The Journal of Neuroscience, February 9, 2005, ():
Presenilin-1-Dependent Transcriptome Changes
J. Neurosci. Mirnics et al.
25: 1571
Supplemental data
Files in this Data Supplement:
- supplemental material
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Supplemental Material 1. Assessment of false discovery ratio (FDR)
FDR was assessed in a permutation test, where equal number of experimental and control microarrays were randomly assigned to two groups. These groups were assessed for gene expression differences with the same analysis as in the experimental – control comparison (top panel). C1-5 denote control samples, E1-5 denote experimental samples. For each analysis, arrows denote comparisons, number on arrow denote the number of genes with changed expression in a permutation. Number of “putatively changed genes” is denoted in parenthesis. Note that in this test, the FDR was <1.5% (<21% for the “putatively changed genes”).
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Supplemental Material 2. qPCR sequences
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Supplemental Material 3. Gene expression differences in the brain of mice with a conditional ablation of mPS1. Abbreviations and table layout are similar to those in Table 1.
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Supplemental Material 4. Gene expression differences in the brain of mice carrying the DE9 hPS1 mutation. Abbreviations and table layout are similar to those in Table 1.
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Supplemental Material 5. 72 gene probesets showing putative expression differences across the cKO and TG comparisons. Although these gene probesets satisfied only 3 of 4 statistical criteria we used in the current study (ALR>|0.20| and p<0.05 in both TG and cKO comparisons), this group also reported an acceptable FDR (20.5%) and very likely contains biologically meaningful data.
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Supplemental Material 6. Hierarchical clustering of gene expression levels for 102 genes that are likely changed in both the TG and cKO comparisons.
Two-way clustering of the normalized expression levels for these genes separated out the mouse genotypes according to their expression phenotype. In the vertical dendrogram each arm represents a single animal (red-cKO; blue-DE9 hPS1, light green-wild type mouse PS1, dark green- wild type hPS1), rows denote gene probesets with NCBI accession numbers. Note that the cKO mice and DE9 mice show the largest Euclidian distance, while the wt mPS1 and wt human PS1 transgenic animals cluster adjacently. For gene names and statistical parameters, see Supplemental Material 5.
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Supplemental Material 7. Intensity-Ratio plot of experiments
In all figurines X axis denotes mean log2 intensity values; Y axis denotes average log2 ratios between the control and experimental conditions. Each black point represents a single gene probeset. Note that the five color-coded genes are regulated in an opposite direction in the cKO and TG comparisons both in the hippocampus and the frontal cortex.
