Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Improving gene set enrichment analysis (GSEA) by using regulation directionality

ABSTRACT: To infer the biological meaning from transcriptome data, it is useful to focus on genes that are regulated by the same regulator, i.e., regulons. Unfortunately, current gene set enrichment analysis (GSEA) tools do not consider whether a gene is activated or repressed by a regulator. This distinction is crucial when analyzing regulons since a regulator can work as an activator of certain genes and as a repressor of other genes, yet both sets of genes belong to the same regulon. Therefore, simply averaging expression differences of the genes of such a regulon will not properly reflect the activity of the regulator. What makes it more complicated is the fact that many genes are regulated by different transcription factors, and current transcriptome analysis tools are unable to indicate which regulator is most likely responsible for the observed expression difference of a gene. To address these challenges, we developed the gene set enrichment analysis program GINtool. Additional features of GINtool are novel graphical representations to facilitate the visualization of gene set analyses of transcriptome data, the possibility to include functional categories as gene sets for analysis, and the option to analyze expression differences within operons, which is useful when analyzing prokaryotic transcriptome and also proteome data.

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE208571 | GEO | 2022/09/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptomic comparison of Listeria monocytogenes and its derivative mutant strain with inactivated lmo0946 gene in exponential phase of growth

Project description:To gain comprehensive knowledge on role of Lmo0946 in physiology of L. monocytogenes, we set on analyzing whole-transcriptome changes induced by inactivation of lmo0946 gene. Remarkably, we identified for the first time a global effect of lmo0946 inactivation on transcriptome of L. monocytogenes with highly induced genes belonging to SOS regulon in absence of any environmental stress.

2023-08-05 | E-MTAB-10809 | biostudies-arrayexpress

Reconstruction of a Pan-regulon for Fur uncovers the conservation of its transcriptional regulation in E. coli

Project description:Regulons for many transcription factors have been elucidated in model strains leading to an understanding of their role in producing physiological states. Comparative analysis of a regulon and its target genes between different strains of the same species is lacking. Ferric uptake regulator (Fur), involved in iron homeostasis, is one of the most conserved TFs, and is present in a wide range of bacteria. Using ChIP-exo experiments, we performed a comprehensive study of Fur binding sites in nine Escherichia coli strains with different lifestyles. 79 of the 431 target genes (18%) found belong to Fur’s core regulon, comprising genes involved in ion transport and metabolism, energy production and conversion, and amino acid metabolism and transport. 179 of the target genes (42%) comprise the accessory regulon, most of which were related to cell wall structure and biogenesis, and virulence factor pathways. The remaining target genes (173 or 40%) were in the unique regulon, with gene functions that were largely unknown. Furthermore, deletion of the fur gene led to distinct phenotypes in growth, motility, antibiotic resistance, and siderophore production. These results provide a more complete understanding of how Fur regulates a set of target genes with surprising variation in closely related bacteria.

2023-08-04 | GSE150501 | GEO

The Fur Pan-regulon in E. coli shows diversity in strain-specific sets of target genes

2023-08-04 | GSE150240 | GEO

A post-transcriptional respiratome regulon in trypanosomes

Project description:Post-transcriptional regulons coordinate the expression of groups of genes in eukaryotic cells, yet relatively few have been characterised. Parasitic trypanosomatids are particularly good models for studies on such mechanisms because they exhibit almost exclusive polycistronic, and unregulated, transcription. Here, we identify the Trypanosoma brucei ZC3H39/40 RNA-binding proteins as regulators of the respiratome; the mitochondrial electron transport chain (complexes I-IV) and the FoF1-ATP synthase (complex V). A high-throughput RNAi screen initially implicated both ZC3H proteins in variant surface glycoprotein (VSG) gene silencing. This link was confirmed and both proteins were shown to form a cytoplasmic ZC3H39/40 complex. Transcriptome and mRNA-interactome analyses indicated that the impact on VSG silencing was indirect, while the ZC3H39/40 complex specifically bound and stabilised transcripts encoding respiratome-complexes. Quantitative proteomic analyses revealed specific positive control of respiratome protein abundance. Our findings establish a link between the mitochondrial respiratome and VSG gene silencing. They also reveal a major respiratome regulon controlled by the conserved trypanosomatid ZC3H39/40 RNA-binding proteins.

2019-11-13 | PXD012450 | Pride

Systems level analyses establish CodY as a multifaceted metabolic regulator integrating metabolism, motility and virulence in Listeria monocytogenes [ChIP-Seq]

Project description:To gain knowledge on L. monocytogenes differential CodY activity, we set on analyzing CodYâ??s regulon in L. monocytogenes in both rich and minimal growth conditions using genome wide sequencing techniques. Remarkably, we identified for the first time a global regulatory role for CodY when BCAAs are limited, that are similar to those within the mammalian niche. Furthermore, our data establish CodY as a central regulator that integrates metabolism, motility, stress responses and virulence in L. monocytogenes. Examination of CodY regulon in rich and minimal conditions.

2016-07-03 | E-GEOD-76821 | biostudies-arrayexpress

Expression data from WT (Ws-2), CBF1,2,3, and CBF2Δc (a truncated CBF2) overexpression

2015-02-28 | GSE55906 | GEO

Proteomic studies of Escherichia coli CFT073 and MG1655

Project description:Here we dissected a regulatory network directed by the conserved iron homeostasis regulator, Ferric Uptake Regulator (Fur), in uropathogenic E. coli strain CFT073. Comparing anaerobic genome-scale Fur DNA binding, with Fur dependent transcript expression and protein levels of the uropathogen to that of commensal E. coli K-12 strain MG1655, showed that the Fur regulon of the core genome is conserved but also includes genes within the pathogenicity/genetic islands. Unexpectedly, regulons indicative of amino acid limitation and the general stress response were also indirectly activated in the uropathogen fur mutant, suggesting that induction of the Fur regulon increases amino acid demand. Using RpoS levels as a proxy, addition of amino acids mitigated the stress. In addition, iron chelation increased RpoS to the same levels as in the fur mutant. The increased amino acid demand of the fur mutant or iron chelated cells was exacerbated by aerobic conditions, which could be partly explained by the O 2 -dependent synthesis of the siderophore aerobactin, encoded within a pathogenicity island. Taken together, this data suggest in the iron-poor environment of the urinary tract, amino acid availability could play a role in the proliferation of this uropathogen, particularly if there is sufficient O 2 to produce aerobactin.

2020-05-27 | PXD017582 | Pride

Hierarchical transcriptional regulation of quorum sensing genes in Vibrio harveyi

Project description:Quorum sensing controls hundreds of genes in vibrios required for cell density-specific behaviors, including bioluminescence, biofilm formation, competence, secretion, and motility. The central regulator in the quorum sensing pathway in vibrios is LuxR/HapR, which directly regulates >100 genes in the 625-gene regulon of Vibrio harveyi. Among these directly regulated genes are 15 transcription factors, which we predicted would comprise the second tier in the hierarchy of the quorum sensing regulon. To better study the mechanism of regulation of the quorum sensing network, we mapped all transcriptional start sites in V. harveyi using dRNA-seq. From these data, we determined the relative position of LuxR binding sites in the promoters of genes directly regulated by LuxR. We confirmed that LuxR directly binds to the promoters of the genes encoding transcription factors and quantified the extent of LuxR activation or repression of transcript levels. Finally, we determined the individual regulons for a subset of transcription factors that have not been previously studied. For regulators such as LysR- or AsnC/Lrp-type transcription factors, the regulons contained >100 genes that contained both unique and overlapping genes with the LuxR regulon. These data support a model in which LuxR directly regulates other transcription factors, which act to further alter the second tier of the gene expression cascade producing cell density behaviors in V. harveyi.

2020-05-15 | GSE144017 | GEO

Expression data from WT (Ws-2), CBF1,2,3, and CBF2M-NM-^Tc (a truncated CBF2) overexpression

Project description:CBF1, CBF2 and CBF3 regulons comprise nearly identical gene sets The vast majority of CBF2 regulon genes were down-regulated less that 50% by overexpression of CBF2M-NM-^Tc, a truncated version of CBF2 We used Affymetrix GeneChips to examine the CBF regulons of plants overexpressing CBF1, CBF2, CBF3 and a truncated version of CBF2, CBF2M-NM-^Tc.

2015-02-28 | E-GEOD-55906 | biostudies-arrayexpress

A transcriptome study of DSF-mediated quorum sensing in Xanthomonas axonopodis pv. citri

Project description:Quorum sensing (QS) in Xanthomonas axonopodis pv. citri, the causal agent of citrus canker, is mediated by a diffusible signal factor (DSF). QS is required for the full virulence of X. axonopodis pv. citri in planta. Mutations in rpfF, rpfC and rpfG, the core genes of QS, decreased the production of extracellular proteases and bacterial motility. Comparison of the transcriptomes of QS mutants with that of the wild type stain revealed that QS temporally regulates the expression of a large set of genes, including genes involved in chemotaxis and flagellar biosynthesis, genes related to metabolism, genes encoding virulence traits such as type II secretion system substates, type III secretion system and effectors. Cross talk between the QS regulon and the HrpG regulon has also been identified by 62 common genes shared by both regulons. The temporal regulation of the QS regulon and cross talk with the HrpG regulon suggest the important role of QS in citrus canker infection, including attachment, invasion and growth in host apoplast.

2012-04-27 | GSE29877 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data