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Fig. 4 | BMC Bioinformatics

Fig. 4

From: Avoiding the pitfalls of gene set enrichment analysis with SetRank

Fig. 4

Example of a visualisation of a significant pathway using the SetRank package. Shown are the interactions between genes in the “Acute Myeloid Leukemia (AML)” gene set of the KEGG DISEASE database. The expression data from dataset GSE14924 CD4, which compared AML patients to healthy subjects, is overlayed on top of the network. Node color reflects the log-fold change; the size of the node label reflects the significance of difference in expression; the node label color reflects the gene rank when sorted by p-value – a rank of 1.0 means the lowest p-value. The node width reflects the global betweenness, i.e. the betweenness of a node in the entire interactome; the node height the local betweenness, i.e. the betweenness in the pathway; the node border color reflects the log-ratio between the local and global betweenness

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