Computational protocol: Comparative transcriptome profiling of amyloid precursor protein family members in the adult cortex

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Protocol publication

[…] If not stated otherwise, data analysis and processing was carried out within the statistical computing environment R, version 2.8.0, using Bioconductor, BioC Release 2.4 []. Raw data was processed with the RMA algorithm (Robust Multiarray Average) developed by Irizarry et al. [] and normalized using quantile normalization [].Hierarchical clustering was carried out using Euclidean distances to calculate the distances between the genes and between the sample groups. Calculated distances were clustered by complete linkage clustering. Expression values for each probe set were normalized to zero mean and unit variance. The values shown thus represent the number of standard deviations above or below the mean expression for each gene. Calculated expression differences for each probe set can be found in the respective additional file.Significant differentially expressed probe sets between two groups were detected by a Significance Analysis of Microarrays (SAM) []. As a cut-off value for significance, we set the false discovery rate (FDR) to 5.33% (WT/APP-/-), 4.96% (WT/APLP2-/-), 4.5% (WT/APPα/α), 4.79% (APPα/α/APP-/-), 5.02% (WT(R6)/APLP2(R1)-/-), and 5.11% (APLP2(R6)-/-/APLP2(R1)-/-).For counting significant differentially expressed genes, probe set identifiers were mapped to Entrez Gene identifiers. If at least one probe set was significant in the SAM, the gene was regarded to be significant as well. If no gene information (Entrez ID) was available for a certain probe set, the probe set was not counted.For group testing (GO terms, pathways) DAVID bioinformatics resources was used []. Gene symbols from each list were taken as input, and redundant entries were discarded. The following gene sets were included into the analysis: GOTERM_BP_FAT (Gene Ontology), Biocarta (Pathways), KEGG_PATHWAY, PANTHER_PATHWAY, REACTOME_PATHWAY. Functional annotation clustering was carried out using the highest classification stringency. […]

Pipeline specifications

Software tools SAM, DAVID
Databases Gene
Application Gene expression microarray analysis
Organisms Mus musculus
Diseases Alzheimer Disease, Machado-Joseph Disease