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The microarray results showed that there were many fewer significantly altered genes following IH (12 up-regulated and 4 down-regulated genes) (Table S1) as compared to CH (94 up-regulated and 70 down-regulated genes) (Table S2).
Although these methods detect fewer significantly enriched pathways, they can potentially produce more relevant results.
An analysis of the genes induced by overexpression of FruM in females identified fewer significantly enriched GO Biological Process categories, as compared to our observations in males.
In contrast, the per-gene regression method identified fewer significantly differentially expressed genes and the p values were larger than those from the other two methods.
Both forms of tumor tissue grouped together when compared to N-NT and, once again, well differentiated tissue had fewer significantly dysregulated miRNAs (245) than papillary tissue (322).
In general, fewer significantly enriched GO terms were found in the comparison between infected and non-infected cells within line (Fig. 2A) than between genetic lines (Fig. 2B).
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However, despite case-control studies that have now exceeded many thousands of subjects and more than 500,000 SNPs, only a few significantly associated SNPs have been identified.
Consistent with observations of little effect on biological parameters and differentially expressed genes, 2ADNT had very few significantly affected GO terms.
Alternative splicing coupled with NMD seems to act on a wide range of genes, but, however, only in a few significantly over-represented functions across mammalian genomes.
Surprisingly, GO term analysis showed that only few significantly enriched biological processes were transcriptionally up-regulated prior to commitment.
However, this is not the case during the early pupal stage, where D. melanogaster and D. simulans cluster together and show the fewest significantly differentially expressed genes.
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