scholarly journals Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

2015 ◽  
Author(s):  
Xiaobei Zhou ◽  
Mark D Robinson
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Comprehensive Evaluation ◽  
Rna Seq ◽  
D Genome ◽  
Differential Gene Expression Analysis ◽  
Differential Gene

A correspondence with respect to: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND and Betel D, Genome Biol 2013, 14:R95

scholarly journals Computational Methods to Study Human Transcript Variants in COVID-19 Infected Lung Cancer Cells

2021 ◽  
Vol 22 (18) ◽  
pp. 9684
Author(s):  
Jiao Sun ◽  
Naima Ahmed Fahmi ◽  
Heba Nassereddeen ◽  
Sze Cheng ◽  
Irene Martinez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Computational Methods ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Rna Seq ◽  
Differential Gene Expression Analysis ◽  
Transcript Variants ◽  
Infected Cells ◽  
Differential Gene

Microbes and viruses are known to alter host transcriptomes by means of infection. In light of recent challenges posed by the COVID-19 pandemic, a deeper understanding of the disease at the transcriptome level is needed. However, research about transcriptome reprogramming by post-transcriptional regulation is very limited. In this study, computational methods developed by our lab were applied to RNA-seq data to detect transcript variants (i.e., alternative splicing (AS) and alternative polyadenylation (APA) events). The RNA-seq data were obtained from a publicly available source, and they consist of mock-treated and SARS-CoV-2 infected (COVID-19) lung alveolar (A549) cells. Data analysis results show that more AS events are found in SARS-CoV-2 infected cells than in mock-treated cells, whereas fewer APA events are detected in SARS-CoV-2 infected cells. A combination of conventional differential gene expression analysis and transcript variants analysis revealed that most of the genes with transcript variants are not differentially expressed. This indicates that no strong correlation exists between differential gene expression and the AS/APA events in the mock-treated or SARS-CoV-2 infected samples. These genes with transcript variants can be applied as another layer of molecular signatures for COVID-19 studies. In addition, the transcript variants are enriched in important biological pathways that were not detected in the studies that only focused on differential gene expression analysis. Therefore, the pathways may lead to new molecular mechanisms of SARS-CoV-2 pathogenesis.

Sign in / Sign up

Export Citation Format

Share Document