Calculating Differentially Expressed Genes (DEGs) from RNA-sequencing requires replicates to estimate gene-wise variability, a requirement that is at times financially or physiologically infeasible in clinics. By imposing restrictive transcriptome-wide assumptions limiting inferential opportunities of conventional methods (edgeR, NOISeq-sim, DESeq, DEGseq), ...
Read More »UTAP – user-friendly transcriptome analysis pipeline
RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such as Illumina Next-Seq have yielded easy-to-operate machines, with high throughput, at a lower ...
Read More »RNA-Seq differential expression analysis – an extended review and a new software tool
The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High...
Read More »For model species, the 3′ RNA-seq method might more accurately detect differential expression
One limitation of the widely used RNA-seq method is that long transcripts are represented by more reads than shorter transcripts, resulting in a biased estimation of expression levels. The 3′ RNA-seq method, which yields only one sequence per transcript, bypasses ...
Read More »A High Resolution Map of the Arabidopsis thaliana Developmental Transcriptome Based on RNA-seq Profiling
Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A.thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding ...
Read More »samExploreR – Exploring reproducibility and robustness of RNA-seq results based on SAM files
Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to ...
Read More »RNA-seq analysis for detecting quantitative trait-associated genes
Many recent RNA-seq studies were focused mainly on detecting the differentially expressed genes (DEGs) between two or more conditions. In contrast, only a few attempts have been made to detect genes associated with quantitative traits, such as obesity index and ...
Read More »Integrating gene expression profiles across different platforms
Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene expression levels. However, considerable discrepancy has been found between DEGs detected ...
Read More »Effect of low-expression gene filtering on detection of differentially expressed genes in RNA-seq data
Researchers from the the Georgia Institute of Technology compare methods for filtering RNA-seq low expression genes and investigate the effect of filtering on detection of differentially expressed genes (DEGs). Although RNA-seq technology has improved the dynamic range of gene expression ...
Read More »Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes
For plant species with unsequenced genomes, cDNA contigs created by de novo assembly of RNA-Seq reads are used as reference sequences for comparative analysis of RNA-Seq datasets and the detection of differentially expressed genes (DEGs). Redundancies in such contigs are ...
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