Self-organising maps (SOMs) cluster the set of differentially expressed genes into related profiles and predict likely downstream targets in each rhombomere: r4 enriched. (A) To uncover underlying trends in the global expression profiles, genes were clustered using SOMs. The 'average' profile of the gene expression pattern contributing to a particular group is shown in each cluster. The number of genes following this pattern is given under each graph. The cluster highlighted in green (that is, enriched in r4) was selected for further study. (B-E') Verification of expression patterns of a selection of genes identified in the r4-enriched SOM. Adjacent to each graph showing a relatively high r4 expression value is a hindbrain flat mount preparation of an in situ hybridisation of the corresponding gene in an E9.5 embryo. In each case, the expression of the gene was either up-regulated or significantly enriched in either all or part of r4. Relative expression and in situ patterns are shown for RARα, Gata2, Lmo1, bHLHb5, Slc12a5, and AldoC. Each of these genes was derived from the same SOM cluster. Gata2 is a known direct downstream target of the r4 patterning gene Hoxb1. The normalised expression is represented graphically for each rhombomere +/- SEM.