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Data reduction and analysis of comparison of treatment groups was normalized, and filtered expression files were analyzed using Partek Genomic Suite.
The second biomathematical workup filtered expression changes with progression from young to old age occurring exclusively in the striatum of PrPmtA and PrPmtB mice, but not in the brainstem/midbrain or cerebellum, nor in WT tissues.
Because the given expression series consists of samples from multiple brain areas with corresponding controls, a better idea of the disease correlation can be seen between statistically filtered expression profiles based on grouping control and disease sets.
We filtered expression data of both replicas for IRDM-G and N-IRDM-G, obtaining, for each cell lines, two distributions of relative absolute differences (DR ≡ |expr1 − expr2|/[expr1 + expr2]) in the mRNA expression of the two considered replicas, one associated to IRDM-G and the other to N-IRDM-G.
When the filtered expression dataset was clustered with three separate datasets including biopsies from breasts of healthy women with high and low content of fatty tissue (two unpublished AHUS-datasets and one published [ 20] dataset), the samples did not cluster according to fat-content (Additional file 3, Figure S2).
The filtered expression data set for MSC-postsenescence and TMC regulated genes were uploaded as tab-delimited text into IPA for generating biological networks.
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A set of 277 genes was generated by filtering expression in adipose tissue.
Raw data derived from individual whole blood gene expression profiles were filtered for expression level, discarding the lowest 20th percentile that represented non-expressed genes, producing a 39,299 gene list.
Gene expression data analyses were completed using a filtered RMA expression value [ 16].
These were later filtered for expression in human cardiac tissue using microarray expression ratios [ 20] extracted from the UCSC genome browser.
Normalized data was then filtered on expression level to obtain a set of genes with expression values in at least one of the comparisons made.
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