eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses

Micallef, Luana; Rodgers, Peter

doi:10.1371/journal.pone.0101717

Cited by 475 publications

(358 citation statements)

References 57 publications

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“…Variation explained by environmental variables only (E), sampling date only (D), season only (S), environment and season combined (ES), environment and sampling date combined (ED), sampling date and season combined (DS), and a combination of all 3 (EDS) were determined following Anderson & Cribble (1998) for variation partitioning on 3 sets of explanatory variables. To visualize the results of the variation partitioning, we generated a Euler diagram with the eulerAPE software (Micallef & Rodgers 2014).…”

Section: Resultsmentioning

confidence: 99%

Spatial and temporal structure of the meroplankton community in a sub-Arctic shelf system

Silberberger¹,

Renaud²,

Espinasse³

et al. 2016

Mar. Ecol. Prog. Ser.

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The early development of many benthic invertebrates involves planktonic larval stages enabling larvae to disperse over large distances and to utilize food from the productive upper water layers. Although many past studies have recognized the importance of this period in the benthic life cycle, knowledge of larval distribution in time and space remains limited, especially for high-latitude regions with pronounced seasonal variability in environmental conditions. Here, we present the first inventory of meroplankton over the continental shelf in the Lofoten− Vesterålen region, northern Norway, over a full annual cycle. Six stations were sampled during 8 sampling events between September 2013 and August 2014. We recorded a total of 65 taxa, a considerably higher diversity than reported in studies from more northern regions. We observed a distinct seasonal pattern with characteristic meroplankton communities defining the seasons: spring, summer, and winter. Abundance and diversity during winter was low, with higher values in spring, and maximum abundances for most taxa in summer. Meroplankton community patterns did not reflect weak environmental spatial structure. Particle tracking was used to identify source and settlement locations of spring and summer communities. Spring and summer communities originated from shore and shelf areas, respectively. Larvae were generally transported toward Andfjord and adjacent shelf regions, irrespective of season. This spatially restricted dispersal and larval settlement highlights the importance of the local benthic communities for the resilience of the ecosystem.

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Section: Resultsmentioning

confidence: 99%

Spatial and temporal structure of the meroplankton community in a sub-Arctic shelf system

Silberberger¹,

Renaud²,

Espinasse³

et al. 2016

Mar. Ecol. Prog. Ser.

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“…A 2-sided p value Ͻ 0.05 was considered statistically significant. Graphics with simultaneous virus occurrence were plotted with the help of the Euler APE v3 software (40).…”

Section: Lc-ms/ms and Data Analyses-lc-ms/msmentioning

confidence: 99%

The Pathogenesis of the Demyelinating Form of Guillain-Barre Syndrome (GBS): Proteo-peptidomic and Immunological Profiling of Physiological Fluids

Ziganshin

Ivanova

Lomakin

et al. 2016

Molecular & Cellular Proteomics

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Acute inflammatory demyelinating polyneuropathy (AIDP) -the main form of Guillain-Barre syndrome-is a rare and severe disorder of the peripheral nervous system with an unknown etiology. One of the hallmarks of the AIDP pathogenesis is a significantly elevated cerebrospinal fluid (CSF) protein level. In this paper CSF peptidome and proteome in AIDP were analyzed and compared with multiple sclerosis and control patients. A total protein concentration increase was shown to be because of even changes in all proteins rather than some specific response, supporting the hypothesis of protein leakage from blood through the blood-nerve barrier. The elevated CSF protein level in AIDP was complemented by activization of protein degradation and much higher peptidome diversity. Because of the studies of the acute motor axonal form, Guillain-Barre syndrome as a whole is thought to be associated with autoimmune response against neurospecific molecules. Thus, in AIDP, autoantibodies against cell adhesion proteins localized at Ranvier's nodes were suggested as possible targets in AIDP. Indeed, AIDP CSF peptidome analysis revealed cell adhesion proteins degradation, however no reliable dependence on the corresponding autoantibodies levels was found. Proteome analysis revealed overrepresentation of Gene Ontology groups related to responses to bacteria and virus infections, which were earlier suggested as possible AIDP triggers. Immunoglobulin blood serum analysis against most common neuronal viruses did not reveal any specific pathogen; however, AIDP patients were more immunopositive in average and often had polyinfections. Cytokine analysis of both AIDP CSF and blood did not show a systemic adaptive immune response or general inflammation, whereas innate immunity cytokines were up-regulated. To supplement the widely-accepted though still unproven autoimmunity-based AIDP mechanism we propose a hypothesis of the primary peripheral nervous system damaging initiated as an innate immunity-associated local inflammation following neurotropic viruses egress, whereas the autoantibody production might be an optional complementary secondary process. Molecular & Cellular

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“…We then used linear contrasts to test the following null hypotheses: (1) no difference between the host races, (2) no difference between the 0 and 24 h treatments, and (3) no difference between the 24 and 48 h treatments. Overlaps of these sets were visualized in an area-proportional Venn diagram using eulerAPE (Micallef and Rodgers, 2014) and tested for significance using Fisher's exact tests.…”

Section: Differential Expression Analysismentioning

confidence: 99%

Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression

Meyers

Powell

Walden

et al. 2016

Journal of Experimental Biology

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The duration of dormancy regulates seasonal timing in many organisms and may be modulated by day length and temperature. Though photoperiodic modulation has been well studied, temperature modulation of dormancy has received less attention. Here, we leverage genetic variation in diapause in the apple maggot fly, Rhagoletis pomonella, to test whether gene expression during winter or following spring warming regulates diapause duration. We used RNAseq to compare transcript abundance during and after simulated winter between an apple-infesting population and a hawthorn-infesting population where the apple population ends pupal diapause earlier than the hawthorn-infesting population. Marked differences in transcription between the two populations during winter suggests that the 'early' apple population is developmentally advanced compared with the 'late' hawthorn population prior to spring warming, with transcripts participating in growth and developmental processes relatively up-regulated in apple pupae during the winter cold period. Thus, regulatory differences during winter ultimately drive phenological differences that manifest themselves in the following summer. Expression and polymorphism analysis identify candidate genes in the Wnt and insulin signaling pathways that contribute to population differences in seasonality. Both populations remained in diapause and displayed a pattern of up-and then down-regulation (or vice versa) of growth-related transcripts following warming, consistent with transcriptional repression. The ability to repress growth stimulated by permissive temperatures is likely critical to avoid mismatched phenology and excessive metabolic demand. Compared with diapause studies in other insects, our results suggest some overlap in candidate genes/pathways, though the timing and direction of changes in transcription are likely species specific.

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eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses

Cited by 475 publications

References 57 publications

Spatial and temporal structure of the meroplankton community in a sub-Arctic shelf system

Spatial and temporal structure of the meroplankton community in a sub-Arctic shelf system

The Pathogenesis of the Demyelinating Form of Guillain-Barre Syndrome (GBS): Proteo-peptidomic and Immunological Profiling of Physiological Fluids

Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression

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