Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Search Page

Filters

My NCBI Filters

Results by year

Table representation of search results timeline featuring number of search results per year.

Year Number of Results
1947 1
1953 1
1954 1
1956 1
1957 1
1958 1
1959 1
1961 1
1963 1
1964 1
1979 1
1980 1
1981 2
1984 2
1987 1
1990 1
1991 1
1994 2
1995 1
1997 1
1999 2
2000 1
2002 1
2004 1
2007 1
2009 2
2010 3
2011 5
2012 20
2013 25
2014 24
2015 32
2016 54
2017 46
2018 65
2019 118
2020 128
2021 130
2022 114
2023 111
2024 35

Text availability

Article attribute

Article type

Publication date

Search Results

859 results

Results by year

Filters applied: . Clear all
Page 1
Interpretation of differential gene expression results of RNA-seq data: review and integration.
McDermaid A, Monier B, Zhao J, Liu B, Ma Q. McDermaid A, et al. Brief Bioinform. 2019 Nov 27;20(6):2044-2054. doi: 10.1093/bib/bby067. Brief Bioinform. 2019. PMID: 30099484 Free PMC article. Review.
We also provide an R/Bioconductor package, Visualization of Differential Gene Expression Results using R, which generates information-rich visualizations for the interpretation of DGE results from three widely used tools, Cuffdiff, DESeq2 and edgeR. The implemented functio …
We also provide an R/Bioconductor package, Visualization of Differential Gene Expression Results using R, which generates information-rich v …
Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2.
Liu S, Wang Z, Zhu R, Wang F, Cheng Y, Liu Y. Liu S, et al. J Vis Exp. 2021 Sep 18;(175). doi: 10.3791/62528. J Vis Exp. 2021. PMID: 34605806
The three protocols of limma, DESeq2 and EdgeR are similar but have different steps among the processes of the analysis. For example, a linear model is used for statistics in limma, while the negative binomial distribution is used in edgeR and DESeq2. Additionally, …
The three protocols of limma, DESeq2 and EdgeR are similar but have different steps among the processes of the analysis. For example, …
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Robinson MD, McCarthy DJ, Smyth GK. Robinson MD, et al. Bioinformatics. 2010 Jan 1;26(1):139-40. doi: 10.1093/bioinformatics/btp616. Epub 2009 Nov 11. Bioinformatics. 2010. PMID: 19910308 Free PMC article.
One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for …
One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that coun …
Integrated Analysis of lncRNA-Mediated ceRNA Network in Lung Adenocarcinoma.
Wu X, Sui Z, Zhang H, Wang Y, Yu Z. Wu X, et al. Front Oncol. 2020 Sep 15;10:554759. doi: 10.3389/fonc.2020.554759. eCollection 2020. Front Oncol. 2020. PMID: 33042838 Free PMC article.
METHODS: We downloaded the RNAseq and miRNAseq data of LUAD from The Cancer Genome Atlas (TCGA) data portal and identified differentially expressed lncRNAs (DElncRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed mRNAs (DEmRNAs) between LUAD and corre …
METHODS: We downloaded the RNAseq and miRNAseq data of LUAD from The Cancer Genome Atlas (TCGA) data portal and identified differentially ex …
Bioinformatic analysis reveals an exosomal miRNA-mRNA network in colorectal cancer.
Ma J, Wang P, Huang L, Qiao J, Li J. Ma J, et al. BMC Med Genomics. 2021 Feb 27;14(1):60. doi: 10.1186/s12920-021-00905-2. BMC Med Genomics. 2021. PMID: 33639954 Free PMC article.
The differential expression analysis was performed using "limma" and "edgeR". Target mRNAs of miRNAs were predicted using FunRich 3.1.3, miRNAtap and multiMiR. ...
The differential expression analysis was performed using "limma" and "edgeR". Target mRNAs of miRNAs were predicted using FunRich 3.1 …
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.
Chen Y, Lun AT, Smyth GK. Chen Y, et al. F1000Res. 2016 Jun 20;5:1438. doi: 10.12688/f1000research.8987.2. eCollection 2016. F1000Res. 2016. PMID: 27508061 Free PMC article.
Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR....
Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edge …
Bioinformatics Analysis Highlight Differentially Expressed CCNB1 and PLK1 Genes as Potential Anti-Breast Cancer Drug Targets and Prognostic Markers.
Fang L, Liu Q, Cui H, Zheng Y, Wu C. Fang L, et al. Genes (Basel). 2022 Apr 7;13(4):654. doi: 10.3390/genes13040654. Genes (Basel). 2022. PMID: 35456460 Free PMC article.
This study characterizes differentially expressed genes (DEGs) based on the TCGA database by using DESeq2, edgeR, and limma. A total of 2032 DEGs, including 1026 up-regulated genes and 1006 down-regulated genes were screened. ...
This study characterizes differentially expressed genes (DEGs) based on the TCGA database by using DESeq2, edgeR, and limma. A total …
Gene Expression Profiling of Skeletal Muscles.
Alto SI, Chang CN, Brown K, Kioussi C, Filtz TM. Alto SI, et al. Genes (Basel). 2021 Oct 28;12(11):1718. doi: 10.3390/genes12111718. Genes (Basel). 2021. PMID: 34828324 Free PMC article.
RNA read counts were analyzed for differential gene expression using the R package edgeR. Differentially expressed genes were filtered using a false discovery rate of less than 0.05 c, a fold-change value of more than twenty, and an association with overrepresented pathway …
RNA read counts were analyzed for differential gene expression using the R package edgeR. Differentially expressed genes were filtere …
859 results