Figure 1

Bioinformatic analysis of microarray expression data. A: The distributions of the raw p-values of all genes for the main effects hypomethylation of LINE-1 retrotransposons (hypo), alteration of chromosome 8 (chrom8) and for the interaction effect (hypo AND chrom8). In each graph the numbers of genes with p-values in the indicated ranges (in increments of 0.02) are shown. The uniform distributions of the p-values for the two main single effects indicate that not more genes are declared significant than expected at random, whereas for the interaction effect a skewed distribution is observed, i.e. significantly small p-values are assigned to a large number of genes. B: The subgraph induced by the top 15 GO terms identified by the classic algorithm for scoring GO terms for enrichment. In this graph, nodes represent GO terms and edges represent parent-child relationships, i.e. an arrow from node A to node B indicates that the genes in B are a subset of the genes in A. Black arrows indicate is-a relationships and red arrows part-of relationships, as defined in the Gene Ontology nomenclature. In general, GO terms are represented by ellipses with the corresponding GO IDs plotted inside. GO IDs surrounded by boxes instead of ellipses indicate the 10 most significant GO terms as identified by enrichment analysis. Color represents the relative significance of enrichment, ranging from dark red (most significant) to light yellow (least significant). Interesting areas in the GO graph defined by significant related GO terms are highlighted by different underlying colors (e.g. red for immune response). C: The subgraph induced by the top 15 GO terms identified by the weight algorithm for scoring GO terms for enrichment. For a detailed description see Fig. 1B. Circles instead of ellipses indicate GO terms that are found significant by the classic algorithm but not by the weight algorithm. see Additional file 3 for a listing of all GO groups in Fig. 1B and 1C