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The algorithm filters out redundant categories by performing conditional enrichment tests that ensure that all the reported enriched categories are statistically significant even after taking into account the enrichment of their ancestor and children nodes in the tree.
GeneCodis also classified a significantly lower number of genes from the input list in the reported enriched GO categories.
Despite this uniformity in the conditions used, we also observed a considerable variability in the number of reported enriched categories and in the P values.
The number of reported enriched categories showed a considerable variability among the different tools used (Table 2), although the same significance threshold (P value<0.05 after correction for multiple testing) and analysis conditions (whole genome as reference background and at least two genes from the input list in the enriched category) were applied in all analyses.
We only reported enriched signatures with corresponding FDR < 0.05.
Previously reported enriched repeat elements in hotspot sequences including THE1B, THE1A, CT-rich, and L2 are also in the list [ 8].
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Here, we report enriched expression of the paraneoplastic antigen-like 5 gene (PNMA5) in association areas but not in primary sensory areas, with the lowest expression level in primary visual cortex.
We report enriched biological processes across a wide range of cellular functions, some of which, including DNA transcription and RNA splicing, were also reported by Liu et al. [ 13].> -wrap-foot> Directiof of effect (Δ beta) is for male relative to female methylation beta value, so that negative values indicate lower methylation in males.
In general, the tools GeneCodis [10] and WebGestalt [11] reported more enriched categories than the other tools, and many of the enriched categories were reported only by GeneCodis (Tables S3, S4, S5).
The findings don't match another study, however, published late 2003, which reported that enriched environments actually increase plaque formation.
The observation that both 'Candidatus Accumulibacter phosphatis' and 'Candidatus Competibacter phosphatis' are able to perform a GAO metabolism but at different rates helps to explain the broad range of HAc-uptake rates reported from enriched 'GAO' cultures.
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