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A Genome-Wide Gene Expression Signature of Environmental Geography in Leukocytes of Moroccan Amazighs

Figure 4

Functional analysis of differentially expressed genes.

(A) Differential expression of the FOS and MYC networks and enriched disease classes. The Ingenuity Pathways Knowledge Base (IPKB) was used to generate networks of interacting genes that are overrepresented in the set of transcripts differentially expressed (based on a 1% FDR cutoff) between the urban and rural samples. The top two networks are focused on the FOS and MYC transcription factors, and every one of the genes that the IPKB indicate as interacting either genetically or biochemically are differentially expressed in this comparison. Network connectivity is indicated as solid edges for direct interactions, and dashed edges for indirect interactions. Transcripts are displayed in green for down-regulated and red for up-regulated, while cellular compartments in which the gene products are localized are also indicated. Gold edges highlight shared interactions. The list of genes, their fold change and P values are listed in Table S3. (B) Overrepresentation of disease classes affected by differentially expressed genes. Some of the Ingenuity Knowledge Database disease bio-function categories enriched (P<0.05) in differentially expressed transcripts (1% FDR) in the three lifestyle pairwise comparisons (grey, urban vs. rural; blue, nomadic vs. urban; green, nomadic vs. rural). Fisher's exact test was used to calculate the P value associated with the probability that the number of genes in each biological function and/or disease assigned to that data set is greater or less than expected by chance given the numbers of genes expressed in leukocytes.

Figure 4

doi: https://doi.org/10.1371/journal.pgen.1000052.g004