shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics

Khomtchouk, Bohdan B.; Hennessy, John L.; Wahlestedt, Claes

doi:10.1371/journal.pone.0176334

Cited by 111 publications

(67 citation statements)

References 29 publications

(18 reference statements)

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“…The heat map was created at Shinyheatmap (http://www .shinyheatmap.com) using Euclidiean distance metrics and complete linkage algorithms (Khomtchouk et al 2017).…”

Section: Gene Expression Profile-input Datamentioning

confidence: 99%

Loss of TLE3 promotes the mitochondrial program in beige adipocytes and improves glucose metabolism

et al. 2019

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Prolonged cold exposure stimulates the recruitment of beige adipocytes within white adipose tissue. Beige adipocytes depend on mitochondrial oxidative phosphorylation to drive thermogenesis. The transcriptional mechanisms that promote remodeling in adipose tissue during the cold are not well understood. Here we demonstrate that the transcriptional coregulator transducin-like enhancer of split 3 (TLE3) inhibits mitochondrial gene expression in beige adipocytes. Conditional deletion of TLE3 in adipocytes promotes mitochondrial oxidative metabolism and increases energy expenditure, thereby improving glucose control. Using chromatin immunoprecipitation and deep sequencing, we found that TLE3 occupies distal enhancers in proximity to nuclear-encoded mitochondrial genes and that many of these binding sites are also enriched for early B-cell factor (EBF) transcription factors. TLE3 interacts with EBF2 and blocks its ability to promote the thermogenic transcriptional program. Collectively, these studies demonstrate that TLE3 regulates thermogenic gene expression in beige adipocytes through inhibition of EBF2 transcriptional activity. Inhibition of TLE3 may provide a novel therapeutic approach for obesity and diabetes.

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“…The heat map was created at Shinyheatmap (http://www .shinyheatmap.com) using Euclidiean distance metrics and complete linkage algorithms (Khomtchouk et al 2017).…”

Section: Gene Expression Profile-input Datamentioning

confidence: 99%

Loss of TLE3 promotes the mitochondrial program in beige adipocytes and improves glucose metabolism

et al. 2019

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“…A heatmap was constructed followed by cluster analysis using shiny heat map tool (Khomtchouk, Hennessy, & Wahlestedt, 2017; http://shinyheatmap.com/). The data used for heatmap construction were normalized based on Z‐scores calculated based on the following formula:

z = \frac{X_{i} - \bar{X}}{σ}

where, X i ,

\overset{X}{true}

and σ stand for raw data, mean and standard deviation for each trait tested.…”

Section: Methodsmentioning

confidence: 99%

Foliar applied zinc increases yield, zinc concentration, and germination in wheat genotypes

et al. 2020

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Human malnutrition associated with zinc (Zn) deficiency is a growing problem in many areas. This study was conducted to assess wheat (Triticum aestivum L.) genotypic variation of grain Zn concentration, grain germination, and grain yield in response to foliar application of Zn. Twenty-four wheat genotypes, including several recombinant inbred lines (RILs) and commercial cultivars, were assessed in two separate experiments; one experiment sprayed with ZnSO 4 ⋅7H 2 O dissolved in water at wheat heading growth stage and one without applying Zn foliar treatment. The range for grain (25.1-63.1) and endosperm (1.2-61.6 mg kg −1 ) Zn concentrations were different between the two Zn treatments. Significant (p = .05) genotype × Zn treatment interactions showed that some genotypes were more responsive to Zn applications than others. The application of Zn increased the Zn concentration in the endosperm in 18 out of the 24 genotypes. For grain, Zn application increased the concentration in the grain in 21 out of the 24 genotypes. Grain yield and germination were increased in the Zn treated cultivars compared with non-treated. In conclusion, foliar application of Zn improved traits in wheat, and identified genetic variation lays the foundation for genotype selection with respect to higher Zn concentration.Abbreviations: CCA, canonical correlation analysis; CIMMYT, international maize and wheat improvement center; DTZ, diphenyl-thiocarbazone; GCV, genotypic coefficients of variations; GE, germination energy; GS, germination speed; GV, germination value; MTG, mean time of germination; PCA, principal component analysis; PCV, phenotypic coefficients of variations; RCBD, randomized complete block design; RIL, recombinant inbred line; TPN, total pixel number.

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“…In recent years, the development of open-source software specially designed for the production of high-quality and interactive plots is becoming very active in various scientific fields [5][6][7]. Novel open source applications have also been developed to customize the graphical output of the Bayesian analysis [8].…”

Section: Introductionmentioning

confidence: 99%

StructuRly: A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis

Criscuolo¹,

Angelini²

2020

PLoS ONE

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Population genetics focuses on the analysis of genetic differences within and betweengroup of individuals and the inference of the populations' structure. These analyses are usually carried out using Bayesian clustering or maximum likelihood estimation algorithms that assign individuals to a given population depending on specific genetic patterns. Although several tools were developed to perform population genetics analysis, their standard graphical outputs may not be sufficiently informative for users lacking interactivity and complete information. StructuRly aims to resolve this problem by offering a complete environment for population analysis. In particular, StructuRly combines the statistical power of the R language with the friendly interfaces implemented using the shiny libraries to provide a novel tool for performing population clustering, evaluating several genetic indexes, and comparing results. Moreover, graphical representations are interactive and can be easily personalized. StructuRly is available either as R package on GitHub, with detailed information for its installation and use and as shinyapps.io servers for those users who are not familiar with R and the RStudio IDE. The application has been tested on Linux, macOS and Windows operative systems and can be launched as a shiny app in every web browser.

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shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics

Cited by 111 publications

References 29 publications

Loss of TLE3 promotes the mitochondrial program in beige adipocytes and improves glucose metabolism

Loss of TLE3 promotes the mitochondrial program in beige adipocytes and improves glucose metabolism

Foliar applied zinc increases yield, zinc concentration, and germination in wheat genotypes

StructuRly: A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis

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