Abstract
High-throughput technologies generate a tremendous amount of expression data on mRNA, miRNA and protein levels. Mining and visualizing the large amount of expression data requires sophisticated computational skills. An easy to use and user-friendly web-server for the visualization of gene expression profiles could greatly facilitate data exploration and hypothesis generation for biologists. Here, we curated and normalized the gene expression data on mRNA, miRNA and protein levels in 23,315, 9009 and 9244 samples, respectively, from 40 tissues (The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GETx)) and 1594 cell lines (Cancer Cell Line Encyclopedia (CCLE) and MD Anderson Cell Lines Project (MCLP)). Then, we constructed the Gene Expression Display Server (GEDS), a web-based tool for quantification, comparison and visualization of gene expression data. GEDS integrates multiscale expression data and provides multiple types of figures and tables to satisfy several kinds of user requirements. The comprehensive expression profiles plotted in the one-stop GEDS platform greatly facilitate experimental biologists utilizing big data for better experimental design and analysis. GEDS is freely available online.
Highlights
The quantification, comparison and visualization of gene expression from mRNA, miRNA and protein levels are key steps in making novel discoveries from different samples
These tools are exceptionally valuable and widely used, some additional quick analyses requested by experimental biologists are not adequately addressed by those existing tools; for example, choosing specific cell lines for further study according to preliminary results, analyzing gene expression from RNA level and protein level as well as phosphorylated protein
Expression Display Server (GEDS), a comprehensive resource for searching and visualizing tissues. Based on these required analyses, we developed the Gene Expression Display Server
Summary
The quantification, comparison and visualization of gene expression from mRNA, miRNA and protein levels are key steps in making novel discoveries from different samples. Genome Atlas (TCGA) [3] and Genotype-Tissue Expression (GTEx) [4] projects produced RNA-Seq and RPPA data for tens of thousands of tumorous and normal tissues GSCALite, cBioPortal and GEPIA mainly focus on the mRNA expression of human cancers and normal tissues These tools are exceptionally valuable and widely used, some additional quick analyses requested by experimental biologists are not adequately addressed by those existing tools; for example, choosing specific cell lines for further study according to preliminary results, analyzing gene expression from RNA level and protein level as well as phosphorylated protein. Expression Display Server (GEDS), a comprehensive resource for searching and visualizing tissues Based on these required analyses, we developed the Gene Expression Display Server Http://bioinfo.life.hust.edu.cn/web/GEDS/), a comprehensive resource for searching and visualizing expression data of genes, miRNAs and proteins to complement the existing tools
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