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Pipeline publication

[…], a public functional genomics data repository. The GSE13535 expression profile is based on the GPL1355 platform ([Rat230_2] Affymetrix Rat Genome 230 2.0 Array). The specimens were acquired at 2 and 18 h after microsphere-injection in a rat model of PE (), and the vehicle-treated samples were considered a control group. A total of 22 specimens were available for the present study, including three vehicle-treated specimens acquired at 2 h, eight microsphere-injection specimens acquired at 2 h, three vehicle-treated specimens acquired at 18 h and eight microsphere-injection specimens acquired at 18 h., The derived genetic data was initially analyzed using affy package () in R software, and the array files were converted into gene expression spectrum data. Robust multi-array average () was then used to standardize the expression spectrum data. Furthermore, the limma package () was used to calculate and analyze the DEGs of the sample groups, as compared with the control group, and the Bayes method was applied for a multiple range test. The DEGs were screened based on a cut-off value, which was set at |logFC| (fold change)>1 and P<0.05., Database for Annotation Visualization and Integrated Discovery (DAVID) () online analytical tools were used to perform KEGG pathway analysis on the DEGs obtained from the experimental specimens. The pathways with a P<0.05 were considered to indicate significant pathways in which the DEGs were involved., The PPI networks of the DEGs at 2 and 18 h after PE initiation were constructed from PPI pairs whose protein interaction scores were >0.4, as determined by the Search Tool for the Retrieval of Interacting Genes/Proteins () online tool. The protein interaction scores were calculated using the following formula ():, Where diff (x) and diff (y) are differential expression assessments of gene x and gene y, respectively. Corr (x, y) represents the correl […]

Pipeline specifications

Software tools affy, limma, DAVID