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To study proteins that are mainly intracellular, i.e. housekeeping proteins, the protein lists were filtered.
Gene lists were filtered in GeneTraffic to include only those genes that displayed at least 2-fold difference and whose coefficient of variance was less than 100% and had a p-value less than 0.05 using a T-test.
Scored lists were filtered again by adjusted p-value (<0.05) and fold change (1.5) and probe sets not meeting these criteria for both strains were excluded yielding a list of 910 probe sets.
Subsequently, the gene lists were filtered at a fold change cut-off of 1.5.
The lists were filtered to include only terms that annotated between two and 250 genes.
Variant lists were filtered against the reference databases and ranked as potential candidates [ 5].
Similar(43)
Each of these gene lists was filtered to avoid multiple entries per list of the same gene.
All p-values from each combination of a biological process and gene list were filtered using a false discovery rate (FDR) at 0.05, clustered and visualized using JAVA Treeview [ 31].
Probe sets list were filtered using limma &/or rankprod-FDR p values depending on the stringency of the statistical tests required for each analysis from the FIESTA viewer interface.
This list was filtered so that no comparison was repeated either with the same target and query, or vice versa.
The gene list was filtered based on the fold change in expression between the two genotypes.
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