Pattern cores and connectedness in cancer gene expression

Noha Yousri, Mohamed S. Kamell, Mohamed A. Ismail

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Citations (Scopus)

Abstract

The huge number of gene expressions resulting from a single microarray experiment, together with the large number of tumor samples, needs efficient methods that can extract hidden information and structure in such data sets. Clustering is a common analysis tool used to find groups of gene expression patterns. However, analysis of large clusters can be an infeasible task in large sets. In this work, a method is proposed to capture the main structure of the data by identifying core gene expressions. This reduces the data to only a subset of representatives used to grasp the main behavior of gene expression. When integrated with clustering, it becomes feasible to analyze clusters of large sizes, and to identify main expression patterns and relations between them. The importance of using a connected-based clustering is emphasized in order to reveal the gradual change between core gene expressions, something which cannot be achieved using traditional clustering algorithms. Analysis is done on breast cancer data to illustrate the significance of the proposed methodology.

Original languageEnglish
Title of host publicationProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Pages100-107
Number of pages8
DOIs
Publication statusPublished - 1 Dec 2007
Externally publishedYes
Event7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE - Boston, MA
Duration: 14 Jan 200717 Jan 2007

Other

Other7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
CityBoston, MA
Period14/1/0717/1/07

Fingerprint

Neoplasm Genes
Gene expression
Cluster Analysis
Gene Expression
Microarrays
Clustering algorithms
Tumors
Breast Neoplasms
Experiments
Neoplasms

Keywords

  • Clustering
  • Connected patterns
  • Density-based cores
  • Gene expression

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Bioengineering

Cite this

Yousri, N., Kamell, M. S., & Ismail, M. A. (2007). Pattern cores and connectedness in cancer gene expression. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE (pp. 100-107). [4375551] https://doi.org/10.1109/BIBE.2007.4375551

Pattern cores and connectedness in cancer gene expression. / Yousri, Noha; Kamell, Mohamed S.; Ismail, Mohamed A.

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. p. 100-107 4375551.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Yousri, N, Kamell, MS & Ismail, MA 2007, Pattern cores and connectedness in cancer gene expression. in Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE., 4375551, pp. 100-107, 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE, Boston, MA, 14/1/07. https://doi.org/10.1109/BIBE.2007.4375551
Yousri N, Kamell MS, Ismail MA. Pattern cores and connectedness in cancer gene expression. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. p. 100-107. 4375551 https://doi.org/10.1109/BIBE.2007.4375551
Yousri, Noha ; Kamell, Mohamed S. ; Ismail, Mohamed A. / Pattern cores and connectedness in cancer gene expression. Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. pp. 100-107
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