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Figure 3 | BMC Genomics

Figure 3

From: What do all the (human) micro-RNAs do?

Figure 3

Directed acyclic graph (DAG [32]) representing the nested Gene Ontology (GO) classification showing the polyhierarchy of functional annotations (GO terms) assigned in the GO category “biological process” to the 2954 genes (Figure1) that supported by empirical evidence from the miRTarBase [18] or TarBase [19] databases or computationally predicted using the TargetScan Human [20] software interact with miRNAs. The figure is based on the GeneTrail web-based analysis tool [24] and represents the results of an over-representation analysis with parameters p-value threshold, t p = 1.0 10−5 and Bonferroni α correction. The figure shows a particular aspect of the polyhierarchy, namely the ORA for the n = 554 (one fifth of all miRNA regulated genes) that were annotated with the GO term “gene expression”. Significant terms are shown as red colored or framed ellipses, with the number of member genes indicated in line three, the expected number of genes in line five and the significance of the deviation between the two numbers given as minus log10 p. The functional area (Table 2) is indicated in yellow, and the leaves of this polyhierarchy at the select p-value threshold are shown in blue indicating the most specific significant GO terms. The vertical succession reflects the height of the terms in the GO polyhierarchy.

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