Presentation Title

Understanding Distributions of Transposable Elements Relative to Gene Functions within the Gene Ontology Directed Acyclic Graph

Project Collaborators

Kristian Brevik (Graduate Student Mentor), Yolanda Chen (Faculty + Project Advisor)

Time

3:00 PM

Location

Silver Maple Ballroom - Biological Sciences

Abstract

Transposable elements (TEs) are short sequences of DNA within genomes, whose location and movement can directly influence the activity of neighboring genes. A mechanism called transposition allows TEs to excise from (and insert themselves onto) a host chromosome, thus disrupting the expression of target and downstream genes. Despite an understanding of this process, little is known about the relative abundance and distribution of TEs, and whether they cluster deterministically or randomly across a genome. Due to the multitude of hierarchical dependencies and connections within a genome, this has proven to be a difficult distinction to make. In order to test the relationship between TEs and groups of genes, we use the network structure of Gene Ontology (GO), which is the largest database curating the knowledge of gene functions. The GO is structured as a directed-acyclic graph (DAG), in which nodes denote specific GO terms, and the hierarchical connections between terms encode information about the dependencies and interactions among gene products. Although we use D. melanogaster as a prototypical species for this study, we discuss our approach for providing a standard analytical pipeline to better understanding the distribution and relative functions of TEs across differing species. In addition, we generate a tool for mapping TE distributions of a given species over the GO network, in order to apply this format broadly.

Primary Faculty Mentor Name

Yolanda Chen

Secondary Mentor NetID

pdodds

Graduate Student Mentors

Kristian Brevik

Status

Graduate

Student College

College of Engineering and Mathematical Sciences

Program/Major

Complex Systems

Primary Research Category

Biological Sciences

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Understanding Distributions of Transposable Elements Relative to Gene Functions within the Gene Ontology Directed Acyclic Graph

Transposable elements (TEs) are short sequences of DNA within genomes, whose location and movement can directly influence the activity of neighboring genes. A mechanism called transposition allows TEs to excise from (and insert themselves onto) a host chromosome, thus disrupting the expression of target and downstream genes. Despite an understanding of this process, little is known about the relative abundance and distribution of TEs, and whether they cluster deterministically or randomly across a genome. Due to the multitude of hierarchical dependencies and connections within a genome, this has proven to be a difficult distinction to make. In order to test the relationship between TEs and groups of genes, we use the network structure of Gene Ontology (GO), which is the largest database curating the knowledge of gene functions. The GO is structured as a directed-acyclic graph (DAG), in which nodes denote specific GO terms, and the hierarchical connections between terms encode information about the dependencies and interactions among gene products. Although we use D. melanogaster as a prototypical species for this study, we discuss our approach for providing a standard analytical pipeline to better understanding the distribution and relative functions of TEs across differing species. In addition, we generate a tool for mapping TE distributions of a given species over the GO network, in order to apply this format broadly.