Fig. 5

Gene function relationships in the latent factor hierarchy. a Hierarchical factor relationships are shown exhibiting a tendency to cluster layer one groups with similar general Gene Ontology enrichments. Lines are shown connecting the top X strongest relationships and the top 1000 genes. Thicker lines indicate higher CorEx relationship probabilities. Representative GO terms for hierarchically clustered groups only are shown in red. Though this figure highlights clustering at layer one and above, many nonclustered layer one factors have very significant annotations as well, detailed in Fig. 2 and the Additional file 1. b In addition to general relationships, specific causal relationships are also detected at the upper layers. Here an example is shown in which noncoding RNAs that are implicated in tumor growth and metastasis via regulation of ribosome activity are isolated in a layer zero group and joined at the higher level to ribosomal structure genes. Noncoding RNA functional annotations are taken from the NCBI Gene database (http://www.ncbi.nlm.nih.gov/gene)