Cited by 424Gene expression and cancer classificationGenomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

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Comparison of software packages for detecting differential expression in RNA-seq studies

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Seyednasrollah, F., Laiho, A., Elo, L. L.·2015·Briefings in Bioinformatics

DOI 10.1093/bib/bbt086PMC PMC4293378

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Abstract

RNA-sequencing (RNA-seq) has rapidly become a popular tool to characterize transcriptomes. A fundamental research problem in many RNA-seq studies is the identification of reliable molecular markers that show differential expression between distinct sample groups. Together with the growing popularity of RNA-seq, a number of data analysis methods and pipelines have already been developed for this task. Currently, however, there is no clear consensus about the best practices yet, which makes the choice of an appropriate method a daunting task especially for a basic user without a strong statistical or computational background. To assist the choice, we perform here a systematic comparison of eight widely used software packages and pipelines for detecting differential expression between sample groups in a practical research setting and provide general guidelines for choosing a robust pipeline. In general, our results demonstrate how the data analysis tool utilized can markedly affect the outcome of the data analysis, highlighting the importance of this choice.

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Authors: Seyednasrollah, F., Laiho, A., & Elo, L. L.
Affiliations: University of Turku (FI)
Corresponding author: Elo, L. L.
ORCID: Seyednasrollah, F.
Laiho, A.
Elo, L. L.
Venue: Briefings in Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2013-12-02
Volume: 16
Issue: 1
Pages: 59-70
ISSN: 1467-5463 (ISSN-L)
1477-4054
DOI: 10.1093/bib/bbt086
PMC: PMC4293378
OpenAlex: W2123579165
Cited by: 421
References: 27
Citations by year: 2026: 8 · 2025: 10 · 2024: 18 · 2023: 35 · 2022: 34 · 2021: 39 · 2020: 41 · 2019: 41 · 2018: 39 · 2017: 55 · 2016: 52 · 2015: 32 · 2014: 16 · 2013: 1
FWCI: 15.09
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
Locations: Briefings in Bioinformatics (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Funders: Academy of Finland
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords: differential gene expression, RNA-seq, software comparison, bioinformatics pipeline, molecular markers, gene expression profiling
MeSH terms: Animals, Data Interpretation, Statistical, Humans, Software, Sequence Analysis, RNA, Mice, Transcriptome

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Comparison of software packages for detecting differential expression in RNA-seq studies

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