Award Date

8-1-2018

Degree Type

Thesis

Degree Name

Master of Science (MS)

Department

Life Sciences

First Committee Member

Mira Han

Second Committee Member

Martin Schiller

Third Committee Member

Philippos Tsourkas

Fourth Committee Member

Qing Wu

Number of Pages

103

Abstract

Despite the long-held assumption that transposons are normally only expressed in the germline, recently we discovered that full length or partial transcripts of LINE1 are frequently found in the somatic cells. However, the extent of variation in LINE1 levels across different tissues and different individuals, and the genes and pathways that are co-expressed with LINE1 are unknown. Co-expressed genes may be candidate genes that are functioning in transposon silencing. Here, we report the extent of variation in L1HS expression levels across cancer tissues and healthy tissues collected for The Cancer Genome Atlas (TCGA). L1HS is overexpressed in most of the cancer types we have studied. Our results confirm earlier reports of higher L1HS expression in the esophagus and stomach tissues. We also show that mitochondrial genes are enriched among the genes whose expression is negatively correlated with L1HS expression and that PHD fingers, bromodomains and KRAB-zinc fingers (KRAB-ZFPs) are enriched among the genes positively co-expressed with L1HS. Additionally, we studied the association of L1HS transcript level with miRNA expression, and we found several candidate miRNAs that are significantly correlated with L1HS expression

Disciplines

Bioinformatics | Biology

Language

English


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