Molecular signatures of neurodegeneration in the cortex of PS1/PS2 double knockout mice

Additional file 1:

Gene expression differences between PSKO and CNT mice regardless of age or brain region. A gene probe was differentially expressed if it reported an > 50% change (|ALR| > 0.585) at a pairwise t-test p < 0.05 between all the PSKO and CNT samples. 72 genes were upregulated, while 41 genes showed reduction in the PSKO samples. The probes from this list are clustered in Additional File 2.

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Additional file 2:

Hierarchical clustering of genes that show differential expression between PSKO and CNT mice regardless of age or brain region. The numerical data are presented in Additional File 1. Gene probes are clustered in rows (denoted by symbols and probe identifiers), microarrays are clustered in columns (denoted by sample identifiers). Each pixel represents a single, color-coded gene expression value form FC or HC form a PSKO or CNT mouse sample at five developmental ages. Shades of red correspond to the magnitude of expression increase; the intensity of blue corresponds to the magnitude of the reduction in gene transcripts. Note that the PSKO and CNT samples, regardless of developmental age or brain region, cluster on different ends of the dendrogram.

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Additional file 3:

Detailed information about the enriched pathways in the PSKO or CNTR mice. This file is a composite of GSEA outputs of BioCarta analysis for individual pathways that showed enrichment in either the PSKO or CNTR mice. For detailed description of output format, consult http://www.broad.mit.edu/cancer/software/gsea/doc/GSEAUserGuideFrame.html webcite

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Additional file 4:

Gene expression differences in the frontal cortex (FC) of PSKO and CNT mice. A gene probe was differentially expressed if it reported > 50% change (|ALR| > 0.585) at a pairwise t-test p < 0.05 between the FC of the PSKO and CNT samples. 70 genes were upregulated, while only 3 genes showed reduction in the PSKO samples. The probes from this list are clustered in Figure 2.

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Additional file 5:

Gene expression differences in the hippocampus (HC) of PSKO and CNT mice. A gene probe was differentially expressed if it reported > 50% change (|ALR| > 0.585) at a pairwise t-test p < 0.05 between the HC of the PSKO and CNT samples. 36 genes were upregulated, while 101 genes showed reduction in the PSKO samples. The probes from this list are clustered in Figure 3.

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Additional file 6:

Developmental expression of Cathepsin and Complement family members in FC and HC. X axis denotes postnatal age, Y axis represent RMA-normalized log2 expression, each colored bar corresponds to a different gene probeset. Note that in both the FC and HC the expression of these genes is relatively steady during postnatal development.

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