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. Author manuscript; available in PMC: 2020 Sep 17.
Published in final edited form as: Methods Mol Biol. 2017;1488:75–120. doi: 10.1007/978-1-4939-6427-7_4

Fig. 13.

Fig. 13

Creating networks and analysis of biological enrichment. From the Trait Collection a network graph depicting relations between gene set members can be constructed using the Graph tool. Display and correlation threshold can be adjusted using the Network Graph interface. Each node represents a gene (probe set) and the edge indicates the correlation (green for negative correlations and red for positive correlations). In this case the network shown in A was given a threshold of r = |0.3| as this represents a signifi cant correlation (p < −0.01) in this data set. Based on the network, a subset of genes (shown in the yellow panel in B) can be selected for enrichment analysis. Select the subset in the Trait Collection and select the Gene Set tool. Enrichment analysis is shown in the background (C), with signifi cant (adjusted p-value or AdjP < 0.05) enrichment of biological function (based on GO annotations) shown in red