Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

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Abstract

A large number of computational methods have been developed for analyzing differential gene expression in RNA-seq data. We describe a comprehensive evaluation of common methods using the SEQC benchmark dataset and ENCODE data. We consider a number of key features, including normalization, accuracy of differential expression detection and differential expression analysis when one condition has no detectable expression. We find significant differences among the methods, but note that array-based methods adapted to RNA-seq data perform comparably to methods designed for RNA-seq. Our results demonstrate that increasing the number of replicate samples significantly improves detection power over increased sequencing depth.

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The transcriptional landscape of the yeast genome defined by RNA sequencing.

U Nagalakshmi, Zhong Wang, K. Waern … (2008)

The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames also were identified for many yeast genes. We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated.

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Moderated statistical tests for assessing differences in tag abundance.

D. Robinson, Gordon K. Smyth (2007)

Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. They are sensitive technologies for measuring gene expression on a genomic scale, without the need for prior knowledge of the genome sequence. As the cost of sequencing DNA decreases, the number of DGE datasets is expected to grow dramatically. Various tests of differential expression have been proposed for replicated DGE data using binomial, Poisson, negative binomial or pseudo-likelihood (PL) models for the counts, but none of the these are usable when the number of replicates is very small. We develop tests using the negative binomial distribution to model overdispersion relative to the Poisson, and use conditional weighted likelihood to moderate the level of overdispersion across genes. Not only is our strategy applicable even with the smallest number of libraries, but it also proves to be more powerful than previous strategies when more libraries are available. The methodology is equally applicable to other counting technologies, such as proteomic spectral counts. An R package can be accessed from http://bioinf.wehi.edu.au/resources/

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Evaluation of DNA microarray results with quantitative gene expression platforms.

Kathryn Keho, Roderick V. Jensen, Cecilie Boysen … (2006)

We have evaluated the performance characteristics of three quantitative gene expression technologies and correlated their expression measurements to those of five commercial microarray platforms, based on the MicroArray Quality Control (MAQC) data set. The limit of detection, assay range, precision, accuracy and fold-change correlations were assessed for 997 TaqMan Gene Expression Assays, 205 Standardized RT (Sta)RT-PCR assays and 244 QuantiGene assays. TaqMan is a registered trademark of Roche Molecular Systems, Inc. We observed high correlation between quantitative gene expression values and microarray platform results and found few discordant measurements among all platforms. The main cause of variability was differences in probe sequence and thus target location. A second source of variability was the limited and variable sensitivity of the different microarray platforms for detecting weakly expressed genes, which affected interplatform and intersite reproducibility of differentially expressed genes. From this analysis, we conclude that the MAQC microarray data set has been validated by alternative quantitative gene expression platforms thus supporting the use of microarray platforms for the quantitative characterization of gene expression.

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Author and article information

Contributors

Franck Rapaport

Raya Khanin

Yupu Liang

Mono Pirun

Azra Krek

Paul Zumbo

Christopher E Mason

Nicholas D Socci

Doron Betel

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central

ISSN (Print): 1465-6906

ISSN (Electronic): 1465-6914

Publication date (Print): 2013

Publication date (Electronic): 10 September 2013

Volume: 14

Issue: 9

Page: R95

Affiliations

[1 ]Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA

[2 ]Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10021, USA

[3 ]Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, 10021, USA

[4 ]Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, 10021, USA

Article

Publisher ID: gb-2013-14-9-r95

DOI: 10.1186/gb-2013-14-9-r95

PMC ID: 4054597

PubMed ID: 24020486

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

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Most cited references 10

The transcriptional landscape of the yeast genome defined by RNA sequencing.

Moderated statistical tests for assessing differences in tag abundance.

Evaluation of DNA microarray results with quantitative gene expression platforms.

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