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Each of these gene lists was filtered to avoid multiple entries per list of the same gene.
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To study proteins that are mainly intracellular, i.e. housekeeping proteins, the protein lists were filtered.
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.
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.
The lists were filtered to include only terms that annotated between two and 250 genes.
Subsequently, the gene lists were filtered at a fold change cut-off of 1.5.
Variant lists were filtered against the reference databases and ranked as potential candidates [ 5].
Both lists were filtered to include only genes that were represented by a unique probe on the microarray chip.
Probe set lists were filtered using raw limma or FDR p-values from the FIESTA viewer interface.
The BLAST lists were filtered for E values better than 10− and amino acid identities of ≥25%.
The latest versions of Varscan 2 (version 2.2.11) and muTect (version 1.1.4) were run under their default parameters, and the candidate lists were filtered following their instructions.
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