T-REx: Transcriptome analysis webserver for RNA-seq Expression data

BMC Genomics
Anne de JongJan Kok

Abstract

Transcriptomics analyses of bacteria (and other organisms) provide global as well as detailed information on gene expression levels and, consequently, on other processes in the cell. RNA sequencing (RNA-seq) has over the past few years become the most accurate method for global transcriptome measurements and for the identification of novel RNAs. This development has been accompanied by advances in the bioinformatics methods, tools and software packages that deal with the analysis of the large data sets resulting from RNA-seq efforts. Based on years of experience in analyzing transcriptome data, we developed a user-friendly webserver that performs the statistical analysis on the gene expression values generated by RNA-seq. It also provides the user with a whole range of data plots. We benchmarked our RNA-seq pipeline, T-REx, using a case study of CodY mutants of Bacillus subtilis and show that it could easily and automatically reproduce the statistical analysis of the cognate publication. Furthermore, by mining the correlation matrices, k-means clusters and heatmaps generated by T-REx we observed interesting gene-behavior and identified sub-groups in the CodY regulon. T-REx is a parameter-free statistical analysis pipeline for R...Continue Reading

References

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Citations

Jun 7, 2017·Environmental Microbiology Reports·Carlos Molina-SantiagoJuan L Ramos
Jan 29, 2017·Applied and Environmental Microbiology·Klara BojanovičKatherine S Long
Nov 21, 2018·Antimicrobial Agents and Chemotherapy·Erika van EijkWiep Klaas Smits
May 12, 2017·Molecular Systems Biology·Xue LiuJan-Willem Veening
Feb 2, 2020·Applied and Environmental Microbiology·Chenxi HuangJan Kok
Mar 25, 2017·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Han-Qin ZhengWen-Chi Chang
Jan 24, 2020·NPJ Biofilms and Microbiomes·Joaquín Caro-AstorgaDiego Romero
Jul 27, 2017·Frontiers in Microbiology·Sandra M CarvalhoLígia M Saraiva
Jan 15, 2021·NPJ Biofilms and Microbiomes·Joaquín Caro-AstorgaDiego Romero
Jun 15, 2021·Nucleic Acids Research·Ashley Mae ConardErica Larschan

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Methods Mentioned

BETA
RNA-seq
MDS

Software Mentioned

EdgeR
SAMtools
DEseq
Cytoscape
NGS
RockHopper
Trex
script
package EdgeR
REx

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