Enrichment or depletion of a GO category within a class of genes: which test?

Rivals, Isabelle; Personnaz, L.; Taing, Lieng; Potier, Marie‐Claude

doi:10.1093/bioinformatics/btl633

Cited by 599 publications

(516 citation statements)

References 32 publications

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“…Relevant lists of genes previously found by DESeq2 to be differentially abundant (that is, all genes found to be differentially abundant in Prochlorococcus by DESeq2 at any time point in co-culture) were imported as SmartTables in PathwayTools. Pathway enrichment/ depletion was tested using default settings (Fisher's exact test P-value o0.1 (Rivals et al, 2007)). …”

Section: Sequence Analysismentioning

confidence: 99%

Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus

2016

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Microbial interactions, whether direct or indirect, profoundly affect the physiology of individual cells and ultimately have the potential to shape the biogeochemistry of the Earth. For example, the growth of Prochlorococcus, the numerically dominant cyanobacterium in the oceans, can be improved by the activity of co-occurring heterotrophs. This effect has been largely attributed to the role of heterotrophs in detoxifying reactive oxygen species that Prochlorococcus, which lacks catalase, cannot. Here, we explore this phenomenon further by examining how the entire transcriptome of Prochlorococcus NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002, with which it was co-cultured for years, separated and then reunited. Significant changes in the Prochlorococcus transcriptome were evident within 6 h of initiating co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48 h experiment, suggesting that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely corresponded to reduced stress conditions for Prochlorococcus, as inferred from the depletion of transcripts encoding DNA repair enzymes and many members of the 'high light inducible' family of stress-response proteins. Later, notable changes were seen in transcripts encoding components of the photosynthetic apparatus (particularly, an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes, suggesting that the introduction of the heterotroph may have induced increased production of reduced carbon compounds for export. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains.

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Section: Sequence Analysismentioning

confidence: 99%

Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus

2016

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“…The statistical significance of the observed overlap in transcript profiles, as well as enrichment of GO terms, was analyzed using hypergeometric tests (Sokal and Rohlf, 1995;Covington and Harmer, 2007;Rivals et al, 2007).…”

Section: Comparison Of Transcript Profilesmentioning

confidence: 99%

Arabidopsis Deadenylases AtCAF1a and AtCAF1b Play Overlapping and Distinct Roles in Mediating Environmental Stress Responses

et al. 2009

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To maintain homeostasis in an ever-changing environment organisms have evolved mechanisms to reprogram gene expression. One central mechanism regulating gene expression is messenger RNA (mRNA) degradation, which is initiated by poly(A) tail shortening (deadenylation). The carbon catabolite repressor 4-CCR4 associated factor1 (CCR4-CAF1) complex is the major enzyme complex that catalyzes mRNA deadenylation and is conserved among eukaryotes. However, the components and functions of this global regulatory complex have not been well characterized in plants. Here we investigate the CAF1 family in Arabidopsis (Arabidopsis thaliana). We identify 11 AtCAF1 homologs and show that a subset of these genes are responsive to mechanical wounding, among them are AtCAF1a and AtCAF1b whose expression levels are rapidly and transiently induced by wounding. The differential expression profiles of the various AtCAF1s suggest that not all AtCAF1 genes are involved in stress-responsive regulation of transcript levels. Comparison of misexpressed genes identified via transcript profiling of Atcaf1a and Atcaf1b mutants at different time points before and after wounding suggests that AtCAF1a and AtCAF1b target shared and unique transcripts for deadenylation with temporal specificity. Consistent with the AtPI4Kγ3 transcript exhibiting the largest increase in abundance in Atcaf1b, AtCAF1b targets AtPI4Kγ3 mRNA for deadenylation. Stress-tolerance assays demonstrate that AtCAF1a and AtCAF1b are involved in mediating abiotic stress responses. However, AtCAF1a and AtCAF1b are not functionally redundant in all cases, nor are they essential for all environmental stresses. These findings demonstrate that these closely related proteins exhibit overlapping and distinct roles with respect to mRNA deadenylation and mediation of stress responses.

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“…According to Rivals et al [18], we chose the hypergeometric statistical model. The reference list of genes was the whole Agilent array.…”

Section: 'Enriched' Termsmentioning

confidence: 99%

Iron-related transcriptomic variations in Caco-2 cells: In silico perspectives

Aubry¹,

Monnier

Chicault

et al. 2008

Biochimie

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The iron absorption by duodenal enterocytes is a key step of its homeostasis. But the control of this absorption is complex and cannot be fully explicated with present knowledge. In a global transcriptome approach, we identified 60 genes over-expressed in hemin (iron) overload in Caco-2 cells, an in vitro model of duodenal enterocytes. The challenge from there was to identify the affected molecular mechanisms and achieve a biological interpretation for that cluster. In that purpose, we built up a functional annotation method combining evidence and literature. Our method identified four pathways in the Process hierarchy of the Gene Ontology (GO): lipid metabolism, amino acid and cofactor metabolism, response to stimulus and transport. The accuracy of this functional profile is supported by the identification of known pathways associated with the iron overload (response to oxidative stress, glutathione metabolism). But our method also suggests new hypotheses on the regulation of iron uptake in Caco-2 cells. It is hypothesized that plasma membrane remodeling and vesicular recycling could be a potential modulator of iron transport proteins activities. These assumptions yet require a biological validation and they will therefore direct further research. Our functional annotation method is a valuable tool designed to help the biologist understand the biological links between the genes of a cluster, elaborate working hypotheses and direct future work. This work is also a validation 'by hand' of a biomedical text-mining system. 4

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Enrichment or depletion of a GO category within a class of genes: which test?

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 599 publications

References 32 publications

Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus

Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus

Arabidopsis Deadenylases AtCAF1a and AtCAF1b Play Overlapping and Distinct Roles in Mediating Environmental Stress Responses

Iron-related transcriptomic variations in Caco-2 cells: In silico perspectives

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