Sentence examples for utilized for differential expression from inspiring English sources

Finally, since the reference transcriptome included several sequence variants (contigs) for many putative genes, combined read counts from contigs within each gene were utilized for differential expression analyses.

reads per sample was exclusively utilized for differential gene expression profiling.

The two methods utilized for determining differential expression of lignocellulolytic Pfams indicated that several GH and carbohydrate binding module (CBM) families relevant to lignocellulose deconstruction were significantly overexpressed in the thermophilic community (Table  5).

Bioconductor DESeq package version 1.10.1 [ 58] was utilized for the differential expression analysis, using two-fold change cutoff, that is, log2 fold change ≥1 or ≤ -1 and an adjusted P-value ≤0.05 as thresholds.

To normalize multiple samples for differential expression analysis, we utilized a "geometric" method as described in Anders and Huber [ 34].

Differential gene expression analysis was conducted using the DESeq package (Anders and Huber 2010) in R, which utilizes a negative binomial distribution to test for differential expression among treatments to better accommodate the well known phenomenon of overdispersion in RNA-seq data.

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Robinson, M. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data.

DEGseq was used for differential expression analysis with the "Fisher's Exact Test" method44.

For differential expression analysis, raw sequences were mapped to transcriptome version WS220 using TopHat229.

RMA normalization was used for differential expression (DE) analysis, as it is considered as standard for this calculation53.