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Gene Function Inference in Deletion Mutants 113.3.2. Exploring Patterns and Functional Units: the ClutrFree GUIThe ClutrFree graphic user interface (GUI) has been designed around twowindows: the pattern and the gene table window. A global view of the patternsimilarities among experiments is displayed in the two tree windows (Fig. 3).• The pattern window: the pattern window shows the pattern inferred by BD (rowsof P). Horizontal arrows allow navigation across patterns for the same experimentsand vertical arrows allow navigation across experiments. The current patternis represented by a highlighted node in the pattern tree (Fig. 3A). Thedisplayed graph is the contribution of each mutant to the current pattern, displayedin an arbitrary unit. Other features in the graphs include the display of persistence(this value is proportional to the thickness of the blue box behind each plottedpoint). Graphics can be exported for publication (see Note 3).• The gene-table window: this window, organized around two tables, displays thedistribution of genes (upper table) and ontologies (lower table) across the differentpatterns (columns of A): on one hand, this is used for functional inference onpatterns to assess the different pathways present in a pattern and linked to a set ofmutants (Fig. 3C). On the other hand, this is used for gene function inference onthe basis of known genes with detailed ontologies present in the pattern. The genetable must be used together with the pattern window to understand which gene islinked to which groups of mutants. In the ontology table (lower table), two valuesare associated for each ontology in each pattern: enrichment (noted e[x], with xbeing the pattern number) and p-value (noted p–v[x], calculated from a hypergeometricdistribution, see ref. 5 for the mathematical details).• The tree windows: there are two tree windows in ClutrFree, one related to the patterns(pattern tree), showing the relationship of patterns across dimensionalities,and one related to the gene membership (membership tree), constructed from thecolumns of A (Fig. 3B,D). Each tree level represents the patterns from a single BDrun, and the levels are sorted from the lower number of patterns (five at the top) tothe higher number of patterns (20 at the bottom). Levels are connected by maximumcorrelation between nodes to infer stable patterns (7). More information,including ontological information can be displayed in the trees (see Note 4).3.3.3. Inference of Pattern FunctionTo understand the pattern function, the lower part of the gene-table windowwill be used, the ontology table. This table permits the assessment of a generalidea for the pattern function, i.e., which pathways are present in this pattern. Thisis an essential step before detailed examination of the list of mutants present inthe pattern, and the list of genes having the highest contribution to the pattern.The procedure for pattern function inference is the following: (see Note 2).1. The ontologies for 15 patterns are displayed, the level that is believed to be optimalfor analysis (see Subheading 3.1.2.). This is done by pressing the [NSol+1]