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Figure 1 | BMC Bioinformatics

Figure 1

From: Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

Figure 1

Schematic representation of the steps in our analyses. (a) Example flow chart of the different steps for calculating gene set coexpression enrichment P e values between each of the 6624 genes in the multi-species network and 902 GO sets. For each gene m i we use the hypergeometric distribution to calculate a coexpression enrichment P e -value (P e (m i , g j )) for whether GO set g j was significantly overrepresented in the top 250 genes with smallest P c -values to m i . (b) The four steps in our analyses. 1. A coexpression network is generated with P c values (multi-species network) or correlation coefficients (single-species network) scoring coexpression between gene pairs. 2. Coexpression enrichment P e values are calculated between each gene and each GO category, such as between GO category 1 and genes A, B, and C and between GO category 2 and genes A, B, and C. 3. A score reflecting GBA is calculated for each GO category (e.g., GO category 1). 4. The interrelationship between pairs of GO categories is quantified, such as that between GO category 1 and GO category 2, which are sibling categories in a Gene Ontology graph, sharing GO category 3 as a common parent.

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