COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses: Table 1.

Moretto, Marco; Sonego, Paolo; Dierckxsens, Nicolas; Brilli, Matteo; Bianco, Luca; Ledezma-Tejeida, Daniela; Gama-Castro, Socorro; Galardini, Marco; Romualdi, Chiara; Laukens, Kris; Collado‐Vides, Julio; Meysman, Pieter; Engelen, Kristof

doi:10.1093/nar/gkv1251

Cited by 65 publications

(90 citation statements)

References 13 publications

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“…Enriched molecular networks ( P < 0.05) were identified using VESPUCCI (http://vespucci.colombos.fmach.it) (Moretto et al . ) based on VitisNet annotation (Grimplet et al . ).…”

Section: Methodsmentioning

confidence: 99%

“…php; Du et al 2010). Enriched molecular networks (P < 0.05) were identified using VESPUCCI (http:// vespucci.colombos.fmach.it) (Moretto et al 2016) based on VitisNet annotation . The MapMan tool (Thimm et al 2004) was used to visualize DE genes in the context of biotic stress pathway using the GrapeGen 12Xv1 annotation version (Lijavetzky et al 2012) as MapMan bins.…”

Section: Rna Sequencing Data Processing and Data Analysismentioning

confidence: 99%

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Molecular analysis of the early interaction between the grapevine flower and Botrytis cinerea reveals that prompt activation of specific host pathways leads to fungus quiescence

Haile

Pilati

Sonego

et al. 2017

Plant Cell & Environment

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Grape quality and yield can be impaired by bunch rot, caused by the necrotrophic fungus Botrytis cinerea. Infection often occurs at flowering, and the pathogen stays quiescent until fruit maturity. Here, we report a molecular analysis of the early interaction between B. cinerea and Vitis vinifera flowers, using a controlled infection system, confocal microscopy and integrated transcriptomic and metabolic analysis of the host and the pathogen. Flowers from fruiting cuttings of the cultivar Pinot Noir were infected with green fluorescent protein (GFP)-labelled B. cinerea and studied at 24 and 96 hours post-inoculation (h.p.i.). We observed that penetration of the epidermis by B. cinerea coincided with increased expression of genes encoding cell-wall-degrading enzymes, phytotoxins and proteases. Grapevine responded with a rapid defence reaction involving 1193 genes associated with the accumulation of antimicrobial proteins, polyphenols, reactive oxygen species and cell wall reinforcement. At 96 h.p.i., the reaction appears largely diminished both in the host and in the pathogen. Our data indicate that the defence responses of the grapevine flower collectively are able to restrict invasive fungal growth into the underlying tissues, thereby forcing the fungus to enter quiescence until the conditions become more favourable to resume pathogenic development.

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“…Enriched molecular networks ( P < 0.05) were identified using VESPUCCI (http://vespucci.colombos.fmach.it) (Moretto et al . ) based on VitisNet annotation (Grimplet et al . ).…”

Section: Methodsmentioning

confidence: 99%

Section: Rna Sequencing Data Processing and Data Analysismentioning

confidence: 99%

Molecular analysis of the early interaction between the grapevine flower and Botrytis cinerea reveals that prompt activation of specific host pathways leads to fungus quiescence

Haile

Pilati

Sonego

et al. 2017

Plant Cell & Environment

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“…In order to extract regulatory interactions from expression data, diverse conditions must be profiled to discriminate between the effects of transcriptional regulators. Previous studies have compiled transcriptomics data from independent research groups to study the transcriptional states and regulation of E. coli [21][22][23][24] . Even after resolving the significant normalization challenge with such disparate datasets, many sources of variation remain that obscure biological signals [25][26][27] .…”

Section: Independent Component Analysis (Ica) Extracts Regulatory Sigmentioning

confidence: 99%

The Escherichia coli Transcriptome Mostly Consists of Independently Regulated Modules

Sastry

Gao

Szubin

et al. 2019

Preprint

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Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we applied unsupervised learning to a compendium of high-quality Escherichia coli RNA-seq datasets to identify 70 statistically independent signals that modulate the expression of specific gene sets. We show that 50 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals was validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provided: (1) a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations, (2) a guide to gene and regulator function discovery, and (3) a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation forms an underlying principle that describes the composition of a model prokaryotic transcriptome.

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“…The high amount of global gene expression data that is currently available offers opportunities to investigate the gene co-expression networks in many organisms. COLOMBOS is a database that integrates a collection of transcriptomics results from both microarray and RNA-seq experiments for several prokaryotic species, including Salmonella 39.…”

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confidence: 99%

In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD

Martínez-Flores

Pérez-Morales

Sánchez-Pérez

et al. 2016

Sci Rep

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A wide variety of Salmonella enterica serovars cause intestinal and systemic infections to humans and animals. Salmonella Patogenicity Island 1 (SPI-1) is a chromosomal region containing 39 genes that have crucial virulence roles. The AraC-like transcriptional regulator HilD, encoded in SPI-1, positively controls the expression of the SPI-1 genes, as well as of several other virulence genes located outside SPI-1. In this study, we applied a clustering method to the global gene expression data of S. enterica serovar Typhimurium from the COLOMBOS database; thus genes that show an expression pattern similar to that of SPI-1 genes were selected. This analysis revealed nine novel genes that are co-expressed with SPI-1, which are located in different chromosomal regions. Expression analyses and protein-DNA interaction assays showed regulation by HilD for six of these genes: gtgE, phoH, sinR, SL1263 (lpxR) and SL4247 were regulated directly, whereas SL1896 was regulated indirectly. Interestingly, phoH is an ancestral gene conserved in most of bacteria, whereas the other genes show characteristics of genes acquired by Salmonella. A role in virulence has been previously demonstrated for gtgE, lpxR and sinR. Our results further expand the regulon of HilD and thus identify novel possible Salmonella virulence genes.

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COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses: Table 1.

Cited by 65 publications

References 13 publications

Molecular analysis of the early interaction between the grapevine flower and Botrytis cinerea reveals that prompt activation of specific host pathways leads to fungus quiescence

Molecular analysis of the early interaction between the grapevine flower and Botrytis cinerea reveals that prompt activation of specific host pathways leads to fungus quiescence

The Escherichia coli Transcriptome Mostly Consists of Independently Regulated Modules

In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD

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