Department of Hematology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France Hervé Dombret Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA ...
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PubMed Central Google Scholar Low DA, Weyand NJ, Mahan MJ. Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect Immun. 2001;69(...
As a result, we identified 11,284 differentially expressed (DE) genes (false discovery rate [FDR]-adjusted P-value ≤ 0.05 and fold change ≥2 or ≤0.5), of which 87.1% (9,830) were also identified as DE genes using DEseq31 and/or edgeR32 (Table S3; Fig. S3). The density ...
Normalization factors were calculated using the iterative DESeq2 method in edgeR (Love et al., 2014, Robinson et al., 2009). DESeq2 estimates the log2 fold change using the MLE method and also calculates the Wald test p-value and BH adjusted p-values. Additionally, a MA and volcano ...
To identify the differentially expressed genes (DEGs) in the three different comparisons, the DESeq2 package (v1.24.0) in R software was utilized. Essentially, DEGs with an |log2 fold change|> 1 and a Q value ≤ 0.05 were considered to be significantly differentially expressed genes ...
Gene-level read counts were calculated using HTSeq (v0.6.1p1; Kim et al., 2015). DESeq2 (v1.18.1) was used for data normalization (Love et al., 2014). All the sequence data from this article can be found in the NCBI database under BioProject PRJNA681368. Author contributions W.C...
To examine motif enrichment for putative ‘active’ sites near differentially expressed genes, RNA-seq data from HT29 cells16were used to identify regions that are likely to be actively controlling transcription. We re-analyzed the published RNA-seq data using DESeq257to identify genes upregulated...
Table 2 Classification of the differential isomiRs across the studied stress in Diff isomiRs. Full size table Among the stress datasets, drought and salt stress revealed the most differentially expressed isomiRs with a total of 7,642 and 401 by mapping-based method and DESeq2 in drought stress...
DESeq2 requires unstandardized read counting data of input genes, rather than standardized RPKM, FPKM, and other data. The count of gene reads was achieved using featureCounts [29]. After difference analysis, it is also required that the Benjamini–Hochberg method be used to correct multiple ...
Quality control of BAM files was performed using Picard Tools v1.86 "CollectRnaSeqMetrics". Gene count matrices were analyzed using DESeq2 [41], and normalized gene expression counts were obtained. We performed principal compo- nent analysis (PCA) to identify groupings or outliers from the data...