Among the 553 SNPs associated with AraC IC50, 140 unique SNPs within or near 123 genes were associated with variation in expression of 843 (563 unique genes) expression probesets (Table S4 and S5).
Staminodia also displayed unique gene expression patterns.
These regions corresponded to 181 gene expression probesets on our Affymetrix Gene 1.0ST arrays, of which 39 (22%) had a strong positive correlation between CN and gene expression (r>0.6).
In the multivariate analysis only location seemed to be associated with gene expression (702 probesets with non-corrected p-value < 0.001, 1007 probesets with FDR < 10%%), while radiological appearance was almost without influence on gene expression (5 probesets with non-corrected p < 0.001, no probesets with FDR below 10%%).
In a GE-biplot, arrays that have approximately the same relative values of gene expression across probesets cluster together.
Of 101 genes (162 probesets) induced by LPS (FDR ≤10%, FC ≥2), CO suppressed the expression of 78% 799 unique genes, 120 probesets), using a liberal selection criteria (FDR ≤20% and FC ≤0.83) to avoid missing important CO effects (Figure 1C).
Unique and shared gene expression was delineated.
Recent studies have shown the need to regularly and automatically re-annotate gene expression probes and probesets [ 7, 31, 35].
Genes and Affymetrix expression probesets were localized on the genome by aligning RefSeq sequences and probeset targets to the genome, NCBI Version 36, using GMAP [ 34].
This list of 134 genes comprised 110 unique genes, and increased expression was observed for 80 (102 probesets) unique genes, while 30 (32 probesets) unique genes showed decreased expression (Table 1).
