Performance Analysis of Gene Expression Data Using Mann–Whitney U Test

Vengatesan, K.; Mahajan, S. B.; Sanjeevikumar, P.; Mangrule, R.; Kala, V.; Pragadeeswaran,

doi:10.1007/978-981-10-4762-6_67

Cited by 7 publications

(5 citation statements)

References 8 publications

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“…To determine the dominantly expressed homoeolog for a given gene pair (homoeolog pairs), their TPM values were compared: Greater or less was recorded, and the relative expression fold—dominant over submissive—was calculated. We also used the non-parametric statistical test of the Mann-Whitney-U test ( 65 ) in the Python package SciPy to identify the significance of differentially expressed gene pairs from a subset of genes. Gene pairs with P value < 0.05 were considered significantly differentially expressed.…”

Section: Methodsmentioning

confidence: 99%

The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids

Zhang,

Cui

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Polyploidization is important to the evolution of plants. Subgenome dominance is a distinct phenomenon associated with most allopolyploids. A gene on the dominant subgenome tends to express to higher RNA levels in all organs as compared to the expression of its syntenic paralogue (homoeolog). The mechanism that underlies the formation of subgenome dominance remains unknown, but there is evidence for the involvement of transposon/DNA methylation density differences nearby the genes of parents as being causal. The subgenome with lower density of transposon and methylation near genes is positively associated with subgenome dominance. Here, we generated eight generations of allotetraploid progenies from the merging of parental genomes Brassica rapa and Brassica oleracea . We found that transposon/methylation density differ near genes between the parental ( rapa : oleracea ) existed in the wide hybrid, persisted in the neotetraploids (the synthetic Brassica napus ), but these neotetraploids expressed no expected subgenome dominance. This absence of B. rapa vs. B. oleracea subgenome dominance is particularly significant because, while there is no negative relationship between transposon/methylation level and subgenome dominance in the neotetraploids, the more ancient parental subgenomes for all Brassica did show differences in transposon/methylation densities near genes and did express, in the same samples of cells, biased gene expression diagnostic of subgenome dominance. We conclude that subgenome differences in methylated transposon near genes are not sufficient to initiate the biased gene expressions defining subgenome dominance. Our result was unexpected, and we suggest a “nuclear chimera” model to explain our data.

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Section: Methodsmentioning

confidence: 99%

The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids

Zhang,

Cui

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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“…Statistical significance was determined by unpaired t -tests or Mann–Whitney tests using the GraphPad Prism v. 7.0 software. The non-parametric Mann–Whitney tests routinely used to improve the analysis of the gene expression data to detect the differences between the median value of the groups with more power and strict approach than the other tests [30]. Differences between groups were considered statistically significant at p < 0.05.…”

Section: Methodsmentioning

confidence: 99%

Characterization and functional analysis of zinc trafficking in the human fungal pathogen Candida parapsilosis

et al. 2022

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The zinc restriction and zinc toxicity are part of host defence, called nutritional immunity. The crucial role of zinc homeostasis in microbial survival within a host is established, but little is known about these processes in the opportunistic human fungal pathogen Candida parapsilosis. Our in silico predictions suggested the presence of at least six potential zinc transporters (ZnTs) in C. parapsilosis —orthologues of ZRC1 , ZRT3 and ZRT101 —but an orthologue of PRA1 zincophore was not found. In addition, we detected a species-specific gene expansion of the novel ZnT ZRT2, as we identified three orthologue genes in the genome of C. parapsilosis . Based on predictions, we created homozygous mutant strains of the potential ZnTs and characterized them. Despite the apparent gene expansion of ZRT2 in C. parapsilosis , only CpZRT21 was essential for growth in a zinc-depleted acidic environment, in addition we found that CpZrc1 is essential for zinc detoxification and also protects the fungi against the elimination of murine macrophages. Significantly, we demonstrated that C. parapsilosis forms zincosomes in a Zrc1-independent manner and zinc detoxification is mediated by the vacuolar importer CpZrc1. Our study defines the functions of C. parapsilosis ZnTs, including a species-specific survival and zinc detoxification system.

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“…A Mann–Whitney analysis 34 (a nonparametric test that compares the medians of two different samples) was performed for the data of Sauter mean diameter between conditions (constant stirred speed and constant power input). Statistical analysis was performed using Statgraphics Centurion XVI software.…”

Section: Methodsmentioning

confidence: 99%

“…where X vol,j is the fraction of accumulated volume of the jth class; X vol,j−1 is the fraction of accumulated volume of the ( j − 1)th class; xj is the fraction of accumulated volume contained in class j; V j is the volume of the jth class; m is the total number of classes; f j is the frequency in the jth class; and d j is the diameter of the jth class. A Mann-Whitney analysis 34 (a nonparametric test that compares the medians of two different samples) was performed for the data of Sauter mean diameter between conditions (constant stirred speed and constant power input). Statistical analysis was performed using Statgraphics Centurion XVI software.…”

Section: Determination Of Bubble Size Distributionmentioning

confidence: 99%

Oxygen transfer and bubble sizes occurring in a pilot‐scale cultivation of Bacillus velezensis 83 for the production of poly(γ‐glutamic acid) under two schemes of power drawn

Pulido‐Durán

Flores

Serrano‐Carreón

et al. 2022

J of Chemical Tech & Biotech

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BACKGROUND The influence of power consumption on oxygen transfer during non‐Newtonian and surfactant‐producing microbial fermentations has been scarcely reported. In this work, we study the oxygen transfer and bubble size distributions in a real 100 L fermentation (producing poly(γ‐glutamic acid)) occurring under constant stirring speed (N) and under constant retrofitted power drawn (Pg/V). RESULTS For constant N fermentations, Pg/V and the volumetric mass transfer coefficient (kLa) decreased 40% and 70% during cultivation, respectively. Fermentations at constant Pg/V showed a decrease similar to that observed for constant N fermentations. Bubble size distributions were also similar for both operational conditions. Although an increase in bubble size was expected at constant N cultivations due to the increasing viscosity of the medium, the Sauter mean diameter (d32) decreased 65%. This singular behavior of d32 was likely caused by surfactin and bacillomycin, metabolites with strong surfactant activity produced by Bacillus velezensis 83 in the cultivations. The use of a constant Pg/V did not counteract the decrease in kLa due to the increase in viscosity. Although the presence of biosurfactants leads to an increase of interfacial transfer area by decreasing d32, the presence of these molecules and the increase in the medium viscosity affected kLa. CONCLUSIONS An atypical behavior of this system was found, especially in d32, different to that based on common correlations found in the literature. A complex interaction among the multiple factors involved in a real bioprocess for poly(γ‐glutamic acid) production was evidenced. © 2022 Society of Chemical Industry (SCI).

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Performance Analysis of Gene Expression Data Using Mann–Whitney U Test

Cited by 7 publications

References 8 publications

The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids

The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids

Characterization and functional analysis of zinc trafficking in the human fungal pathogen Candida parapsilosis

Oxygen transfer and bubble sizes occurring in a pilot‐scale cultivation of Bacillus velezensis 83 for the production of poly(γ‐glutamic acid) under two schemes of power drawn

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