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Significant enrichments of GO terms were computed based on hypergeometric distributions using FUNC [ 80] by comparing the numbers of a given GO term in the target group with the numbers in the background group.
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We used Fisher's exact right-side test based on hypergeometric distribution and corrected for multiplicity testing by the Bonferroni method.
We calculated the probability values based on hypergeometric distribution instead of chi-square distribution, which is used in the original ACME.
Based on hypergeometric distribution, we carried out a function enrichment analysis between the progression-related sub-network and the whole human biological network.
For cellular pathway analysis, MetaCore is based on hypergeometric distribution, SAM-GSA uses "Maxmean" statistic, and GSEA uses modified Kolmogorov-Smirnov statistic.
P values were calculated based on hypergeometric distribution analysis.
Methods based on hypergeometric distribution, if properly implemented, are also fast.
Significantly altered KEGG pathways were identified using a P-value based on hypergeometric distribution.
And significantly altered KEGG pathway were identified using a P-value based on hypergeometric distribution.
Significantly enriched components defined in Gene Ontology (GO) were determined based on hypergeometric distribution analysis [ 38].
Significantly altered pathways were determined by p-values calculated based on hypergeometric distribution with Benjamini correction.
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