T, Kruhøffer M, Jensen JL, Marcussen N, Hamilton-Dutoit S, Wolf H, Orntoft TF. Identifying distinct classes of bladder carcinoma using microarrays. Nat Genet 2003, 33:90-96. 10.1038/ng1061, 12469123.
20. Broët P, Lewin A, Richardson S, Dalmasso C, Magdelenat H. A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments. Bioinformatics 2004, 20(16):2562-2571. 10.1093/bioinformatics/bth285, 15117756.
21. Mardia KV, Kent JT, Bibby JM. Multivariate analysis 1979, London: Academic Press Inc.