Computational protocol: High Phosphorus Diet-Induced Changes in NaPi-IIb Phosphate Transporter Expression in the Rat Kidney: DNA Microarray Analysis

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Protocol publication

[…] The CEL files were quantified with the DFW using statistical language R (http://www.r-project) and Bioconductor (http://www.bioconductor.org/) . Hierarchical clustering was performed using the pvclust() function in R. To identify DEGs, the RP method was applied to DFW quantified data, with the number of permutations set at 1,000. Probe sets with an FDR <0.05 were regarded as having different expression levels between the two groups (i.e. were differently expressed). The annotation file for the Rat Genome 230 2.0 Array was downloaded from the Affymetrix web site (August 10, 2010, Rat230_2.na31.annot.csv).Gene-annotation enrichment analysis of DEGs was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/) and Quick GO (http://www.ebi.ac.uk/QuickGO/) . EASE scores, which are modified Fisher's exact test p-values , were used to extract statistically overrepresented GO terms from the DEGs; Benjamini and Hochberg FDR corrections were used to correct the results by multiple testing. GO terms with FDR-corrected p-values of <0.05 were regarded as significantly enriched. […]

Pipeline specifications

Software tools Pvclust, DAVID, QuickGO
Application Gene expression microarray analysis
Organisms Rattus norvegicus
Diseases Phosphorus Metabolism Disorders
Chemicals Phosphorus, Sodium