ArticleBMC genomics2015
T-REx: Transcriptome analysis webserver for RNA-seq Expression data.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- Transcriptome analysis and prediction of the metabolic state of stress-induced viable but non-culturable Bacillus subtilis cells.Scientific reports · 2022Article
- G-Quadruplex DNA as a Target in Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action.Journal of medicinal chemistry · 2022Article
- Second Messenger c-di-GMP Modulates Exopolysaccharide Pea-Dependent Phenotypes via Regulation ofApplied and environmental microbiology · 2022Article
- Adaptation of Bacillus thuringiensis to Plant Colonization Affects Differentiation and Toxicity.mSystems · 2021Article
- An Organogold Compound as Potential Antimicrobial Agent against Drug-Resistant Bacteria: Initial Mechanistic Insights.ChemMedChem · 2021Article
- TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.Nucleic acids research · 2021Article
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- Mechanism of Resistance Development inPharmaceuticals (Basel, Switzerland) · 2021Article
- Analyses of competent and non-competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence.Environmental microbiology · 2020Article
- Lysis of a Lactococcus lactis Dipeptidase Mutant and Rescue by Mutation in the Pleiotropic Regulator CodY.Applied and environmental microbiology · 2020Article
- Biofilm formation displays intrinsic offensive and defensive features ofNPJ biofilms and microbiomes · 2020Article
- Genome Location Dictates the Transcriptional Response to PolC Inhibition inAntimicrobial agents and chemotherapy · 2019Article
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- Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network.PloS one · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscriptomics 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.
resultsBased 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.
conclusionT-REx is a parameter-free statistical analysis pipeline for RNA-seq gene expression data that is dedicated for use by biologists and bioinformaticians alike. The tables and figures produced by T-REx are in most cases sufficient to accurately mine the statistical results. In addition to the stand-alone version, we offer a user-friendly webserver that only needs basic input ( http://genome2d.molgenrug.nl ).
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