Pluto Bioinformatics

GSE136165: Efficient Identification of Multiple Pathways: RNA-Seq Analysis of Livers from 56Fe Ion Irradiated Mice

Bulk RNA sequencing

Background: mRNA interactions with each other and other signaling molecules define different biological pathways and functions. Researchers have been investigating various tools to analyze these types of interactions. In particular, gene co-expression network methods have proved useful in finding and analyzing these molecular interactions. Many different analytical pipelines to identify these interactions networks have been proposed with the aim of identifying an optimal partition of the network where the individual modules are neither too small to make any general inference or too large to be biologically interpretable. Results: In this study, we propose a new pipeline to perform gene co-expression network analysis. The proposed pipeline uses WGCNA, a widely used software to perform different aspects of gene co-expression network analysis and modularity maximization algorithm to analyze novel RNA-Seq data to understand the effects of low-dose 56Fe ion irradiation on the formation of hepatocellular carcinoma in mice. The network results along with experimental validation show that using WGCNA combined with Modularity provide a more biologically interpretable network in our dataset. Our pipeline showed better performance than the existing clustering algorithm in WGCNA in finding modules and identified a module with mitochondrial subunits that are supported by mitochondrial complex assay. Conclusions: We present a pipeline that can reduce the problem of parameter selection with the existing algorithm in WGCNA for comparable RNA-Seq datasets which may assist in future research to discover novel mRNA interactions and their downstream molecular effects. SOURCE: Anna Nia (anna.nia@ucla.edu) - Mark R. Emmett University of Texas Medical Branch