Differential expression analysis for sequence count data

Anders Simon ¹

Huber Wolfgang ¹

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European Molecular Biology Laboratory, heidelberg, Germany |

Publication type: Journal Article

Publication date: 2010-10-28

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DOI: 10.1186/gb-2010-11-10-r106

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PubMed ID: 20979621

Abstract

High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.

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Citations by journals

	100 200 300 400 500 600
PLoS ONE	PLoS ONE, 553, 4.61% PLoS ONE 553 publications, 4.61%
Scientific Reports	Scientific Reports, 466, 3.88% Scientific Reports 466 publications, 3.88%
BMC Genomics	BMC Genomics, 464, 3.87% BMC Genomics 464 publications, 3.87%
Nature Communications	Nature Communications, 254, 2.12% Nature Communications 254 publications, 2.12%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 212, 1.77% International Journal of Molecular Sciences 212 publications, 1.77%
Frontiers in Plant Science	Frontiers in Plant Science, 200, 1.67% Frontiers in Plant Science 200 publications, 1.67%
Nucleic Acids Research	Nucleic Acids Research, 165, 1.38% Nucleic Acids Research 165 publications, 1.38%
Cell Reports	Cell Reports, 147, 1.23% Cell Reports 147 publications, 1.23%
Bioinformatics	Bioinformatics, 144, 1.2% Bioinformatics 144 publications, 1.2%
Frontiers in Microbiology	Frontiers in Microbiology, 139, 1.16% Frontiers in Microbiology 139 publications, 1.16%
BMC Plant Biology	BMC Plant Biology, 125, 1.04% BMC Plant Biology 125 publications, 1.04%
PLoS Genetics	PLoS Genetics, 115, 0.96% PLoS Genetics 115 publications, 0.96%
BMC Bioinformatics	BMC Bioinformatics, 111, 0.93% BMC Bioinformatics 111 publications, 0.93%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 109, 0.91% Proceedings of the National Academy of Sciences of the United States of America 109 publications, 0.91%
eLife	eLife, 106, 0.88% eLife 106 publications, 0.88%
Frontiers in Genetics	Frontiers in Genetics, 97, 0.81% Frontiers in Genetics 97 publications, 0.81%
Methods in Molecular Biology	Methods in Molecular Biology, 90, 0.75% Methods in Molecular Biology 90 publications, 0.75%
Nature	Nature, 87, 0.73% Nature 87 publications, 0.73%
PeerJ	PeerJ, 84, 0.7% PeerJ 84 publications, 0.7%
Genome Research	Genome Research, 80, 0.67% Genome Research 80 publications, 0.67%
Genes	Genes, 73, 0.61% Genes 73 publications, 0.61%
Cell	Cell, 72, 0.6% Cell 72 publications, 0.6%
Gene	Gene, 65, 0.54% Gene 65 publications, 0.54%
Plant Journal	Plant Journal, 59, 0.49% Plant Journal 59 publications, 0.49%
Oncotarget	Oncotarget, 57, 0.48% Oncotarget 57 publications, 0.48%
Science	Science, 54, 0.45% Science 54 publications, 0.45%
G3: Genes, Genomes, Genetics	G3: Genes, Genomes, Genetics, 54, 0.45% G3: Genes, Genomes, Genetics 54 publications, 0.45%
Molecular Ecology	Molecular Ecology, 51, 0.43% Molecular Ecology 51 publications, 0.43%
Applied and Environmental Microbiology	Applied and Environmental Microbiology, 50, 0.42% Applied and Environmental Microbiology 50 publications, 0.42%
	100 200 300 400 500 600

Citations by publishers

	500 1000 1500 2000 2500 3000 3500
Springer Nature	Springer Nature, 3021, 25.18% Springer Nature 3021 publications, 25.18%
Elsevier	Elsevier, 1716, 14.3% Elsevier 1716 publications, 14.3%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 785, 6.54% Public Library of Science (PLoS) 785 publications, 6.54%
Wiley	Wiley, 729, 6.08% Wiley 729 publications, 6.08%
Frontiers Media S.A.	Frontiers Media S.A., 695, 5.79% Frontiers Media S.A. 695 publications, 5.79%
Oxford University Press	Oxford University Press, 661, 5.51% Oxford University Press 661 publications, 5.51%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 648, 5.4% Multidisciplinary Digital Publishing Institute (MDPI) 648 publications, 5.4%
American Society for Microbiology	American Society for Microbiology, 233, 1.94% American Society for Microbiology 233 publications, 1.94%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 152, 1.27% Cold Spring Harbor Laboratory 152 publications, 1.27%
Taylor & Francis	Taylor & Francis, 120, 1% Taylor & Francis 120 publications, 1%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 117, 0.98% American Association for the Advancement of Science (AAAS) 117 publications, 0.98%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 109, 0.91% Proceedings of the National Academy of Sciences (PNAS) 109 publications, 0.91%
eLife Sciences Publications	eLife Sciences Publications, 106, 0.88% eLife Sciences Publications 106 publications, 0.88%
PeerJ	PeerJ, 84, 0.7% PeerJ 84 publications, 0.7%
Genetics Society of America	Genetics Society of America, 80, 0.67% Genetics Society of America 80 publications, 0.67%
The Company of Biologists	The Company of Biologists, 78, 0.65% The Company of Biologists 78 publications, 0.65%
Impact Journals	Impact Journals, 75, 0.63% Impact Journals 75 publications, 0.63%
American Association for Cancer Research (AACR)	American Association for Cancer Research (AACR), 72, 0.6% American Association for Cancer Research (AACR) 72 publications, 0.6%
Hindawi Limited	Hindawi Limited, 62, 0.52% Hindawi Limited 62 publications, 0.52%
American Chemical Society (ACS)	American Chemical Society (ACS), 59, 0.49% American Chemical Society (ACS) 59 publications, 0.49%
EMBO press	EMBO press, 51, 0.43% EMBO press 51 publications, 0.43%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 49, 0.41% American Society for Biochemistry and Molecular Biology 49 publications, 0.41%
SAGE	SAGE, 48, 0.4% SAGE 48 publications, 0.4%
American Society of Plant Biologists	American Society of Plant Biologists, 43, 0.36% American Society of Plant Biologists 43 publications, 0.36%
American Society for Clinical Investigation	American Society for Clinical Investigation, 41, 0.34% American Society for Clinical Investigation 41 publications, 0.34%
Spandidos Publications	Spandidos Publications, 40, 0.33% Spandidos Publications 40 publications, 0.33%
Mary Ann Liebert	Mary Ann Liebert, 38, 0.32% Mary Ann Liebert 38 publications, 0.32%
Wolters Kluwer Health	Wolters Kluwer Health, 36, 0.3% Wolters Kluwer Health 36 publications, 0.3%
Rockefeller University Press	Rockefeller University Press, 35, 0.29% Rockefeller University Press 35 publications, 0.29%
	500 1000 1500 2000 2500 3000 3500

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