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Gene Function Inference in Deletion Mutants 133. The most significant ontologies are explored for each pattern by sorting them inorder of decreasing enrichment value. This is done by clicking on the columnheader (alternatively, the ontologies can be sorted by increasing p-values by pressingshift+clicking on the column header).4. The five most enriched ontologies are visualized for all the 15 patterns of thecurrent level. The obtained functions are shown in Table 3 for patterns 5, 9, 11,14, and 15 (see Note 2).The last step of this procedure is the linkage of mutants present in the patternof genes of the ontologies found. This permits a finer understanding of thepathways present in the pattern. This is done by examination of the mutants thatare absent or present from the corresponding pattern because those absentmutants are the ones that are affecting the pathways in the functional unit owingto the gene knockout. There is no clearly established cutoff for considering amutant to be present/absent from a pattern but a rule of thumb is that mutantwith an amplitude less than 10% of the maximum amplitude in the pattern canbe considered absent from it (and correspondingly, a mutant with an amplitudegreater or equal to 10% of the maximum amplitude will be considered present).See Fig. 4 for an example.In the following, it is assumed that the files from the website have beenloaded into ClutrFree. If BD is rerun, the pattern numbers may change (seeNote 2). The detailed step-by-step procedure is as follows:1. The Pattern window is brought up and the patterns obtained are displayed with BDset for 15 solutions by pressing the “\/” key as much as necessary until the 15pattern experiment appears.2. Pattern 1 is selected by pressing “>>” or “