scholarly journals Bayesian estimation of differential transcript usage from RNA-seq data

2017 ◽  
Vol 16 (5-6) ◽  
Author(s):  
Panagiotis Papastamoulis ◽  
Magnus Rattray
Keyword(s):  
Bayesian Methods ◽  
Bayesian Model ◽  
Bayes Factor ◽  
Null Model ◽  
Rna Seq ◽  
Mcmc Sampling ◽  
False Discovery ◽  
Fully Bayesian ◽  
Per Gene ◽  
Generation Sequencing

AbstractNext generation sequencing allows the identification of genes consisting of differentially expressed transcripts, a term which usually refers to changes in the overall expression level. A specific type of differential expression is differential transcript usage (DTU) and targets changes in the relative within gene expression of a transcript. The contribution of this paper is to: (a) extend the use of cjBitSeq to the DTU context, a previously introduced Bayesian model which is originally designed for identifying changes in overall expression levels and (b) propose a Bayesian version of DRIMSeq, a frequentist model for inferring DTU. cjBitSeq is a read based model and performs fully Bayesian inference by MCMC sampling on the space of latent state of each transcript per gene. BayesDRIMSeq is a count based model and estimates the Bayes Factor of a DTU model against a null model using Laplace’s approximation. The proposed models are benchmarked against the existing ones using a recent independent simulation study as well as a real RNA-seq dataset. Our results suggest that the Bayesian methods exhibit similar performance with DRIMSeq in terms of precision/recall but offer better calibration of False Discovery Rate.

Distinguishing Normative Processes From Noise

2016 ◽  
Vol 79 (4) ◽  
pp. 311-332 ◽  
Author(s):  
Jonathan H. Morgan ◽  
Kimberly B. Rogers ◽  
Mao Hu
Keyword(s):  
Bayesian Methods ◽  
Bayesian Model ◽  
Stepwise Regression ◽  
Bayesian Model Averaging ◽  
Model Averaging ◽  
Ground Truth ◽  
Model Specification ◽  
Affect Control Theory ◽  
False Discovery ◽  
Social Events

This research evaluates the relative merits of two established and two newly proposed methods for modeling impressions of social events: stepwise regression, ANOVA, Bayesian model averaging, and Bayesian model sampling. Models generated with each method are compared against a ground truth model to assess performance at variable selection and coefficient estimation. We also assess the theoretical impacts of different modeling choices. Results show that the ANOVA procedure has a significantly lower false discovery rate than stepwise regression, whereas Bayesian methods exhibit higher true positive rates and comparable false discovery rates to ANOVA. Bayesian methods also generate coefficient estimates with less bias and variance than either stepwise regression or ANOVA. We recommend the use of Bayesian methods for model specification in affect control theory.

The Spirit of Cromwell’s Rule

2018 ◽  
Author(s):  
Timothy McGrew
Keyword(s):  
Bayesian Methods ◽  
Bayesian Model ◽  
Bayesian Probability ◽  
Standard Textbook ◽  
Per Se

One of the central complaints about Bayesian probability is that it places no constraints on individual subjectivity in one’s initial probability assignments. Those sympathetic to Bayesian methods have responded by adding restrictions motivated by broader epistemic concerns about the possibility of changing one’s mind. This chapter explores some cases where, intuitively, a straightforward Bayesian model yields unreasonable results. Problems arise in these cases not because there is something wrong with the Bayesian formalism per se but because standard textbook illustrations teach us to represent our inferences in simplified ways that break down in extreme cases. It also explores some interesting limitations on the extent to which successive items of evidence ought to induce us to change our minds when certain screening conditions obtain.

scholarly journals Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1423
Author(s):  
André Albuquerque ◽  
Cristina Óvilo ◽  
Yolanda Núñez ◽  
Rita Benítez ◽  
Adrián López-Garcia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Muscle Growth ◽  
Rna Seq ◽  
Next Generation Sequencing Technology ◽  
Pig Breeds ◽  
Nfkb Activation ◽  
Main Gene ◽  
Slow Type ◽  
Longissimus Lumborum ◽  
Generation Sequencing

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

scholarly journals A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula)

2021 ◽  
Author(s):  
Gangjun Zhao ◽  
Caixia Luo ◽  
Jianning Luo ◽  
Junxing Li ◽  
Hao Gong ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Recessive Gene ◽  
Genomic Region ◽  
Dwarf Mutant ◽  
Rna Seq ◽  
Dwarf Phenotype ◽  
Sponge Gourd ◽  
Response To Stress ◽  
Luffa Acutangula ◽  
Generation Sequencing

Abstract Key message A dwarfism gene LacDWARF1 was mapped by combined BSA-Seq and comparative genomics analyses to a 65.4 kb physical genomic region on chromosome 05. Abstract Dwarf architecture is one of the most important traits utilized in Cucurbitaceae breeding because it saves labor and increases the harvest index. To our knowledge, there has been no prior research about dwarfism in the sponge gourd. This study reports the first dwarf mutant WJ209 with a decrease in cell size and internodes. A genetic analysis revealed that the mutant phenotype was controlled by a single recessive gene, which is designated Lacdwarf1 (Lacd1). Combined with bulked segregate analysis and next-generation sequencing, we quickly mapped a 65.4 kb region on chromosome 5 using F2 segregation population with InDel and SNP polymorphism markers. Gene annotation revealed that Lac05g019500 encodes a gibberellin 3β-hydroxylase (GA3ox) that functions as the most likely candidate gene for Lacd1. DNA sequence analysis showed that there is an approximately 4 kb insertion in the first intron of Lac05g019500 in WJ209. Lac05g019500 is transcribed incorrectly in the dwarf mutant owing to the presence of the insertion. Moreover, the bioactive GAs decreased significantly in WJ209, and the dwarf phenotype could be restored by exogenous GA3 treatment, indicating that WJ209 is a GA-deficient mutant. All these results support the conclusion that Lac05g019500 is the Lacd1 gene. In addition, RNA-Seq revealed that many genes, including those related to plant hormones, cellular process, cell wall, membrane and response to stress, were significantly altered in WJ209 compared with the wild type. This study will aid in the use of molecular marker-assisted breeding in the dwarf sponge gourd.

scholarly journals Erratum: Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

2014 ◽  
Vol 32 (11) ◽  
pp. 1166-1166 ◽  
Author(s):  
Sheng Li ◽  
Scott W Tighe ◽  
Charles M Nicolet ◽  
Deborah Grove ◽  
Shawn Levy ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Next Generation ◽  
Generation Sequencing

Uncertainty of prior and posterior model probability: Implications for interpreting Bayes factors

2021 ◽  
Author(s):  
John K. Kruschke
Keyword(s):  
Posterior Distribution ◽  
Bayesian Model ◽  
Model Comparison ◽  
Bayes Factor ◽  
Bayes Factors ◽  
Prior Model ◽  
Bayesian Hypothesis Testing ◽  
Bayesian Model Comparison ◽  
Posterior Model Probability ◽  
Model Probability

In most applications of Bayesian model comparison or Bayesian hypothesis testing, the results are reported in terms of the Bayes factor only, not in terms of the posterior probabilities of the models. Posterior model probabilities are not reported because researchers are reluctant to declare prior model probabilities, which in turn stems from uncertainty in the prior. Fortunately, Bayesian formalisms are designed to embrace prior uncertainty, not ignore it. This article provides a novel derivation of the posterior distribution of model probability, and shows many examples. The posterior distribution is useful for making decisions taking into account the uncertainty of the posterior model probability. Benchmark Bayes factors are provided for a spectrum of priors on model probability. R code is posted at https://osf.io/36527/. This framework and tools will improve interpretation and usefulness of Bayes factors in all their applications.

scholarly journals Grouped False-Discovery Rate for Removing the Gene-set-Level Bias of RNA-seq

2013 ◽  
Vol 9 ◽  
pp. EBO.S13099 ◽  
Author(s):  
Tae Young Yang ◽  
Seongmun Jeong
Keyword(s):  
False Discovery Rate ◽  
Rna Seq ◽  
Gene Set ◽  
False Discovery

scholarly journals Genetic effect in leaf and xylem transcriptome variations among Eucalyptus urophylla x grandis hybrids in field conditions

2018 ◽  
Vol 67 (1) ◽  
pp. 57-65
Author(s):  
Alexandre Vaillant ◽  
Astrid Honvault ◽  
Stéphanie Bocs ◽  
Maryline Summo ◽  
Garel Makouanzi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Variance Components ◽  
Genetic Effect ◽  
Field Conditions ◽  
Eucalyptus Urophylla ◽  
Rna Seq ◽  
Intermediate Phenotypes ◽  
False Discovery ◽  
Hybrid Clones ◽  
Selection Of

Abstract To assess the genetic and environmental components of gene-expression variation among trees we used RNA-seq technology and Eucalyptus urophylla x grandis hybrid clones tested in field conditions. Leaf and xylem transcriptomes of three 20 month old clones differing in terms of growth, repeated in two blocks, were investigated. Transcriptomes were very similar between ramets. The number of expressed genes was significantly (P<0.05) higher in leaf (25,665±634) than in xylem (23,637±1,241). A pairwise clone comparisons approach showed that 4.5 to 14 % of the genes were diffe­rentially expressed (false discovery rate [FDR]<0.05) in leaf and 7.1 to 16 % in xylem. An assessment of among clone variance components revealed significant results in leaf and xylem in 3431 (248) genes (at FDR<0.2) and 160 (3) (at FDR<0.05), respectively. These two complementary approa­ches displayed correlated results. A focus on the phenylpro­panoid, cellulose and xylan pathways revealed a large majo­rity of low expressed genes and a few highly expressed ones, with RPKM values ranging from nearly 0 to 600 in leaf and 10,000 in xylem. Out of the 115 genes of these pathways, 45 showed differential expression for at least one pair of geno­type, five of which displaying also clone variance compo­nents. These preliminary results are promising in evaluating whether gene expression can serve as possible ‘intermediate phenotypes’ that could improve the accuracy of selection of grossly observable traits.

scholarly journals NGS comparison of Downy and Powdery mildew resistance genomic regions between 'Regent' and 'Red Globe'

2021 ◽  
Author(s):  
Carel Jacobus van Heerden ◽  
Phylli Burger ◽  
Johan Theodorus Burger ◽  
Renée Prins
Keyword(s):  
Next Generation Sequencing ◽  
Powdery Mildew ◽  
Downy Mildew ◽  
Genetic Factors ◽  
Powdery Mildew Resistance ◽  
Negative Impact ◽  
Chromosome 15 ◽  
Genomic Regions ◽  
Per Gene ◽  
Generation Sequencing

Powdery and downy mildew have a large negative impact on grape production worldwide. Quantitative trait loci (QTL) mapping projects have identified several loci for the genetic factors responsible for resistance to these pathogens. Several of these studies have focused on the cultivar Regent, which carries the resistance loci to downy mildew on chromosome 18 (Rpv3), as well powdery mildew on chromosome 15 (Ren3, Ren9). Several other minor resistance loci have also been identified on other chromosomes. Here we report on the re-sequencing of the Regent and Red Globe (susceptible) genomes using next generation sequencing. While the genome of Regent has more SNP variants than Red Globe, the distribution of these variants across the two genomes is not the same, nor is it uniform. The variation per gene shows that some genes have higher SNP density than others and that the number of SNPs for a given gene is not always the same for the two cultivars. In this study, we investigate the effectiveness of studying the variation of non-synonymous to synonymous SNP ratio's between resistant and susceptible cultivars in the target QTL regions as a strategy to narrow down the number of likely candidate genes for Rpv3, Ren3 and Ren9.

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