Abstract
DNA methylation is an epigenetic mechanism that cells use to control gene expression. DNA methylation has become one of the hottest topics in cancer research, especially for abnormally hypermethylated tumor suppressor genes or hypomethylaed oncogenes research. The analysis of DNA methylation data determines the differential hypermethlated or hypomethylated genes that are candidate to be cancer biomarkers. Visualization the DNA methylation status may lead to discover new relationships between hypomethylated and hypermethylated genes, therefore this paper applied a mathematical modelling theory called formal concept analysis for visualizing DNA methylation status.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Scott Poethig, R.: Life with 25,000 Genes. Genome Research 11, 313–316 (2001)
Bq, L., Huang, T., Liu, L., Cai, Y., Chou, K.: Identification of Colorectal Cancer Related Genes with mRMR and Shortest Path in Protein-Protein Interaction Network. PLoS One, vol 7, e33393 (2012)
Lynch, A.G., Dunning, M.J., Iddawela, M., Barbosa-Morais, N.L., Ritchie, M.E.: Considerations for the processing and analysis of GoldenGate-based two-colour illumina platforms. Statistical Methods in Medical Research 18, 437–452 (2009)
Florescu, A., Parrella, P., Fazio, V.M., Cojocaru, D.: Study of MIR- 200c and MIR-9 methylation on patients with breast cancer. Analele Stiintifice ale Universitatii Alexandru Ioan Cuza din Iasi Sec. II a. Genetica si Biologie Moleculara 13, 1–6 (2012)
Strachan, T., Read, A.P.: Human Molecular Genetics, 2nd edn. Wiley-LISS, New York (1999)
Smale, T., Kadonaga, T.: The RNA polymerase II core promoter. Annual Review of Biochemistry 72, 449–479 (2003)
Ganter, B., Wille, R.: Formal Concept Analysis, mathematical foundations, 1st edn. Springer (1999)
Kaytoue, M., Duplessis, S., Napoli, A.: Using Formal Concept Analysis for the Extraction of Groups of Co-expressed Genes. In: Modelling, Computation and Optimization in Information Systems and Management Sciences (MCO), vol. 14, pp. 439–449 (2008)
Bediaga, N., Acha, A., Guerra, I., Viguri, A., del Carmen Albaina, M., Ruiz, I., Rezola, R., Alberdi, M.J., Dopazo, J., Montaner, D., Renobales, M., Fernandez, A., John, F., Fraga, M., Li-loglou, T., de Pancorbo, M.M.: DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Research 12, R77 (2010)
Castellanos-Garzn, J.A., Garca, C.A., Novais, P., Daz, F.: A visual analytics frame-work for cluster analysis of DNA microarray data. Expert Systems with Applications 40, 758–774 (2013)
Yanagawa, M., Ikemot, K., Kawauchi, S., Furuya, T., Yamamoto, S., Oka, M., Oga, A., Nagashima, Y., Sasaki, K.: Luminal A and luminal B (HER2 negative) subtypes of breast cancer consist of a mixture of tumors with different genotype. BMC Research Notes 5, 376 (2012)
Goldhirsch, A., Wood, W.C., Coates, A.S., Gelber, R.D., Thrlimann, B., Senn, H.-J.: Strategies for subtypes-dealing with the diversity of breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer. Ann. Oncol. 22, 1736–1747 (2011)
Goldhirsch, A., Wood, W.C., Coates, A.S., Gelber, R.D., Thrlimann, B., Senn, H.-J.: Strategies for subtypes-dealing with the diversity of breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer. Ann. Oncol. 22, 1736–1747 (2011)
Gene Expression Omnibus, GEO, http://www.ncbi.nlm.nih.gov/geo/
Bediaga, N., Acha, A., Guerra, I., Viguri, A., del Carmen Albaina, M., Ruiz, I., Rezola, R., Alberdi, M.J., Dopazo, J., Montaner, D., Renobales, M., Fernandez, A., John, F., Fraga, M., Li-loglou, T., de Pancorbo, M.M.: DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Research 12, R77 (2010)
Amin, I.I., Kassim, S.K., Hassanien, A.E., Hefny, H.: Formal concept analysis for mining hypermethylated genes in breast cancer tumor subtypes. In: 12th International Conference on Intelligent Systems Design and Applications (ISDA), Kochi, India, pp. 764–769 (2012)
Amin, I.I., Kassim, S.K., Hassanien, A.E., Hefny, H.: Applying formal concept anal-ysis for visualizing DNA methylation status among breast cancer tumors subtypes. In: 9th International Computer Engineering (ICENCO 2013) Conference, Cairo, Egypt, pp. 37–42 (2013)
Amin, I.I., Kassim, S.K., Hassanien, A.E., Hefny, H.: Using formal concept analysis for mining hyomethylated genes among breast cancer tumors subtypes. In: IEEE International Conference on Advances in Computing, Communications and Informatics (ICACCI 2013), Mysore, India, pp. 521–526 (2013)
Gentleman, R., Carey, V., Huber, W., Hahne, F.: Genefilter: methods for filtering genes from microarray experiments (2006)
Slawski, M., Boulesteix, A.: GeneSelector: Stability and Aggregation of ranked gene lists (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer International Publishing Switzerland
About this paper
Cite this paper
Amin, I.I., Hassanien, A.E., Hefny, H.A., Kassim, S.K. (2014). Visualizing and Identifying the DNA Methylation Markers in Breast Cancer Tumor Subtypes. In: Kömer, P., Abraham, A., Snášel, V. (eds) Proceedings of the Fifth International Conference on Innovations in Bio-Inspired Computing and Applications IBICA 2014. Advances in Intelligent Systems and Computing, vol 303. Springer, Cham. https://doi.org/10.1007/978-3-319-08156-4_17
Download citation
DOI: https://doi.org/10.1007/978-3-319-08156-4_17
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-08155-7
Online ISBN: 978-3-319-08156-4
eBook Packages: EngineeringEngineering (R0)