Interestingly, only 60% of these validated fusions appeared in the high-confidence enriched list produced using RNA and defuse filtering parameters.
Together with an expanded and enriched list of candidate genes, the interest of such an approach is also dependent on accurate assessment of environmental exposure.
We used EASE analyses, as implemented by DAVID (Dennis et al. 2003), to identify biological process, cellular component, and molecular function gene ontology terms that were statistically enriched in lists of DEGs.
We compared each tissue enriched gene list to each of our mutant misexpression lists (sti q<.001, sti q<.01, dFmr1 q<.001, and dFmr1 q<.01).
Interestingly, five of these eight pathways (marked * in Table 5) are among the top five significantly enriched pathways listed in our study.
GO analysis identified unique biological or molecular functions for each gene network; the transcripts, their corresponding modules, and the functional categories for which the modules are enriched are listed in Table S5.
The TFs whose transcription factor binding sites (TFBSs) were found enriched are listed in Table 4.
Information of superarray enriched our list with members of the Rel, NF-κB, and IκB families.
*Terms also enriched in list of genes designated as meiocyte genes.
By applying length, %GC and conservation thresholds we have significantly enriched our list of IGRs for known structured RNAs.
With the use of systemic and integrated analysis of functional annotation information by using the DAVID, novel enriched gene list with functional modularity was analyzed.
