CellExpress: A comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system
Journal
Database
Journal Volume
2018
Journal Issue
2018
Date Issued
2018
Author(s)
Abstract
With the advancement of high-throughput technologies, gene expression profiles in cell lines and clinical samples are widely available in the public domain for research. However, a challenge arises when trying to perform a systematic and comprehensive analysis across independent datasets. To address this issue, we developed a web-based system, CellExpress, for analyzing the gene expression levels in more than 4000 cancer cell lines and clinical samples obtained from public datasets and user-submitted data. First, a normalization algorithm can be utilized to reduce the systematic biases across independent datasets. Next, a similarity assessment of gene expression profiles can be achieved through a dynamic dot plot, along with a distance matrix obtained from principal component analysis. Subsequently, differentially expressed genes can be visualized using hierarchical clustering. Several statistical tests and analytical algorithms are implemented in the system for dissecting gene expression changes based on the groupings defined by users. Lastly, users are able to upload their own microarray and/or next-generation sequencing data to perform a comparison of their gene expression patterns, which can help classify user data, such as stem cells, into different tissue types. In conclusion, CellExpress is a user-friendly tool that provides a comprehensive analysis of gene expression levels in both cell lines and clinical samples. The website is freely available at http://cellexpress.cgm.ntu.edu.tw/. Source code is available at https://github.com/LeeYiFang/Carkinos under the MIT License. ? The Author(s) 2018. Published by Oxford University Press.
Other Subjects
animal; DNA microarray; gene expression profiling; gene expression regulation; genetics; human; metabolism; neoplasm; nucleic acid database; tumor cell line; Animals; Cell Line, Tumor; Databases, Nucleic Acid; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Humans; Neoplasms; Oligonucleotide Array Sequence Analysis
Publisher
Oxford University Press
Type
journal article