Archives—December 2012

Grad Seminar MS Defense: Xiang Li

Poplar Gene Expression Data Analysis Pipeline

Thursday, December 13  4pm
Fisher 325

MS Defense:  Xiang Li
Advisor: Hairong Wei

Abstract: Analyzing large-scale gene expression data is tedious and time-consuming. To solve this problem, we develop a set of pipeline tools for rapid processing poplar gene expression data. In our pipeline tools, DEG pipeline is designed to identify biologically important genes that are differentially expressed under certain condition in multiple time points. Pathway analysis is designed to evaluate the expression of a set of genes catalyzing biological pathways. Domain pipeline evaluates the output from DEG pipeline. It is designed to figure out the enriched protein domains related to DEGs. GO pipeline also evaluates the output from DEG pipeline and attempts to figure out the enriched GO terms.

Our pipeline tools can analyze both microarray gene data and high-throughput gene data. These two types of data are obtained by two different technologies. A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. High throughput sequencing, also called as the next-generation sequencing, is a new technology to measure gene expression levels by sequencing MicroRNAs (miRNAs), and obtain each miRNA’s copy numbers in cells or tissues.

We also develop an on-line tool for the pipelines to facilitate users to analyze their data. Besides the analyses mentioned above, it can also perform GO hierarchy analysis, i.e. construct GO trees by taking a list of GO terms as input.