Figure 4

Connectivity between genes in the functional clusters. (A) Deregulated pathways. Matrix shows pathways (columns) enriched in the genes more activated in the damaged cells that overlap significantly with functional clusters (rows). Only pathways and clusters overlapping with higher-tail hyper-geometric p-value at most 0.001 (indicated in red) are reported. Abbreviations of pathway names: SI, snare interactions; U, ubiquitin. (B). Deregulated complexes. Top left: The Exon junction (EJ) complex and five spliceosome complexes (rows) are overrepresented (best hyper test, see Methods) in the genes more activated in DNA-damage by the regulators ATM, RelA and p53 (columns). Only complexes with a p-value at most 10^-5 (indicated in red) are reported. Genes in those complexes overlap significantly with the functional cluster MRNA/RNA processing. Right: Graph representation of the genes (round nodes shaded in violet by their average deregulation scores) in the complexes (rounded square nodes). Edges represent gene - complex membership. Abbreviations are reported in Additional file 2, Table S1. Pathways and complexes carry information about relations between their member genes. Therefore, these enrichment results broaden our view on the connectivity within the sets of genes in the functional clusters.