The Significance of Digital Gene Expression Profiles

Audic, Stéphane; Claverie, Jean‐Michel

doi:10.1101/gr.7.10.986

Cited by 2,600 publications

(2,158 citation statements)

References 30 publications

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“…RNA‐Seq data were mapped to the T. urticae genome (version 200909) (http://bioinformatics.psb.ugent.be/orcae/overview/Tetur) using the Torrent Mapping Alignment Program v3.4.1 (ThermoFisher Scientific, Grand Island, NY, USA) to obtain Reads Per Kb per Million reads (RPKM), and the differential gene expression analysis to identify differentially expressed genes (DEGs) between two different DGE libraries was conducted using the method described by Audic and Claverie (Audic & Claverie, 1997). The false discovery rate (FDR) method determines the p ‐value threshold for multiple testing by controlling the FDR value.…”

Section: Methodsmentioning

confidence: 99%

Adaptation of acaricide stress facilitates Tetranychus urticae expanding against Tetranychus cinnabarinus in China

Wang

et al. 2017

Ecology and Evolution

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The two‐spotted spider mite, Tetranychus urticae, and the carmine spider mite, Tetranychus cinnabarinus, are invasive and native species in China, respectively. Compared with T. cinnabarinus, T. urticae has expanded into most parts of China and has become the dominant species of spider mite since 1983, when it was first reported in China. However, the mechanism of the demographic conversion has not been illuminated. In this study, one T. urticae field population and one T. cinnabarinus field population were isolated from the same plant in the same field, and the toxicological characteristics were compared between these two species. Laboratory bioassays demonstrated that T. urticae was more tolerant to commonly used acaricides than T. cinnabarinus. The activities of detoxification enzymes were significantly greater in T. urticae, and the fold changes of enzymes activities in T. urticae were also greater following exposure to acaricides. Furthermore, more metabolism‐related genes were upregulated at a basal level, and more genes were induced in T. urticae following exposure to acaricides. The comparison of proteins and genes between both species led credence to the hypothesis that T. urticae was more resistant to acaricides, which was the reason explaining the expansion of invasive T. urticae against native T. cinnabarinus. Laboratory simulation experiments demonstrated that following the application of acaricides, the composition of a mixed T. urticae/T. cinnabarinus population would change from a T. cinnabarinus‐dominant to a T. urticae‐dominant population. This study not only reveals that T. urticae possesses stronger detoxification capacity than its sibling species T. cinnabarinus, which facilitated its persistent expansion in China, but also points to the need to accurately identify Tetranychus species and to develop species‐specific management strategies for these pests.

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Section: Methodsmentioning

confidence: 99%

Adaptation of acaricide stress facilitates Tetranychus urticae expanding against Tetranychus cinnabarinus in China

Wang

et al. 2017

Ecology and Evolution

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“…Significant DEGs were defined and identified according to the method of Audic and Claverie (1997). The criteria for the data in this present study were a false discovery rate (FDR) value of ≤0.001 and an absolute log 2 ratio value of ≥1, where the ratio is the ratio of gene expression at a non-zero time point profile relative to the corresponding control.…”

Section: Identification Of Differentially Expressed Genes (Degs) Andmentioning

confidence: 99%

“…DEGs were defined and identified based on digital gene expression profiles as described previously (Audic and Claverie, 1997). As a result, we obtained 9060 unique DEGs after removing redundant DEGs.…”

Section: Selection and Initial Analysis Of Significant Degsmentioning

confidence: 99%

RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses

Shi

Huang

et al. 2014

Molecular Immunology

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“…We employed the Audic-Claverie test (Audic and Claverie, 1997) for direct comparisons of tag frequencies between libraries. This test was used to identify genes with significantly altered expression levels by estimation of p-value (p in the text) for the comparison.…”

Section: Statistical Filtering Of Expression Datamentioning

confidence: 99%

Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults

Ruzanov

Riddle

Marra

et al. 2007

Experimental Gerontology

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SummaryWe used Serial Analysis of Gene Expression (SAGE) to compare the global transcription profiles of long-lived mutant daf-2 adults and dauer larvae, aiming to identify aging-related genes based on similarity of expression patterns. Genes that are expressed similarly in both long-lived types potentially define a common life-extending program. Comparison of eight SAGE libraries yielded a set of 120 genes, the expression of which was significantly different in long-lived worms versus normal adults. The gene annotations indicate a strong link between oxidative stress and life span, further supporting the hypothesis that metabolic activity is a major determinant in longevity. The SAGE data show changes in mRNA levels for electron transport chain components, elevated expression of glyoxylate shunt enzymes and significantly reduced expression for components of the TCA cycle in longer-lived nematodes. We propose a model for enhanced longevity through a cytochrome c oxidase-mediated reduction in reactive oxygen species commonly held to be a major contributor to aging.

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The Significance of Digital Gene Expression Profiles

Cited by 2,600 publications

References 30 publications

Adaptation of acaricide stress facilitates Tetranychus urticae expanding against Tetranychus cinnabarinus in China

Adaptation of acaricide stress facilitates Tetranychus urticae expanding against Tetranychus cinnabarinus in China

RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses

Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults

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