DNA co-methylation analysis suggests novel functional associations between gene pairs in breast cancer samples

Human Molecular Genetics

Volumn 22, Issue 15, 2013, Pages

  Akulenko, Ruslan ^a   Helms, Volkhard ^a  

^a SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST CANCER; CHROMOSOME; COMETHYLATION; CONTROLLED STUDY; DNA METHYLATION; FEMALE; GENE EXPRESSION; GENE LOCATION; GENETIC ASSOCIATION; GENETIC DISTANCE; HUMAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; BREAST TUMOR; EPIGENETICS; EPISTASIS; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; PROMOTER REGION;

BREAST NEOPLASMS; DNA METHYLATION; EPIGENOMICS; EPISTASIS, GENETIC; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HUMANS; PROMOTER REGIONS, GENETIC;

EID: 84880313808     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddt158     Document Type: Article

References (35)

1. Russo, V.E.A., Martienssen, R.A. and Riggs, A.D. (1996) Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory Press, Plainview, NY.
2. Bird, A. (2002) DNA methylation patterns and epigenetic memory. Genes Dev., 16, 6-21.
3. Kriaucionis, S. and Bird, A. (2003) DNA methylation and Rett syndrome. Hum. Mol. Genet., 12, R221-R227.
4. Ehrlich, M., Gama-Sosa, M.A., Huang, L.H., Midgett, R.M., Kuo, K.C., McCune, R.A. and Gehrke, C. (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucl. Acids Res., 10, 2709-2721.
5. Yoder, J.A., Walsh, C.P. and Bestor, T.H. (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet., 13, 335-340.
6. Chan, M.F., Liang, G. and Jones, P.A. (2000) Relationship between transcription and DNA methylation. Curr. Top. Microbiol. Immunol., 249, 75-86.
7. Reik, W. and Walter, J. (1998) Imprinting mechanisms in mammals. Curr. Opin. Genet. Dev., 8, 154-164.
8. Jones, P.A. and Baylin, S.B. (2002) The fundamental role of epigenetic events in cancer. Nat. Rev. Genet., 3, 415-428.
9. Laird, P.W. (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
10. Kulis, M. and Esteller, M. (2010) DNA methylation and cancer. Adv. Genet., 70, 27-56.
11. Koboldt, D.C., Fulton, R.S., McLellan, M.D., Schmidt, H., Kalicki-Veizer, J., McMichael, J.F., Fulton, L.L., Dooling, D.J., Ding, L., Mardis, E.R. et al. (2012) Comprehensive molecular portraits of human breast tumors. Nature, 490, 61-70.
12. Catteau, A. and Morris, J.R. (2002) BRCA1 methylation: a significant role in tumour development? Semin. Cancer Biol., 12, 359-371.
13. Holm, K., Hegardt, C., Staaf, J., Vallon-Christersson, J., Jonsson, G., Olsson, H., Borg, A. and Ringner, M. (2010) Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res., 12, R36.
14. Yang, X., Yan, L. and Davidson, N.E. (2001) DNA methylation in breast cancer. Endocr. Relat. Cancer, 8, 115-127.
15. Huang, Y., Nayak, S., Jankowitz, R., Davidson, N.E. and Oesterreich, S. (2011) Epigenetics in breast cancer: what's new? Breast Cancer Res., 13, 225.
16. Bock, C. and Lengauer, T. (2008) Computational epigenetics. Bioinformatics, 24, 1-10.
17. Barekati, Z., Radpour, R., Kohler, C., Zhang, B., Toniolo, P., Lenner, P., Lv, Q., Zheng, H. and Zhong, X.Y. (2010) Methylation profile of TP53 regulatory pathway and mtDNA alterations in breast cancer patients lacking TP53 mutations. Hum. Mol. Genet., 19, 2936-2946.
18. Horan, K., Jang, C., Bailey-Serres, J., Mittler, R., Shelton, C., Harper, J.F., Zhu, J.K., Cushman, J.C., Gollery, M. and Girke, T. (2008) Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol., 147, 41-57.
19. Azuaje, F.J., Wang, H., Zheng, H., Léonard, F., Rolland-Turner, M., Zhang, L., Devaux, Y. and Wagner, D.R. (2011) Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells. BMC Syst. Biol., 5, 46.
20. Xiao, X., Li, D., Gao, L., Li, X., Wang, Q., Zhang, S. and Liu, Z. (2012) Screening for cancer associated MiRNAs through co-gene, co-function and co-pathway analysis. Comput. Biol. Med., 42, 624-630.
21. Li, Y., Zhu, J., Tian, G., Li, N., Li, Q., Ye, M., Zheng, H., Yu, J., Wu, H., Sun, J. et al. (2010) The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol., 8, e1000533.
22. Tessema, M., Yingling, C.M., Grimes, M.J., Thomas, C.L., Liu, Y., Leng, S., Joste, N. and Belinsky, S.A. (2012) Differential epigenetic regulation of TOX subfamily high mobility group box genes in lung and breast cancers. PLoS One, 7, e34850.
23. Mosca, E., Alfieri, R., Merelli, I., Viti, F., Calabria, A. and Milanesi, L. (2010) A multilevel data integration resource for breast cancer study. BMC Syst. Biol., 4, 76.
24. Bock, C. (2012) Analysing and interpreting DNA methylation data. Nat. Rev. Genet., 13, 705-719.
25. Hansen, K.D., Timp, W., Bravo, H.C., Sabunciyan, S., Langmead, B., McDonald, O.G., Wen, B., Wu, H., Liu, Y., Diep, D. et al. (2011) Increased methylation variation in epigenetic domains across cancer types. Nat. Genet., 43, 768-775.
26. Bock, C., Beerman, I., Lien, W.H., Smith, Z.D., Gu, H., Boyle, P., Gnirke, A., Fuchs, E., Rossi, D.J. and Meissner, A. (2012) DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol. Cell, 47, 633-647.
27. Fiegl, H., Jones, A., Hauser-Kronberger, C., Hutarew, G., Reitsamer, R., Jones, R.L., Dowsett, M., Mueller-Holzner, E., Windbichler, G., Daxenbicher, G. et al. (2008) Methylated NEUROD1 promoter is a marker for chemosensitivity in breast cancer. Clin. Cancer Res., 14, 3494-3502.
28. Golmoghaddam, H., Pezeshki, A.M., Ghaderi, A. and Doroudchi, M. (2011) CD1a and CD1d genes polymorphisms in breast, colorectal and lung cancers. Pathol. Oncol. Res., 17, 669-675.
29. La Rocca, G., Anzalone, R., Corrao, S., Magno, F., Rappa, F., Marasa, S., Czarnecka, A.M., Marasa, L., Sergi, C., Zummo, G. et al. (2008) CD1a down-regulation in primary invasive ductal breast carcinoma may predict regional lymph node invasion and patient outcome. Histopathology, 52, 203-212.
30. Krupp, M., Maass, T., Marquardt, J.U., Staib, F., Bauer, T., König, R., Biesterfeld, S., Galle, P.R., Tresch, A. and Teufel, A. (2011) The functional cancer map: a systems-level synopsis of genetic deregulation in cancer. BMC Med. Genomics, 4, 53.
31. Schlicker, A. and Albrecht, M. (2008) FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res., 36, D434-D439.
32. Resnik, P. (1999) Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language. J. Artif. Intell. Res., 11, 95-130.
33. Lin, D. (1998) An information-theoretic definition of similarity. In Proceedings of the 15th International Conference on Machine Learning, Madison, WI, 296-304.
34. Schlicker, A., Domingues, F.S., Rahnenführer, J. and Lengauer, T. (2006) A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics, 7, 302.
35. Huang, D.W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat. Protoc., 4, 44-57.