Evaluating statistical analysis models for RNA sequencing experiments

Reeb, Pablo; Steibel, Juan P.

doi:10.3389/fgene.2013.00178

Cited by 33 publications

(50 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Robles et al (2012) likewise compared 3 methods and found inflated type I error rates for some methods and conservative performance from others. Reeb and Steibel (2013) compared 3 methods using "plasmodes" (resampled data) and found inflated type I error rates for small significance levels. Guo, Li, Ye, and Shyr (2013) compare 6 methods and conclude that all "suffer from over-sensitivity".…”

Section: Discussionmentioning

confidence: 99%

Excess False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

Rocke

Ruan

Zhang

et al. 2015

Preprint

View full text Add to dashboard Cite

Motivation: An important property of a valid method for testing for differential expression is that the false positive rate should at least roughly correspond to the p-value cutoff, so that if 10,000 genes are tested at a p-value cutoff of 10 −4 , and if all the null hypotheses are true, then there should be only about 1 gene declared to be significantly differentially expressed. We tested this by resampling from existing RNA-Seq data sets and also by matched negative binomial simulations.Results: Methods we examined, which rely strongly on a negative binomial model, such as edgeR, DESeq, and DESeq2, show large numbers of false positives in both the resampled real-data case and in the simulated negative binomial case. This also occurs with a negative binomial generalized linear model function in R. Methods that use only the variance function, such as limma-voom, do not show excessive false positives, as is also the case with a variance stabilizing transformation followed by linear model analysis with limma. The excess false positives are likely caused by apparently small biases in estimation of negative binomial dispersion and, perhaps surprisingly, occur mostly when the mean and/or the dispersion is high, rather than for low-count genes. Contact:dmrocke@ucdavis.edu, lruan@ucdavis.edu, yilzhang@ucdavis.edu, gt4636b@gatech.edu, bpdurbin@ucdavis.edu, saviran@ucdavis.edu.Supplementary Information: The computational tools developed for this study are freely available via our website http://dmrocke.ucdavis.edu/software.html. They can be downloaded as R code or run directly through an interactive web-based shiny application to reproduce the analysis presented here per a user's choice of dataset and the methods to be evaluated.

show abstract

Section: Discussionmentioning

confidence: 99%

Excess False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

Rocke

Ruan

Zhang

et al. 2015

Preprint

View full text Add to dashboard Cite

show abstract

“…Principal component analysis (PCA) of the twelve liver transcriptomes was applied to examine the contribution of each transcript to the separation of the classes3435. Then, fastq formatted reads from the two diploid parents and two hybrid offspring were mapped to the reference genome using TopHat23637.…”

Section: Methodsmentioning

confidence: 99%

Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae

Ren

Tao

et al. 2016

Sci Rep

View full text Add to dashboard Cite

Hybridization and polyploidization are considered important driving forces that form new epigenetic regulations. To study the changing patterns of expression accompanying hybridization and polyploidization, we used RNA-seq and qRT-PCR to investigate global expression and homoeologue expression in diploid and tetraploid hybrids of Carassius auratus red var. (♀) (R) and Cyprinus carpio (♂) (C). By comparing the relative expression levels between the hybrids and their parents, we defined the expression level dominance (ELD) and homoeologue expression bias (HEB) in liver tissue. The results showed that polyploidization contributed to the conversion of homoeologue ELD. In addition, hybridization had more effect on the change in HEB than polyploidization, while polyploidization had more effect on the change of global gene expression than hybridization. Meanwhile, similar expression patterns were found in growth-related genes. The results suggested that hybridization and polyploidization result in differential degrees of maternal HEB in three tissues (liver, muscle and ovary) tested. The results of this study will increase our understanding of the underlying regulation mechanism of rapid growth in diploid hybrids and allotetraploids. The differential degrees of global expression and homoeologue expression contribute to growth heterosis in newly formed hybrids, ensuring the on-going success of allotetraploid speciation.

show abstract

“…Transcriptome de novo assembly was carried out with a short-reads assembly program (Trinity) [54], using three independent software modules called Inchworm, Chrysalis, and Butterfly. Principal component analysis (PCA) of nine liver transcriptomes was applied to examine the contribution of each transcript to the separation of the classes [55, 56] (Additional file 9). …”

Section: Methodsmentioning

confidence: 99%

Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish

Ren

Tang

et al. 2017

BMC Genomics

View full text Add to dashboard Cite

BackgroundPolyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. The gene expression of diverged genomes and regulatory interactions are still unclear in lower vertebrates.ResultsWe generated 229 million cleaned reads (42.23 Gbp) from triploid of maternal grass carp (Ctenopharyngodon idellus, Cyprininae, 2n = 48) × paternal blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48) and their diploid parents using next-generation sequencing. In total, 157,878 contigs were assembled and 15,444 genes were annotated. We examined gene expression level changes among the parents and their triploid offspring. The mechanisms of dosage compensation that reduced triploid expression levels to the diploid state were determined in triploid fish. In this situation, novel gene expression and gene silencing were observed. Then, we established a model to determine the extent and direction of expression level dominance (ELD) and homoeolog expression bias (HEB) based on the relative expression level among the parents and their triploid offspring.ConclusionsOur results showed that the genome-wide ELD was biased toward maternal genome in triploid. Extensive alterations in homoeolog expression suggested a combination of regulatory and epigenetic interactions through the transcriptome network. Additionally, the expression patterns of growth genes provided insights into the relationship between the characteristics of growth and underlying mechanisms in triploids. Regulation patterns of triploid state suggest that various expression levels from the initial genomic merger have important roles in adaptation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3424-5) contains supplementary material, which is available to authorized users.

show abstract

Evaluating statistical analysis models for RNA sequencing experiments

Cited by 33 publications

References 41 publications

Excess False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

Excess False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae

Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish

Contact Info

Product

Resources

About