CirGO: an alternative circular way of visualising gene ontology terms

Kuznetsova, Irina; Lugmayr, Artur; Siira, Stefan J.; Rackham, Oliver; Filipovska, Aleksandra

doi:10.1186/s12859-019-2671-2

Cited by 105 publications

(90 citation statements)

References 26 publications

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“… Metabolite profiling revealed alterations in the citric acid cycle that normalizes with age. Proteomic analyses of samples from 10‐ and 30‐week‐old Mrps12 +/+ and Mrps12 ep / ep mice revealed an enrichment in proteins that are involved in citric acid cycle‐related biological processes, by gene ontology analyses. Detailed CirGO graphs (Kuznetsova et al , ) of enriched biological processes are provided in Appendix Figures S1 and S2. Respiratory chain subunit proteins and citric acid cycle enzymes that were altered in abundance are labeled in green and black, respectively, within a heatmap of all significantly altered proteins within the proteomic dataset. Data information: In (A), data are presented as box plots of the fold change ( x ‐axis) of metabolites; horizontal middle lines represent the mean, and the box ranges are the upper and lower quartiles, with the whiskers showing the highest and lowest observations of results obtained from five to six mice from each genotype. Only metabolites whose abundance was significantly changed between Mrps12 +/+ and Mrps12 ep / ep mice, after Benjamini–Hochberg correction (FDR 0.01), are graphed.…”

Section: Resultsmentioning

confidence: 99%

“…The data were normalized to 18S rRNA. Mitochondrial DNA (mtDNA) was measured using quantitative PCR, and values were normalized to the β‐2‐microglobulin ( B2m ) gene. Proteomic analyses of samples from 30‐week‐old Mrps12 +/+ and Mrps12 ha / ha mice revealed an enrichment in proteins with significantly changed levels that are involved in cardiac and mitochondrial metabolic processes, by gene ontology analyses. Detailed CirGO graphs (Kuznetsova et al , ) of enriched biological processes are provided in Appendix Figure S3. Respiratory chain subunit proteins that were significantly changed in abundance are labeled in green within a heatmap of all significantly altered proteins within the proteomic dataset. Data information: In (A), autoradiographs and stained gels are representative of results obtained from six mice from each genotype. In (B, C), data are presented as mean ± SD of results obtained from five to six mice from each genotype.…”

Section: Resultsmentioning

confidence: 99%

“…B Proteomic analyses of samples from 10and 30-week-old Mrps12 +/+ and Mrps12 ep/ep mice revealed an enrichment in proteins that are involved in citric acid cyclerelated biological processes, by gene ontology analyses. Detailed CirGO graphs (Kuznetsova et al, 2019) of enriched biological processes are provided in Appendix Figures S1 and S2. C Respiratory chain subunit proteins and citric acid cycle enzymes that were altered in abundance are labeled in green and black, respectively, within a heatmap of all significantly altered proteins within the proteomic dataset.…”

Section: Discussionmentioning

confidence: 99%

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Stress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation

et al. 2019

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Translation fidelity is crucial for prokaryotes and eukaryotic nuclear‐encoded proteins; however, little is known about the role of mistranslation in mitochondria and its potential effects on metabolism. We generated yeast and mouse models with error‐prone and hyper‐accurate mitochondrial translation, and found that translation rate is more important than translational accuracy for cell function in mammals. Specifically, we found that mitochondrial mistranslation causes reduced overall mitochondrial translation and respiratory complex assembly rates. In mammals, this effect is compensated for by increased mitochondrial protein stability and upregulation of the citric acid cycle. Moreover, this induced mitochondrial stress signaling, which enables the recovery of mitochondrial translation via mitochondrial biogenesis, telomerase expression, and cell proliferation, and thereby normalizes metabolism. Conversely, we show that increased fidelity of mitochondrial translation reduces the rate of protein synthesis without eliciting a mitochondrial stress response. Consequently, the rate of translation cannot be recovered and this leads to dilated cardiomyopathy in mice. In summary, our findings reveal mammalian‐specific signaling pathways that respond to changes in the fidelity of mitochondrial protein synthesis and affect metabolism.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Stress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation

et al. 2019

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“…The tissue-specific expression profiles and intra-individual variations in the functional content of polymorphic sites were statistically tested using the WEGO v2.0 online tool [59] and visualised using a combination of the REVIGO online server [60] and CirGO [61]. The signal of pervasive selection (the ratio of non-synonymous to synonymous amino acid substitution, dN/dS ratio) in one particular liver transcript with an exceptionally high number of polymorphic sites was tested using a fixed-effects likelihood model [62] implemented in the online server Datamonkey [63].…”

Section: Transcriptome Assembly Variant Calling and Functional Annotmentioning

confidence: 99%

De Novo Transcriptome Assembly and Annotation of Liver and Brain Tissues of Common Brushtail Possums (Trichosurus vulpecula) in New Zealand: Transcriptome Diversity after Decades of Population Control

Emami‐Khoyi

Parbhu

Ross

et al. 2020

Genes

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The common brushtail possum (Trichosurus vulpecula), introduced from Australia in the mid-nineteenth century, is an invasive species in New Zealand where it is widespread and forms the largest self-sustained reservoir of bovine tuberculosis (Mycobacterium bovis) among wild populations. Conservation and agricultural authorities regularly apply a series of population control measures to suppress brushtail possum populations. The evolutionary consequence of more than half a century of intensive population control operations on the species’ genomic diversity and population structure is hindered by a paucity of available genomic resources. This study is the first to characterise the functional content and diversity of brushtail possum liver and brain cerebral cortex transcriptomes. Raw sequences from hepatic cells and cerebral cortex were assembled into 58,001 and 64,735 transcripts respectively. Functional annotation and polymorphism assignment of the assembled transcripts demonstrated a considerable level of variation in the core metabolic pathways that represent potential targets for selection pressure exerted by chemical toxicants. This study suggests that the brushtail possum population in New Zealand harbours considerable variation in metabolic pathways that could potentially promote the development of tolerance against chemical toxicants.

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“…Semantic similarity measure to use: SimRel. Next, CirGO [134] was used to plot a concise version of the GO analysis.…”

Section: Gene Ontology and Pathways Analysismentioning

confidence: 99%

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

Nilo-Poyanco

Moraga

Benedetto

et al. 2020

Preprint

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BackgroundFruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.ResultsTo accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2,740 proteins, using the peach genome reference v1. After data pre-treatment, 1,663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively.ConclusionsShotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

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CirGO: an alternative circular way of visualising gene ontology terms

Cited by 105 publications

References 26 publications

Stress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation

Stress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation

De Novo Transcriptome Assembly and Annotation of Liver and Brain Tissues of Common Brushtail Possums (Trichosurus vulpecula) in New Zealand: Transcriptome Diversity after Decades of Population Control

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

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