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The primary set of genes become inactivated, perhaps through mutation, leaving only the alternate pathway operating.
Further studies suggest that mtUPR is regulated via a 2 stage process, involving the transcriptional activation of a primary set of genes (chop, c/ebpβ) which subsequently activate transcription of mtUPR responsive genes containing the CHOP element [13].
Phenotypic assessment indicates that the bound-induced genes have a higher likelihood of requirement for growth fitness under the H2O2-induced stress condition than do the unbound-induced genes (Figure 5D), indicating that the bound-induced genes are the primary set of genes that are regulated by Atf1/Pcr1 in response to H2O2.
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Additionally, participation in various collaborative projects, such as the Reference Genome project (8), or the Protein Ontology (8) defines primary sets of genes to work based on community input.
To account for the likelihood that the primary sets of gene models used do not provide perfect accounting of all gene-encoding regions within the assemblies, we exercised a translated nucleotide BLAST (tBLASTn) and carried out genome-wide gene prediction using genBlastG [ 52].
This set of genes then becomes the primary set of candidate genes driving the disease.
In total, 2057 unique genes were included across all gene lists, and were used as the primary set of candidate genes.
Figure S1 shows the complete distribution of individual gene coverage percentages using our primary set of 910 genes for the Illumina 610 Quad microarray in each population.
In addition to our primary set of 910 genes, the mouse systems genetics method (Chesler and colleagues, submitted) that identified 7,842 additional genes with potential biological relevance to addiction through mouse QTL and gene expression correlation analysis and the GIN prioritization scores reflect this quantitative assessment of biological relevance.
Table 1 shows the number of supplementary SNPs needed to tag all common variants in various populations for our primary set of 910 genes that are biologically relevant to addiction.
Based on these data, we defined six primary sets of EDM2 or WNK8 target genes (Table 1; gene sets 1-6; Additional Files 1, 2, 3, 4, 5, 6) and derived six additional secondary sets of their targets (Table 1; gene sets 7 - 12; Additional Files 7, 8, 9, 10, 11, 12).
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