{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T08:56:11Z","timestamp":1776502571134,"version":"3.51.2"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,6]],"date-time":"2019-02-06T00:00:00Z","timestamp":1549411200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/H002286\/1"],"award-info":[{"award-number":["BB\/H002286\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/J00247X\/1"],"award-info":[{"award-number":["BB\/J00247X\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/M010066\/1"],"award-info":[{"award-number":["BB\/M010066\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/M004155\/1"],"award-info":[{"award-number":["BB\/M004155\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>RNA-seq experiments are usually carried out in three or fewer replicates. In order to work well with so few samples, differential gene expression (DGE) tools typically assume the form of the underlying gene expression distribution. In this paper, the statistical properties of gene expression from RNA-seq are investigated in the complex eukaryote, Arabidopsis thaliana, extending and generalizing the results of previous work in the simple eukaryote Saccharomyces cerevisiae.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We show that, consistent with the results in S.cerevisiae, more gene expression measurements in A.thaliana are consistent with being drawn from an underlying negative binomial distribution than either a log-normal distribution or a normal distribution, and that the size and complexity of the A.thaliana transcriptome does not influence the false positive rate performance of nine widely used DGE tools tested here. We therefore recommend the use of DGE tools that are based on the negative binomial distribution.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The raw data for the 17 WT Arabidopsis thaliana datasets is available from the European Nucleotide Archive (E-MTAB-5446). The processed and aligned data can be visualized in context using IGB (Freese et al., 2016), or downloaded directly, using our publicly available IGB quickload server at https:\/\/compbio.lifesci.dundee.ac.uk\/arabidopsisQuickload\/public_quickload\/ under \u2018RNAseq&amp;gt;Froussios2019\u2019. All scripts and commands are available from github at https:\/\/github.com\/bartongroup\/KF_arabidopsis-GRNA.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz089","type":"journal-article","created":{"date-parts":[[2019,2,5]],"date-time":"2019-02-05T07:33:02Z","timestamp":1549351982000},"page":"3372-3377","source":"Crossref","is-referenced-by-count":10,"title":["How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in\n                    <i>Arabidopsis thaliana<\/i>"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2812-0525","authenticated-orcid":false,"given":"Kimon","family":"Froussios","sequence":"first","affiliation":[{"name":"Division of Computational Biology, University of Dundee , Dundee, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9068-9654","authenticated-orcid":false,"given":"Nick J","family":"Schurch","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, University of Dundee , Dundee, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katarzyna","family":"Mackinnon","sequence":"additional","affiliation":[{"name":"Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marek","family":"Gierli\u0144ski","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, University of Dundee , Dundee, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C\u00e9line","family":"Duc","sequence":"additional","affiliation":[{"name":"Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK"},{"name":"GReD, Facult\u00e9 de M\u00e9decine 28 , place Henri Dunant BP 38 - 63001 CLERMONT-FERRAND"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gordon G","family":"Simpson","sequence":"additional","affiliation":[{"name":"Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK"},{"name":"Division of Plant Sciences, School of Life Sciences, University of Dundee , Dundee, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9014-5355","authenticated-orcid":false,"given":"Geoffrey J","family":"Barton","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, University of Dundee , Dundee, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,2,6]]},"reference":[{"key":"2023013108050502800_btz089-B1","doi-asserted-by":"crossref","first-page":"R106.","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol"},{"key":"2023013108050502800_btz089-B2","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/35048692","article-title":"Analysis of the genome sequence of the flowering plant Arabidopsis thaliana","volume":"408","year":"2000","journal-title":"Nature"},{"key":"2023013108050502800_btz089-B3","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Series B Methodol"},{"key":"2023013108050502800_btz089-B4","doi-asserted-by":"crossref","first-page":"e17820.","DOI":"10.1371\/journal.pone.0017820","article-title":"Evaluating gene expression in C57BL\/6J and DBA\/2J mouse striatum using RNA-Seq and microarrays","volume":"6","author":"Bottomly","year":"2011","journal-title":"PLoS One"},{"key":"2023013108050502800_btz089-B5","doi-asserted-by":"crossref","first-page":"94.","DOI":"10.1186\/1471-2105-11-94","article-title":"Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments","volume":"11","author":"Bullard","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023013108050502800_btz089-B6","doi-asserted-by":"crossref","first-page":"e576.","DOI":"10.7717\/peerj.576","article-title":"Error estimates for the analysis of differential expression from RNA-seq count data","volume":"2","author":"Burden","year":"2014","journal-title":"PeerJ"},{"key":"2023013108050502800_btz089-B7","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1093\/bioinformatics\/btt015","article-title":"Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression","volume":"29","author":"Busby","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013108050502800_btz089-B8","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1007\/s00709-012-0448-9","article-title":"On the physiological significance of alternative splicing events in higher plants","volume":"250","author":"Carvalho","year":"2013","journal-title":"Protoplasma"},{"key":"2023013108050502800_btz089-B9","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1080\/00031305.1990.10475751","article-title":"A suggestion for using powerful and informative tests of normality","volume":"44","author":"D'Agostino","year":"1990","journal-title":"Am. Stat"},{"key":"2023013108050502800_btz089-B10","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1093\/bib\/bbs046","article-title":"A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis","volume":"14","author":"Dillies","year":"2013","journal-title":"Brief. Bioinform"},{"key":"2023013108050502800_btz089-B11","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013108050502800_btz089-B12","doi-asserted-by":"crossref","first-page":"150.","DOI":"10.1186\/1471-2164-6-150","article-title":"Proposed methods for testing and selecting the ERCC external RNA controls","volume":"6","year":"2005","journal-title":"BMC Genomics"},{"key":"2023013108050502800_btz089-B13","doi-asserted-by":"crossref","first-page":"17","DOI":"10.2307\/3001420","article-title":"The significance of deviations from the expectation in a Poisson series","volume":"6","author":"Fisher","year":"1950","journal-title":"Biometrics"},{"key":"2023013108050502800_btz089-B14","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1093\/biostatistics\/kxt053","article-title":"Differential expression analysis of RNA-seq data at single-base resolution","volume":"15","author":"Frazee","year":"2014","journal-title":"Biostatistics"},{"key":"2023013108050502800_btz089-B15","doi-asserted-by":"crossref","first-page":"2089","DOI":"10.1093\/bioinformatics\/btw069","article-title":"Integrated genome browser: visual analytics platform for genomics","volume":"32","author":"Freese","year":"2016","journal-title":"Bioinformatics"},{"key":"2023013108050502800_btz089-B16","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nbt.3269","article-title":"Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation","volume":"33","author":"Gaidatzis","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2023013108050502800_btz089-B17","doi-asserted-by":"crossref","first-page":"3625","DOI":"10.1093\/bioinformatics\/btv425","article-title":"Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment","volume":"31","author":"Gierlinski","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013108050502800_btz089-B18","doi-asserted-by":"crossref","first-page":"S2.","DOI":"10.1186\/1471-2164-14-S8-S2","article-title":"Evaluation of read count based RNAseq analysis methods","volume":"14 (Suppl. 8)","author":"Guo","year":"2013","journal-title":"BMC Genomics"},{"key":"2023013108050502800_btz089-B19","doi-asserted-by":"crossref","first-page":"422.","DOI":"10.1186\/1471-2105-11-422","article-title":"baySeq: empirical Bayesian methods for identifying differential expression in sequence count data","volume":"11","author":"Hardcastle","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023013108050502800_btz089-B20","doi-asserted-by":"crossref","first-page":"D1003","DOI":"10.1093\/nar\/gku1200","article-title":"Araport: the Arabidopsis information portal","volume":"43","author":"Krishnakumar","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023013108050502800_btz089-B21","doi-asserted-by":"crossref","first-page":"R29.","DOI":"10.1186\/gb-2014-15-2-r29","article-title":"voom: precision weights unlock linear model analysis tools for RNA-seq read counts","volume":"15","author":"Law","year":"2014","journal-title":"Genome Biol"},{"key":"2023013108050502800_btz089-B22","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1093\/bioinformatics\/btt087","article-title":"EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments","volume":"29","author":"Leng","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013108050502800_btz089-B23","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1177\/0962280211428386","article-title":"Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data","volume":"22","author":"Li","year":"2013","journal-title":"Stat. Methods Med. Res"},{"key":"2023013108050502800_btz089-B24","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/biostatistics\/kxr031","article-title":"Normalization, testing, and false discovery rate estimation for RNA-sequencing data","volume":"13","author":"Li","year":"2012","journal-title":"Biostatistics"},{"key":"2023013108050502800_btz089-B25","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"2023013108050502800_btz089-B26","doi-asserted-by":"crossref","first-page":"550.","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023013108050502800_btz089-B27","doi-asserted-by":"crossref","DOI":"10.1515\/1544-6115.1826","article-title":"Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates","volume":"11","author":"Lund","year":"2012","journal-title":"Stat. Appl. Genet. Mol. Biol"},{"key":"2023013108050502800_btz089-B28","first-page":"293.","article-title":"Transform methods for testing the negative binomial hypothesis","volume":"65","author":"Meintanis","year":"2005","journal-title":"Statistica"},{"key":"2023013108050502800_btz089-B29","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"2023013108050502800_btz089-B30","doi-asserted-by":"crossref","first-page":"e25.","DOI":"10.1093\/nar\/gku1273","article-title":"Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns","volume":"43","author":"Moulos","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023013108050502800_btz089-B31","first-page":"1","article-title":"RNA-Seq: a method for comprehensive transcriptome analysis","volume":"11","author":"Nagalakshmi","year":"2010","journal-title":"Curr. Protoc. Mol. Biol"},{"key":"2023013108050502800_btz089-B32","volume-title":"R: A Language and Environment for Statistical Computing.","year":"2011"},{"key":"2023013108050502800_btz089-B33","doi-asserted-by":"crossref","first-page":"R95.","DOI":"10.1186\/gb-2013-14-9-r95","article-title":"Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data","volume":"14","author":"Rapaport","year":"2013","journal-title":"Genome Biol"},{"key":"2023013108050502800_btz089-B34","doi-asserted-by":"crossref","first-page":"e47.","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023013108050502800_btz089-B35","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023013108050502800_btz089-B36","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1261\/rna.053959.115","article-title":"How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?","volume":"22","author":"Schurch","year":"2016","journal-title":"RNA"},{"key":"2023013108050502800_btz089-B37","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1093\/bib\/bbt086","article-title":"Comparison of software packages for detecting differential expression in RNA-seq studies","volume":"16","author":"Seyednasrollah","year":"2015","journal-title":"Brief. Bioinform"},{"key":"2023013108050502800_btz089-B38","doi-asserted-by":"crossref","first-page":"2517","DOI":"10.1093\/bioinformatics\/btu324","article-title":"compcodeR\u2013an R package for benchmarking differential expression methods for RNA-seq data","volume":"30","author":"Soneson","year":"2014","journal-title":"Bioinformatics"},{"key":"2023013108050502800_btz089-B39","doi-asserted-by":"crossref","first-page":"91.","DOI":"10.1186\/1471-2105-14-91","article-title":"A comparison of methods for differential expression analysis of RNA-seq data","volume":"14","author":"Soneson","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023013108050502800_btz089-B40","doi-asserted-by":"crossref","first-page":"2213","DOI":"10.1101\/gr.124321.111","article-title":"Differential expression in RNA-seq: a matter of depth","volume":"21","author":"Tarazona","year":"2011","journal-title":"Genome Res"},{"key":"2023013108050502800_btz089-B41","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protoc"},{"key":"2023013108050502800_btz089-B42","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1093\/bioinformatics\/btp612","article-title":"DEGseq: an R package for identifying differentially expressed genes from RNA-seq data","volume":"26","author":"Wang","year":"2010","journal-title":"Bioinformatics"},{"key":"2023013108050502800_btz089-B43","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1007\/s11357-012-9410-1","article-title":"Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome","volume":"35","author":"Wood","year":"2013","journal-title":"Age (Dordr)"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/18\/3372\/48975135\/bioinformatics_35_18_3372.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/18\/3372\/48975135\/bioinformatics_35_18_3372.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,14]],"date-time":"2024-07-14T11:06:01Z","timestamp":1720955161000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/18\/3372\/5307752"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,2,6]]},"references-count":43,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2019,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz089","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/090753","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9,15]]},"published":{"date-parts":[[2019,2,6]]}}}