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In all other cases, you have to specify the appropriate reference set under Custom.
This option is especially attractive if you're only interested in more general functional profiling anyway.Hypergeometric or binomial test for overrepresentation.The darkest orange nodes which are furthest down the hierarchy are probably the ones that you're looking for.A list of genes that are significantly upregulated in a microarray experiment).E.g., when performing Bonferroni control of the fwer at level.05, you would be 95 certain that that the over-represented categories that you identified contain no false positives.However, if you're not testing against a Cytoscape network, but instead you.g.Should there be a substantial contribution of genes in the 'metabolism' category other than 'protein modification' genes, than the metabolism node should be bigger in size (which is not the case here) and darker in color.
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