Abstract
The current DNA sequencing technologies and their high-throughput yield, allowed the thrive of genomic and transcriptomic experiments but it also have generated big data problem. Due to this exponential growth of sequencing data, also the complexity of managing, processing and interpreting it in order to generate results, has raised. Therefore, the demand of easy-to-use friendly software and websites to run bioinformatic tools is imminent. In particular, RNA-Seq and differential expression analysis have become a popular and useful method to evaluate the genetic expression change in any organism. However, many scientists struggle with the data analysis since most of the available tools are implemented in a UNIX-based environment. Therefore, we have developed the web server IDEAMEX (Integrative Differential Expression Analysis for Multiple EXperiments). The IDEAMEX pipeline needs a raw count table for as many desired replicates and conditions, allowing the user to select which conditions will be compared, instead of doing all-vs.-all comparisons. The whole process consists of three main steps (1) Data Analysis: that allows a preliminary analysis for quality control based on the data distribution per sample, using different types of graphs; (2) Differential expression: performs the differential expression analysis with or without batch effect error awareness, using the bioconductor packages, NOISeq, limma-Voom, DESeq2 and edgeR, and generate reports for each method; (3) Result integration: the obtained results the integrated results are reported using different graphical outputs such as correlograms, heatmaps, Venn diagrams and text lists. Our server allows an easy and friendly visualization for results, providing an easy interaction during the analysis process, as well as error tracking and debugging by providing output log files. The server is currently available and can be accessed at http://www.uusmb.unam.mx/ideamex/ where the documentation and example input files are provided. We consider that this web server can help other researchers with no previous bioinformatic knowledge, to perform their analyses in a simple manner.
Highlights
Transcriptomics experiments have been used widely to measure the RNA levels expressed in tissues or cells from practically any organism
We introduce the IDEAMEX web server (Integrative Differential Expression Analysis for Multiple EXperiments) that uses as input an RNA sequencing (RNA-Seq) raw count table in text format and generates results using bioconductor packages NOISeq, limma-voom, DESeq2 and edgeR
We demonstrate the functionality of IDEAMEX, using RNA-Seq data from a previous publication (Olvera et al, 2017) where the differential expression analysis in tilapia liver was performed, in addition to other datasets used as examples to test the website
Summary
Transcriptomics experiments have been used widely to measure the RNA levels expressed in tissues or cells from practically any organism. This approach has been used since the implementation of Northern blots hybridization analysis and was scaled up by the development of microarray technology. Transcriptomics has been improved with the aid of sequencing technologies which recently have been replacing microarrays by using RNA sequencing (RNA-Seq) experiments to evaluate gene expression at a genome-wide scale. Either microarrays or RNA-Seq technologies have generated a massive amount of data results that demands ad hoc methods to fully analyze and compare gene expression between different conditions, tissues or cell populations for a given organism. The differential expression analysis is probably the most important step that allows the user to interpret the biological information regarding the expression profiles of a given organism under different conditions
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