Figure 1 - uploaded by Jerome Mariette
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A six lists Edwards-Venn diagram. This Venn diagram displays overlaps between six different biological samples. The icon, located on the top-right, allows users to download the diagram as a PNG file. The middle-right switch button panel allows to activate or dis-activate lists to access a specific intersection count. Charts showing the list size and intersection size repartition located underneath the diagram.
Source publication
Background
Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input li...
Contexts in source publication
Context 1
... diagrams with up to four lists are easy to read and understand but Venn diagrams with more than four lists, are much harder to interpret. To solve this problem, the Edwards-Venn [2] representation introduces new shapes providing a clearer view, shown in the example of Figure 1. Table 1 present the main packages with their main features (maximum number of input lists, input data formats, Venn diagram layouts, application types and output formats). ...
Context 2
... display five or six lists diagrams, in a user-friendly manner, jvenn implements several features. First, the lay- out can be switched between the standard layout and the Edwards-Venn layout (Figure 1) which gives a clearer graphical representation for six lists diagrams. To enhance the figure's readability for the classical six lists Venn chart, some count values are not shown and some are display outside the chart, using lines to line the count to its cor- responding area. ...
Context 3
... jvenn handles only six list at most, six out of the seven lists were selected for further processing: we left out the median normalization method because, for one hand, this method is very similar to several other methods (as shown in the article) and, for the other hand, we believe that median is a poor estimate of the sequencing length, which is the bias that normalization methods try to correct. The lists were uploaded to the jvenn application and a Venn diagram was obtained, using an Edwards layout, which is shown in Figure 1. ...
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Citations
... Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify significant genera that differed between the sample types (cow colostrum, cow feces, and calf feces) and the two breeds of cattle (Hanwoo and Holstein) [34]. The UpSet plot was generated with the R package UpSetR [35] and the Venn diagram was constructed using the jvenn tool to display the common and unique genera among the samples [36]. ...
This study aimed to evaluate rotavirus transmission to calves and analyze microbial communities in cow milk and neonatal calf feces within dairy and beef cattle. A total of 20 cattle, Hanwoo (n = 10), and Holstein (n = 10) were allotted for the study, with each breed comprising five cows and five calves. Colostrum samples were obtained from the dam, while feces were obtained from both the dam and calf. Group A rotavirus was identified in the fecal samples through real-time reverse transcription PCR (RT-qPCR). Bacterial communities present in the colostrum and bovine feces were explored using 16S rRNA metagenomic sequencing. The RT-qPCR results showed that the Cq value of one calf and one cow in the Holstein group was < 35, confirming the presence of rotavirus, whereas the Cq value in the Hanwoo group was > 35, indicating a negative result. For the bacterial communities, significant differences (p < 0.05) were found between the colostrum and fecal samples from the dams and calves, but there were no significant differences between Hanwoo and Holstein cattle. Alpha diversity analysis showed that the Chao1 and Shannon indices revealed significant differences (p < 0.05) among the sample types (cow colostrum, cow feces, and calf feces). The bacterial communities in various sample types from both Hanwoo and Holstein cattle were dominated by the phyla Firmicutes, Proteobacteria, and Bacteroidetes. In addition, the genera shared between the cow colostrum and calf fecal microbiota were higher than those shared between cow and calf feces. Overall, the current study detected rotavirus in Holstein but not in Hanwoo cattle; however, no clear evidence showed the transmission of rotavirus from dam to calf. Moreover, significant variations in bacterial compositions were observed among calf feces, cow feces, and colostrum samples, suggesting the presence of unique microbial profiles.
... A nominal p-value < 0.05 and |log2FC| > 1 were applied as the cutoff criteria, and the resultant genes that satisfied both the cutoffs were considered statistically significant DEGs. To determine common DEGs between the datasets, we used the Jvenn web application [31]. ...
Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors globally, significantly affecting liver functions, thus necessitating the identification of biomarkers and effective therapeutics to improve HCC-based disabilities. This study aimed to identify prognostic biomarkers, signaling cascades, and candidate drugs for the treatment of HCC through integrated bioinformatics approaches such as functional enrichment analysis, survival analysis, molecular docking, and simulation. Differential expression and functional enrichment analyses revealed 176 common differentially expressed genes from two microarray datasets, GSE29721 and GSE49515, significantly involved in HCC development and progression. Topological analyses revealed 12 hub genes exhibiting elevated expression in patients with higher tumor stages and grades. Survival analyses indicated that 11 hub genes (CCNB1, AURKA, RACGAP1, CEP55, SMC4, RRM2, PRC1, CKAP2, SMC2, UHRF1, and FANCI) and three transcription factors (E2F1, CREB1, and NFYA) are strongly linked to poor patient survival. Finally, molecular docking and simulation identified seven candidate drugs with stable complexes to their target proteins: tozasertib (−9.8 kcal/mol), tamatinib (−9.6 kcal/mol), ilorasertib (−9.5 kcal/mol), hesperidin (−9.5 kcal/mol), PF−562271 (−9.3 kcal/mol), coumestrol (−8.4 kcal/mol), and clofarabine (−7.7 kcal/mol). These findings suggest that the identified hub genes and TFs could serve as valuable prognostic biomarkers and therapeutic targets for HCC-based disabilities.
... Considering the potential impact of height [32] , we calculated several muscle mass indices as follows: (Table S1) according to the reference criteria [33]. Children with sufficient MDL had good or excellent scores in all four muscle mass indices, and those with insufficient MDL had insufficient or severe muscle mass in one or more muscle mass indices (Fig. S1) [34]. ...
... All analyses, excluding the Venn diagram [34,39], were conducted with R 4.3.1, and two-sided P < 0.05 was considered statistically significant. ...
Some trace elements have been found to be associated with muscle mass and muscle function; however, evidence in children is limited, and it remains unclear which trace elements are more relevant. We aimed to explore the association of levels of individual and combined essential trace elements and muscle development level (MDL) in young children. Muscle mass was measured by body composition analysis, and trace elements were determined by using inductively coupled plasma mass spectrometry (ICP-MS). Logistic regression, restricted cubic spline (RCS) and weighted quantile sum regression (WQS) were used to assess the individual and joint associations between trace element levels and MDL. We enrolled 2851 children: 1595 boys (55.9%) and mean age 7.1 years (range 6.8–7.3). The proportion of insufficient muscle mass in the whole body, limbs, upper and lower limbs was 1.9%, 6.5%, 44.9% and 4.6%, respectively. The odds of insufficient MDL decreased with the fourth versus first quartile of zinc (OR = 0.67, 95% CI: 0.51–0.89), manganese (OR = 0.80, 95% CI: 0.65–1.00), and cobalt (OR = 0.89, 95% CI: 0.81–0.99) and was increased with the fourth quartile of nickel (OR = 2.23, 95% CI: 1.72–2.89) and selenium (OR = 1.51, 95% CI: 1.14–1.98). The RCS yielded similar results, except for the discrepancy in high cobalt levels. The odds of insufficient MDL decreased with the combination of nine trace elements (OR = 0.84, 95% CI: 0.73–0.97), primarily zinc (weight = 0.297), manganese (weight = 0.198) and cobalt (weight = 0.173). Insufficient MDL in young children was mainly in upper limbs. Low levels of zinc, manganese, and cobalt, individually or combined, were significantly associated with risk of insufficient MDL. Further foods rich in zinc, manganese, and cobalt should be suggested to supplement in diet, and increase exercise of upper limbs to improve insufficient MDL in the young children should be needed.
... In this dataset, published by our group, we determined in an unbiased manner which genes and pathways are differentially regulated during mouse colonic inflammation followed by tissue regeneration. From this publication, we obtained supplementary dataset 1, containing all the DEGs, which were compared with the upregulated genes in irradiated crypts cells in bulk using jvenn program 68 . Functional enrichment analysis using enrichR (v.2.1) 69 was performed on the genes shared between these two datasets (that is, DEGs in DSS kinetics and upregulated genes in irradiated crypts compared to control). ...
Uncontrolled regeneration leads to neoplastic transformation1–3. The intestinal epithelium requires precise regulation during continuous homeostatic and damage-induced tissue renewal to prevent neoplastic transformation, suggesting that pathways unlinking tumour growth from regenerative processes must exist. Here, by mining RNA-sequencing datasets from two intestinal damage models4,5 and using pharmacological, transcriptomics and genetic tools, we identified liver X receptor (LXR) pathway activation as a tissue adaptation to damage that reciprocally regulates intestinal regeneration and tumorigenesis. Using single-cell RNA sequencing, intestinal organoids, and gain- and loss-of-function experiments, we demonstrate that LXR activation in intestinal epithelial cells induces amphiregulin (Areg), enhancing regenerative responses. This response is coordinated by the LXR-ligand-producing enzyme CYP27A1, which was upregulated in damaged intestinal crypt niches. Deletion of Cyp27a1 impaired intestinal regeneration, which was rescued by exogenous LXR agonists. Notably, in tumour models, Cyp27a1 deficiency led to increased tumour growth, whereas LXR activation elicited anti-tumour responses dependent on adaptive immunity. Consistently, human colorectal cancer specimens exhibited reduced levels of CYP27A1, LXR target genes, and B and CD8 T cell gene signatures. We therefore identify an epithelial adaptation mechanism to damage, whereby LXR functions as a rheostat, promoting tissue repair while limiting tumorigenesis.
... The results were visualized using the online tool jvenn (https://jvenn.toulouse.inrae.fr/app/example.html) 49 . ...
FAR-RED IMPAIRED RESPONSE 1 (FAR1) is a class of transposase-derived transcription factors that play a very important role in the initiation of the photosensitive pigment A (phyA) signaling pathway. Despite their importance, the understanding of the function of FAR1 genes in quinoa is still limited, especially regarding how they affect the spike sprouting response. Quinoa has gained global attention in recent years for its health benefits and potential for sustainable agriculture. In our study, the CqFAR1 gene set in quinoa was characterized using HMMER (PF03101) and BLAST analyses, and 87 genes were identified. The 87 CqFAR1 genes were systematically classified into five groups that showed a high degree of conservation in gene structure and motif composition. Tissue expression profiles of the CqFAR1 gene indicated that the CqFAR1 gene plays a key role throughout the growth and development of quinoa, especially at mid (leaf) and end (spike) stages. By RT-qPCR analysis, we observed significant differences in the expression of the CqFAR1 gene at different developmental stages. Notably, the CqFAR1 gene showed significant expression enhancement at the early stage of quinoa spike sprouting. The results are useful for understanding the role of the CqFAR1 gene in quinoa growth and development and provide theoretical support for quinoa breeding.
... f r / a p p / e x a m p l e . h t m l ) [78]. Gene e n r i c h m e n t analysis was performed separately for each pairwise comparison. ...
Background
Bisphenol S (BPS) is the main substitute for bisphenol A (BPA), a well-known plasticiser and endocrine disruptor. BPS disrupts ovarian function in several species. Moreover, a few studies have reported that the effects of BPS might be modulated by the metabolic status, and none have characterised the granulosa cell (GC) proteome after chronic BPS exposure.
Objectives
This study aimed to decipher the mechanisms of action of chronic BPS exposure on the proteome of ewe GCs while considering the interaction between a deliberate contrasted metabolism and reproductive function.
Methods
Forty ewes were split into two groups with contrasted diets: restricted (R, n = 20) and well-fed (WF, n = 20). The R and WF ewes were subdivided according to the dose of BPS administered through the diet (0–50 µg/kg/day), forming four groups: R0, R50, WF0 and WF50. After 3-month BPS daily exposure, GCs were recovered during the pre-ovulatory stage and proteins were analysed by nano-liquid chromatography coupled with tandem mass spectrometry.
Results
Chronic exposure to BPS affected the GC proteome differently according to the ewe metabolic status. Fifty-nine out of 958 quantified proteins were differentially abundant between groups and are mainly involved in carbohydrate and lipid pathways. Unsupervised hierarchical clustering of differentially abundant proteins (DAPs) identified four clusters of 34, 6, 5 and 14 proteins according to the BPS exposure and diet interaction. Pairwise comparisons between groups also revealed a strong effect of BPS exposure and diet interaction. Functional analysis of DAPs highlighted that BPS upregulated β-glucuronidase (GUSB; p = 0.002), a protein especially able to deconjugate bisphenol glucuronides (BP-g). Moreover, among unexposed ewes, GUSB was detected only in well-fed ewes.
Discussion
Conjugation of glucuronides inhibits the oestrogenic activity of bisphenols. Upregulation of GUSB in ewes dosed with BPS would prolong the oestrogenic effects of BPS by deconjugating BPS-g into free BPS. In addition, literature has reported an up-regulation of GUSB in people suffering from obesity. Therefore, people suffering from obesity could be subjected to prolonged and aggravated exposure to BPS. These data highlighted the deleterious effects of BPS and its interaction with metabolic status.
... The web-based Interactive Venn diagram viewer jvenn (Bardou et al., 2014) was used to analyse and visualise the shared presence of archaeal, bacterial and eukaryotic ASVs among the different typologies and identify a core community. Afterwards the same tool was used to visualise shared ASVs among the typology core community for archaea, bacteria and eukaryotes depending on seasons. ...
... All graphs were drawn using the ggplot2 package in R (45). The Venn diagram based on bacterial and fungal ASV was drawn using the online software jvenn (46). Bacterial and fungal biomarkers were identified using Linear discriminant analysis Effect Size (LEfSe) (47), with an LDA threshold score of 4.0 and a significance level of P < 0.05. ...
Fungi and bacteria often occupy very similar niches; they interact closely with each other, and bacteria can provide direct or indirect benefits to plants that form mutualistic interactions with fungi. In orchids, successful seed germination largely depends on compatible mycorrhizal fungi, but whether and how bacteria contribute to seed germination and protocorm development remains largely unknown. Here, we performed field and laboratory experiments to assess the potential role of bacteria in mediating seed germination and protocorm development in the terrestrial orchid Gymnadenia conopsea . Our results suggested that bacterial and fungal communities differ between developmental stages in the germination process. The diversity of bacterial and fungal communities and their interaction network in germinating seeds (Stage 1) differed significantly from those in later developmental stages (Stages 2–5). Pseudomonas gradually became the dominant bacterial group as the protocorms matured and showed a positive association with Ceratobasidiaceae fungi. Seed germination tests in vitro demonstrated that co-inoculation of Ceratobasidium sp. GS2 with Pseudomonas isolates significantly improved protocorm growth and development, suggesting that the observed increase in Pseudomonas abundance during protocorm development directly or indirectly improves the growth of germinating seeds. Overall, our findings indicate that bacteria may exert non-negligible effects on seed germination of orchids and, therefore, offer valuable perspectives for future strategies for conservation and cultivating orchid species.
IMPORTANCE
It is well known that orchid seeds depend on mycorrhizal fungi to supply the necessary nutrients that support germination in natural environments. Apart from fungi, bacteria may also be involved in the germination process of orchid seeds, but so far, their role has not been intensively studied. This research provides evidence that bacterial community composition changes during seed germination of the terrestrial orchid Gymnadenia conopsea . Interestingly, in vitro experiments showed that Pseudomonas spp., which were the most dominant bacteria in the later germination stages, improved protocorm growth. These results suggest that bacteria contribute to the germination of orchid seeds, which may open new perspectives to apply bacteria as a biofertilizer in the introduction and restoration of G . conopsea populations.
... To normalize the datasets, UniProt [25] was used. The resulting targets were visualized as Venn diagrams by jvenn [26]. ...
Background
The intestinal epithelial barrier is the first line of defense against pathogens and noxious substances entering the body from the outside world. Through proliferation and differentiation, intestinal stem cells play vital roles in tissue regeneration, repair, and the maintenance of intestinal homeostasis. Inflammatory bowel disease (IBD) is caused by the disruption of intestinal homeostasis through the invasion of toxic compounds and pathogenic microorganisms. Hylotelephium erythrostictum (Miq.) H. Ohba (H. erythrostictum) is a plant with diverse pharmacological properties, including antioxidant, anti-inflammatory, antidiabetic, and antirheumatic properties. However, the roles of H. erythrostictum and its bioactive compounds in the treatment of intestinal injury are unknown.
Methods
We examined the protective effects of H. erythrostictum water extract (HEWE) and H. erythrostictum butanol extract (HEBE) on Drosophila intestinal injury caused by dextran sodium sulfate (DSS) or Erwinia carotovoracarotovora 15 (Ecc15).
Results
Our findings demonstrated that both HEWE and HEBE significantly prolonged the lifespan of flies fed toxic compounds, reduced cell mortality, and maintained intestinal integrity and gut acid‒base homeostasis. Furthermore, both HEWE and HEBE eliminated DSS-induced ROS accumulation, alleviated the increases in antimicrobial peptides(AMPs) and intestinal lipid droplets caused by Ecc15 infection, and prevented excessive ISC proliferation and differentiation by inhibiting the JNK, EGFR, and JAK/STAT pathways. In addition, they reversed the significant changes in the proportions of the gut microbiota induced by DSS. The bioactive compounds contained in H. erythrostictum extracts have sufficient potential for use as natural therapeutic agents for the treatment of IBD in humans.
Conclusion
Our results suggest that HEWE and HEBE are highly effective in reducing intestinal inflammation and thus have the potential to be viable therapeutic agents for the treatment of gut inflammation.
Clinical trial number
Not applicable.
... The target genes of the differentially expressed miRNA were predicted using the online software on the websites TargetScan, mischemia-reperfusion DIP and microDB. The comparison of the 6 data sets was analyzed by jvenn, and the Venn diagram was drawn [26]. Jvenn was also used to compare the differences between the three miRNA target genes and the differential genes of the three chips and to screen the differentially expressed miRNAs and genes with targeted binding relationships. ...
Background
MicroRNAs (miRNAs) are critical regulators of cancer progression, prompting our investigation into the specific function of miR-630 in pancreatic cancer stem cells (PCSCs). Analysis of miRNA and mRNA expression data in PCSCs revealed downregulation of miR-630 and upregulation of PRKCI, implying a potential role for miR-630 in PCSC function and tumorigenicity.
Results
Functional assays confirmed that miR-630 directly targets PRKCI, leading to the suppression of the Hedgehog signaling pathway and consequent inhibition of PCSC self-renewal and tumorigenicity in murine models. This study unveiled the modulation of the PRKCI-Hedgehog signaling axis by miR-630, highlighting its promising therapeutic potential for pancreatic cancer (PC) treatment.
Conclusions
MiR-630 emerges as a pivotal regulator in PCSC biology, opening up new avenues for targeted interventions in PC. The inhibitory effect of miR-630 on PCSC behavior underscores its potential as a valuable therapeutic target, offering insights into innovative treatment strategies for this challenging disease.
