Tag Archives: differentially expressed genes

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 ...

The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

In recent years, different technologies have been used to measure genome-wide gene expression levels and to study the transcriptome across many types of tissues and in response to in vitro treatments. However, a full understanding of gene regulation in any ...