The modules are listed by values representing their status (induced or repressed).
You can break it down into meal categories, such as breakfast, lunch, dinner, snack, and dessert or food groups, such as cereal, fruits, vegetables, meats, dairy, etc. Prioritize the list by nutritional value.
For each category we sort the gene list by p-values and examine the positions of the p-values of its known members in this sorted list.
This strategy made use of a subset of genes as input to produce a ranked list (by P-values) of the GO attributes that are enriched among the input gene subset [24].
A one-way analysis of variance with respect to the "drug treatment" factor was performed to generate the sorted gene list by P values.
In Table 5 and Table 6 we list by P-value the top 50 new ABA-induced genes and ABA-repressed genes in guard cells not previously reported by any of the 11 previous ABA microarray studies that we evaluated.
To determine which genes showed the most significant gene expression changes, we further refined our lists of disease-altered and region-enriched genes, by first including only genes with a fold change >1.4, then sorting each list by P-value (the top ten genes of each comparison are presented in Table 3).
BD-L metagene values for the cell lines, as calculated from the Neve et al. [ 21] data set, are listed by increasing value.
The top 100 proteins exhibited an average fold increase of 3.8 (median 3.2, range 1.6 128.7) in the tenofovir arm, listed by p value in Figure 6.
Supplementary Table S1 shows a ranking of the most frequent contigs from the total EST contig list by normalized frequency value.
Then the following hypergeometric test will assess the overrepresentation of the TF target genes in the differentially expressed gene list by a p-value of ∑ i = m min (n, M ) C M i C N − M n − i C N n.
