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Finally, through functional enrichment analysis on our highly prioritized candidate gene network, we identified a small number of pathways that are key in early neural development, providing further support for their potential role in ASD.
In turn, relatively few interactions are confined to a small number of pathways (Fig. 2B).
In all cases, classifiers with a small number of pathways (three to six) achieved a high level of accuracy (83% to 95%).
Empirical studies have shown the proposed approach is able to identify a small number of pathways with nice prediction performance.
We used KEGG pathway identifiers since they are generic and allow maintaining a small number of pathways in the network.
Given the small number of pathways in the RNA-only sets no set-difference analysis was needed (Additional file 1: Figure S6).
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Using a more recent network of GI and PI edges from the BioGRID [17] (as of October 2007), we find 50.6% of 3020 pathways exhibiting GO enrichment, as compared to Ulitsky and Shamir, who find less than 36% of their smaller number of pathways enriched, on a similar but slightly older network (see Table 1).
This could reflect the smaller number of categories used in this analysis compared to the 12 used by Vinogradov [ 13] or the smaller number of pathways studied.
This can be shown not to result from the smaller number of pathways, but rather because of the increase in their individual reproducibility.
Thus, numerous "upper" pathways funnel into a small number of "lower" pathways.
In all they found that for only a relatively small fraction (15%, 18/120) of possible pathways, all five steps increased resistance, suggesting that a relatively small number of possible pathways are accessible to natural selection.
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