Skip to Main Content
 

Global Search Box

 
 
 
 

Files

File List

Full text release has been delayed at the author's request until May 15, 2025

ETD Abstract Container

Abstract Header

A multi-cancer study of CpG island methylator phenotype and its complex set of mutational associations

Salyer, Owen G
http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1714142225218414

Abstract Details

2024, Bachelor of Science (BS), Ohio University, Computer Science.
CpG sites occur at an irregularly high frequency at regions of the genome called CpG islands; in normal samples, CpG islands are typically unmethylated. When a number of these CpG islands are instead hypermethylated in a cancer sample the sample is referred to as possessing CpG island methylator phenotype (CIMP). CIMP has been well-defined (and was first reported) in colorectal cancers, but research has also been performed on numerous cancer types such as gliomas, melanomas, and leukemia. The goal of the work presented here is to analyze the differences in gene mutation and expression between samples with CIMP (CIMP+) and samples without CIMP (CIMP-) across multiple cancer types. First we perform a coverage analysis to find the sets of genes and mutations which best correlate with CIMP+ samples while minimizing correlation with CIMP- samples. The cancer types used in these analyses are colorectal cancer (COADREAD), stomach cancer (STAD), and uterine corpus endometrial carcinoma (UCEC). The results from each tumor type are combined to create a synthesized set of mutations and mutated genes which correlate with CIMP+ samples. We then perform differential expression analysis on RNA-Seq data from The Cancer Genome Atlas (TCGA) to determine genes that are differentially expressed in CIMP+ samples when compared to CIMP- samples. We find 890 mutations and mutated genes with strong positive correlation to CIMP, many of which are also differentially expressed between CIMP+ and CIMP- samples. Among these mutated and differentially expressed genes are numerous genes in the MSigDB KRAS down-signaling gene set. This analysis furthers our understanding of CIMP and cancer in general and may give more insight into the differences between the genomic characteristics of CIMP-positive and CIMP-negative cancers.
Lonnie R. Welch (Advisor)
58 p.
Computer Science
computer science; bioinformatics; genomics; computational biology

Recommended Citations

Citations

  • Salyer, O. G. (2024). A multi-cancer study of CpG island methylator phenotype and its complex set of mutational associations [Undergraduate thesis, Ohio University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1714142225218414

    APA Style (7th edition)

  • Salyer, Owen. A multi-cancer study of CpG island methylator phenotype and its complex set of mutational associations. 2024. Ohio University, Undergraduate thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1714142225218414.

    MLA Style (8th edition)

  • Salyer, Owen. "A multi-cancer study of CpG island methylator phenotype and its complex set of mutational associations." Undergraduate thesis, Ohio University, 2024. http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1714142225218414

    Chicago Manual of Style (17th edition)

ouhonors1714142225218414
© 2024, all rights reserved.
This open access ETD is published by Ohio University Honors Tutorial College and OhioLINK.