Visualization of gene expression data from Chinese hamster ovary (CHO) cells
Date
2017
Authors
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Publisher
University of Delaware
Abstract
Recombinant therapeutic proteins have become one of the preferred treatments for many human diseases. CHO cell lines are the most frequently used mammalian cell system for the production of therapeutic proteins. With the increasing number of studies in CHO cells, understanding the basic information of CHO cells is essential to make further improvements in therapeutic protein production. As the genome sequence provides a basis for genetic engineering and transcriptomic data profiles gene expression information, a platform that allows scientists to quickly go through CHO cell genome and transcriptome information will be extremely helpful. Reference genome sequences and transcriptome annotation information of CHO cells can be visualized by JBrowse on CHOgenome.org, a publicly available website. However, currently no tool allows users to easily visualize gene expression levels under certain conditions from previous experiments. To build a tool for gene expression data visualization, custom Python scripts were created to load transcriptomic data from previous studies and generate new files in a JBrowse acceptable format, which enables the visualization of mRNA expression data in JBrowse. The tool made up by these Python scripts is named ‘ExpressGENiE’, and can process data either from RNA-Seq or DNA microarray experiments by choosing certain functions. Through the use of ‘ExpressGENiE’, new files that contain gene expression data are generated and can be visualized on the JBrowse instance available on CHOgenome.org. This now enables users to easily find the expression level of certain genes from publicly-available experiments.
Description
Keywords
Biological sciences, Applied sciences, Bioinformatics, CHO, DNA microarray, Data visualization, NGS data, RNA sequencing