Computational protocol: Unilateral nephrectomy diminishes ischemic acute kidney injury through enhanced perfusion and reduced pro-inflammatory and pro-fibrotic responses

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Protocol publication

[…] The Affymetrix Clariom D array detects all known, coding rat genes. Normalized gene expression data was analysed in the open source software Multiexperiment Viewer version 4.9.0, which is part of the TM4 microarray software suite []. The statistical analysis was done by employing the Significance Analysis of Microarrays (SAM)-method []. The number of permutations was set to 200, S0 (the exchangeability factor, which was set to the Tusher et al method []), and the k-nearest neighbours method for imputation of missing data with k = 10 was used. Unpaired two-class analysis was performed. A false discovery rate (FDR) of 10% was selected in the functional enrichment and specific pathway analysis. Functional enrichment analysis was done by using the DAVID Bioinformatics Resources 6.8 []. The following criteria defined the threshold of an enriched category: a modified Fischer Exact p-value of < 0.05 (> 1.3 after -log10 transformation), and n ≥ 2 genes represented in a category. For further pathway analysis the Ingenuity ® Pathway Analysis (IPA) software (Qiagen Bioinformatics, Hilden, Germany) was used. […]

Pipeline specifications

Software tools TM4, SAM, DAVID, IPA
Application Gene expression microarray analysis
Organisms Rattus norvegicus
Diseases Acute Kidney Injury
Chemicals Sodium