Computational protocol: Effects of internal low-dose irradiation from 131I on gene expression in normal tissues in Balb/c mice

Similar protocols

Protocol publication

[…] The web-based BioArray Software Environment system (BioArray Solutions, Ltd., Warren, NJ, USA) was used for data preprocessing and quantile normalization of the raw signal intensities, according to the recommendations given by Illumina. Further analysis was conducted using Nexus Expression 2.0 (BioDiscovery, El Segundo, CA, USA) using log2-transformed, normalized expression values and a variance filter.The Benjamini-Hochberg method was used to control the false discovery rate []. Differential gene expression (at least 1.5-fold change) was deemed statistically significant if the p value after adjustment for multiple testing with the Benjamini-Hochberg method was lower than 0.01.Affected biological processes were determined by identifying gene sets associated with different Gene Ontology [GO] terms. A p value cutoff of 0.05 was used. The GO data was further categorized into seven parental biological processes: metabolic processes, transport, cellular processes, system processes, developmental processes, immune response, and response to stimulus and stress. Gene expression data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus [GEO:GSE32014]. […]

Pipeline specifications

Software tools BASE, Nexus Expression
Databases GEO
Application WGS analysis
Organisms Mus musculus