Date of Award


Document Type


Degree Name

Master of Science (MS)

Legacy Department



Chen, Chin-Fu

Committee Member

Luo , Feng

Committee Member

Tomkins , Jeff

Committee Member

Cao , Weiguo


Aberrant DNA methylation in the genome is associated with human cancers. Tumor cells can undergo an overall loss of DNA methylation in non-coding repetitive regions (including the Alu elements) and at the same time maintain hypermethylation in the CpG islands in promoter region of multiple genes. We are interested in understanding the pattern of DNA methylation in the promoters of genes that may mediate the tumor genesis in colon cells. Recent literature survey suggested that about two dozens of genes, when mutated or undergone changes in DNA methylation, can directly promote the development of colon cancers. We downloaded the promoter sequences of these possible colon cancer causing genes from the Human Genome Browser for bioinformatics analysis and investigation of the sequence features on their Alu elements, transcription factor binding sites, and CpG islands. Our results suggest that sequence conservation of the flanking transcription factor binding sites plays an important role in protecting their flanking CpG islands from hypermethylation. In addition, colon cancer genes may harbor a lower density Alu element when compared to control random genes. We selected 4 characteristics of DNA sequences for machine learning and prediction of colon cancer genes.

Included in

Genetics Commons