Additional File 1:

Left: the two possible connectivity topologies between three genes. Each grey line can be any of the seven types of interaction represented on the right. Right: the different types of interaction between two genes and their products. Boxes: genes; green arrows: transcriptional regulation only; dashed lines with circles: protein-protein interaction of the genes products. 1-3: only transcriptional regulation without known ppi interaction, (1 and 2 are distinguished to account for different combinations in the diagrams on the left). 4: protein-protein interaction only. 5-7: transcriptional regulation and interaction between the genes products (without details on the role of the ppi interaction complex). The set of all possible three genes patterns is obtained with all the combinations of the interaction types shown on the right on the topologies shown on the left. The statistically significant patterns form a subset of 8 three genes motifs shown in Figure 1

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Additional File 2:

The list of the motif instances found for the yeast Saccharomyces cerevisiae. Each line corresponds to a different realization and contains the most used non-ambiguous name of the involved genes, ordered according to their position in the motif. First column contains the motifs type according to Figure 1; columns 2 to 4 correspond respectively to the genes positions a, b and c as indicated in figure 1

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Additional File 3:

The Excel file contains the list of genes found in motif realizations with their biological functions as given by the MIPS database using the FunCat ontology, and different statistics on function occurrences and distribution. The data is presented in three sheets with different viewpoints: First sheet, "Functions by genes": gives a list of all genes found in motifs instances with standard, main and alternative names, motifs and positions within motifs where these genes are found (according to types and positions as defined in Figure 1), and finally biological functions. Second sheet, "Functions by positions": gives motifs and positions within motifs grouped according to functions. For each represented function in FunCat, the first three columns indicate the number, the fraction and the names of the genes found in motifs instances having this function. The following columns indicate the details for each motif type with: the number of genes involved in the given motif with the given function, the fraction of all genes within motifs having this position and this function, the fraction of genes for this function that are at this position, and the fraction of genes at this position having this function. Third sheet, "Genes by positions": gives standard and main name of genes found at each position

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