Figure 3
Number of commonly or statistically differentially regulated genes in wild type and aak-2 mutants in response to oxidative stress and examples. (A) Venn diagram showing numbers of commonly up or (B) down-regulated genes with statistically significant gene expression level changes in wild type and aak-2 mutants in response to oxidative stress relative to wild type (overlapping regions) as well as numbers of genes up or down-regulated exclusively in stressed wild type or stressed aak-2 mutants relative to wild type (non-overlapping regions). Numbers in brackets indicate genes that showed the most difference in gene expression relative to wild type between the two libraries, stressed wild type and stressed aak-2 (i.e. genes that showed significant changes in one library (i.e. Log2 ratio relative to wild type greater or less than |0.7|, p-val < 0.01), but showed negligible changes (i.e. Log2 ratio relative to wild type greater or less than ~|0.3|) or significantly changed in the opposite direction in the other library). For instance, there is a relatively large subset of genes in brackets (125) significantly up-regulated in aak-2 mutants in response to oxidative stress but either insignificantly regulated or significantly down-regulated in wild type under oxidative stress. (C) UCSC browser view of hsp-16.2 and hsp-16.41 with the sequence reads aligned to the gene models. Four samples (Stressed wild type (N2), Stressed aak-2, Unstressed wild type (N2), Unstressed aak-2) are shown. It is evident hsp-16.2 and hsp-16.41 are much more highly expressed in stressed wild type and stressed aak-2 mutants compared to unstressed wild type and unstressed aak-2 mutants, especially in stressed aak-2 mutants. Note: The scales for the minimum and maximum number of reads for the four samples are different. (D) UCSC browser view of fat-7 with the sequence reads aligned to the gene model. Four samples (Stressed wild type, Stressed aak-2, Unstressed wild type, Unstressed aak-2) are shown. As indicated by the number of sequence reads mapped, fat-7 is much more highly expressed in aak-2 mutants (stressed and unstressed) compared to wild type (stressed and unstressed). Note: The scales for the minimum and maximum number of reads for the four samples are different.