Gene Expression: edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test

Dimont, Emmanuel; Shi, Jiantao; Kirchner, Rory; Hide, Winston

doi:10.1101/008409

Cited by 12 publications

(14 citation statements)

References 12 publications

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“…The number of reads aligned to each predicted transcript or intron was calculated by FeatureCounts (Liao et al ., ). Differential expression analysis of genes was performed with R package edgeRun (Dimont et al ., ) with the Benjamini and Hochberg's algorithm to control the false discovery rate (FDR). Genes with a FDR below 0.05 and log 2 fold‐change at least 1 were considered to be differently expressed genes.…”

Section: Methodsmentioning

confidence: 99%

The FgSRP1 SR‐protein gene is important for plant infection and pre‐mRNA processing in Fusarium graminearum

Zhang

Gao

Sun

et al. 2017

Environmental Microbiology

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The versatile functions of SR (serine/arginine-rich) proteins in pre-mRNA splicing and processing are modulated by reversible phosphorylation. Previous studies showed that FgPrp4, the only protein kinase among spliceosome components, is important for intron splicing and the FgSrp1 SR protein is phosphorylated at five conserved sites in Fusarium graminearum. In this study, we showed that the Fgsrp1 deletion mutant rarely produced conidia and caused only limited symptoms on wheat heads and corn silks. Deletion of FgSRP1 also reduced ascospore ejection and deoxynivalenol (DON) production. Interestingly, FgSRP1 had two transcript isoforms due to alternative splicing and both of them were required for its normal functions in growth and DON biosynthesis. FgSrp1 localized to the nucleus and interacted with FgPrp4 in vivo. Deletion of all four conserved phosphorylation sites but not individual ones affected the FgSRP1 function, suggesting their overlapping functions. RNA-seq analysis showed that the expression of over thousands of genes and splicing efficiency in over 140 introns were affected. Taken together, FgSRP1 is important for conidiation, and pathogenesis and alternative splicing is important for its normal functions. The FgSrp1 SR protein is likely important for pre-mRNA processing or splicing of various genes in different developmental and infection processes.

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Section: Methodsmentioning

confidence: 99%

The FgSRP1 SR‐protein gene is important for plant infection and pre‐mRNA processing in Fusarium graminearum

Zhang

Gao

Sun

et al. 2017

Environmental Microbiology

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“…We investigated differential transcript abundances between treatments and controls with the EdgeR statistical package (Dimont et al, 2015). Metatranscriptomic responses to ADOC.…”

Section: Changes In Bacterioplankton Community Compositionmentioning

confidence: 99%

“…Metatranscriptomic responses to ADOC. We investigated differential transcript abundances between treatments and controls with the EdgeR statistical package (Dimont et al, 2015). As many as 4450 genes for the Arctic experiment and 2444 genes for Antarctica (728 transcripts in common) were significantly differentially expressed between treatment and control after 24 h of ADOC exposure.…”

Section: Changes In Bacterioplankton Community Compositionmentioning

confidence: 99%

Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters

Cerro‐Gálvez

Casal

Lundin

et al. 2019

Environmental Microbiology

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Summary Thousands of semi‐volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny‐Ålesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.

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“…Raw data were mapped to the human genome [30] using Bowtie2 2.2.6 [31]. Expression levels were evaluated using RSEM v1.2.25 [32] and differential expression between control samples and treated samples was performed using the edgeRun package [33]. Gene and transcript annotation used in the analysis correspond to Gencode v23, and molecular functions and assignations to the Gene Ontology Consortium [34] were performed with the Blast2 GO program [35].…”

Section: Transcriptomicsmentioning

confidence: 99%

Biological Activity of Polynesian Calophyllum inophyllum Oil Extract on Human Skin Cells

et al. 2016

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Oil from the nuts of Calophyllum inophyllum, locally called "Tamanu oil" in French Polynesia, was traditionally used for wound healing and to cure various skin problems and ailments. The skin-active effect of "Tamanu oil emulsion" was investigated on human skin cells (keratinocytes and dermal fibroblasts) and showed cell proliferation, glycosaminoglycan and collagen production, and wound healing activity. Transcriptomic analysis of the treated cells revealed gene expression modulation including genes involved in the metabolic process implied in O-glycan biosynthesis, cell adhesion, and cell proliferation. The presence of neoflavonoids as bioactive constituents in Tamanu oil emulsion may contribute to these biological activities. Altogether, consistent data related to targeted histological and cellular functions brought new highlights on the mechanisms involved in these biological processes induced by Tamanu oil effects in skin cells.

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Gene Expression: edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test

Cited by 12 publications

References 12 publications

The FgSRP1 SR‐protein gene is important for plant infection and pre‐mRNA processing in Fusarium graminearum

The FgSRP1 SR‐protein gene is important for plant infection and pre‐mRNA processing in Fusarium graminearum

Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters

Biological Activity of Polynesian Calophyllum inophyllum Oil Extract on Human Skin Cells

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