miRTarVis: an interactive visual analysis tool for microRNA-mRNA expression profile data

Jung, Daekyoung; Kim, Bohyoung; Freishtat, Robert J.; Giri, Manta; Hoffman, Eric P.; Seo, Jinwook

doi:10.1186/1753-6561-9-s6-s2

Cited by 75 publications

(88 citation statements)

References 24 publications

(30 reference statements)

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“…The family data set distributed for GAW19 is an expanded version of that used for GAW18, which has been previously described in detail [1]. We provide here only a brief summary of this data set.…”

Section: Methodsmentioning

confidence: 99%

“…Data distributed for the workshop included whole genome sequence (WGS) and gene expression in 959 individuals in a set of 20 Mexican American families [1] and whole exome sequence in a set of 1943 unrelated Mexican American individuals drawn from a larger multi-ethnic case/control study [2]. The genotype calls provided for odd-numbered autosomes previously underwent quality control screening and were pre-cleaned.…”

Section: Introductionmentioning

confidence: 99%

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Omics-squared: human genomic, transcriptomic and phenotypic data for genetic analysis workshop 19

et al. 2016

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BackgroundThe Genetic Analysis Workshops (GAW) are a forum for development, testing, and comparison of statistical genetic methods and software. Each contribution to the workshop includes an application to a specified data set. Here we describe the data distributed for GAW19, which focused on analysis of human genomic and transcriptomic data.MethodsGAW19 data were donated by the T2D-GENES Consortium and the San Antonio Family Heart Study and included whole genome and exome sequences for odd-numbered autosomes, measures of gene expression, systolic and diastolic blood pressures, and related covariates in two Mexican American samples. These two samples were a collection of 20 large families with whole genome sequence and transcriptomic data and a set of 1943 unrelated individuals with exome sequence. For each sample, simulated phenotypes were constructed based on the real sequence data. ‘Functional’ genes and variants for the simulations were chosen based on observed correlations between gene expression and blood pressure. The simulations focused primarily on additive genetic models but also included a genotype-by-medication interaction. A total of 245 genes were designated as ‘functional’ in the simulations with a few genes of large effect and most genes explaining < 1 % of the trait variation. An additional phenotype, Q1, was simulated to be correlated among related individuals, based on theoretical or empirical kinship matrices, but was not associated with any sequence variants. Two hundred replicates of the phenotypes were simulated. The GAW19 data are an expansion of the data used at GAW18, which included the family-based whole genome sequence, blood pressure, and simulated phenotypes, but not the gene expression data or the set of 1943 unrelated individuals with exome sequence.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Omics-squared: human genomic, transcriptomic and phenotypic data for genetic analysis workshop 19

et al. 2016

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“…As in past years, a simulated phenotype data set was also provided. A brief description of the data sets follows while a more detailed description can be found in Blangero et al [1]. …”

Section: Genetic Analysis Workhop 19mentioning

confidence: 99%

“…In addition, a normally-distributed trait, Q1, was simulated that was not influenced by any genetic variants, but was correlated between family members (in the family data set). The simulation model is described in detail in Blangero et al [1]. …”

Section: Genetic Analysis Workhop 19mentioning

confidence: 99%

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Genetic Analysis Workshop 19: methods and strategies for analyzing human sequence and gene expression data in extended families and unrelated individuals

et al. 2016

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Genetic Analysis Workshop 19 provided a platform for developing and evaluating statistical methods to analyze whole-genome sequence and gene expression data from a pedigree-based sample, as well as whole-exome sequence data from a large cohort of unrelated individuals. In this article we present an overview of the data sets, the GAW experience, and summaries of the contributions arranged into nine methodological themes.

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Cross‐kingdom regulation by plant‐derived miRNAs in mammalian systems

Yang,

Feng

2023

Anim Models and Exp Med

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MicroRNAs (miRNAs) are small noncoding RNA molecules ubiquitously distributed across diverse organisms, serving as pivotal regulators of genetic expression. Notably, plant‐derived miRNAs have been demonstrated to have unique bioactivity and certain stability in mammalian systems, thereby facilitating their capacity for cross‐kingdom modulation of gene expression. While there is substantial evidence supporting the regulation of mammalian cells by plant‐derived miRNAs, several questions remain unanswered. Specifically, a comprehensive investigation of the mechanisms underlying the stability and transport of plant miRNAs and their cross‐kingdom regulation of gene expression in mammals remains to be done. In this review, we summarized the origin, processing, and functional mechanisms of plant miRNAs in mammalian tissues and circulation, emphasizing their greater resistance to mammalian digestion and circulation systems compared to animal miRNAs. Additionally, we introduce four well‐known plant miRNAs that have been extensively studied for their functions and mechanisms in mammalian systems. By delving into these aspects, we aim to offer a fundamental understanding of this intriguing field and shed light on the complex interactions between plant miRNAs and mammalian biology.

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miRTarVis: an interactive visual analysis tool for microRNA-mRNA expression profile data

Cited by 75 publications

References 24 publications

Omics-squared: human genomic, transcriptomic and phenotypic data for genetic analysis workshop 19

Omics-squared: human genomic, transcriptomic and phenotypic data for genetic analysis workshop 19

Genetic Analysis Workshop 19: methods and strategies for analyzing human sequence and gene expression data in extended families and unrelated individuals

Cross‐kingdom regulation by plant‐derived miRNAs in mammalian systems

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