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| Status |
Public on Sep 30, 2022 |
| Title |
GINtool: Transcriptome analysis using regulon, functional category, and operon information |
| Organism |
Bacillus subtilis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
When analysing transcriptome data, threshold values are chosen to decide whether the regulation of a gene is relevant or not, however this may result in the loss of valuable information. To overcome this problem it can be useful to analyse regulons instead of individual genes, to harness the statistical power of combining genes. Another advantage of a regulon-based analysis is that it provides direct insights into the activity of regulatory pathways, which is the essence of transcriptome analyses. We have developed a software tool called GINtool that can use regulon information to analyse transcriptome data. GINtool includes the option to take the activity mode of a regulator in account, which is important when a regulator can function both as an activator and repressor. GINtool also contains two novel graphical representations that greatly facilitate the visual inspection of regulon-based transcriptome analyses. Additional features of GINtool include the evaluation of transcriptome data using functional categories, and the analysis of gene expression differences within operons. To ease the analyses and downstream processing of figures, GINtool has been developed as an add-in for Excel.
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| Overall design |
To illustrate the use of GINtool, we used original RNA-seq data from a B. subtilis strain overexpressing the industrial-relevant xylanase XynA and compared this with RNA-seq data from a strain that does not express XynA. Data have been collected from two independent biological replicates.
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| Contributor(s) |
Wang B, van der Kloet F, Kes M, Luirink J, Hamoen LW |
| Citation(s) |
38294221 |
| Submission date |
Jul 19, 2022 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Biwen Wang |
| E-mail(s) |
B.wang@uva.nl
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| Organization name |
University of Amsterdam
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| Department |
Swammerdam Institute for Life Science
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| Lab |
Bacterial Cell Biology
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| Street address |
Work, Science Park 904,1098 XH,Amsterdam,The Netherlands
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| City |
Amsterdam |
| ZIP/Postal code |
1098 XH |
| Country |
Netherlands |
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| Platforms (1) |
| GPL28092 |
NextSeq 550 (Bacillus subtilis) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA860153 |
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