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10 Bidautcomputing the maximum correlation between patterns (or between the Amatrix columns for the membership tree).ClutrFree has the capability to visualize simultaneously multiple functionalunits and to permit the comparison of the presence/absence of genes across severalfunctional units. In this section, it will be explored how to launch ClutrFreeand verify the proper format and organization of the data. The exploration willthen be detailed of functional ontologies associated with each pattern to obtaina general idea of the function. Finally Subheading 3.3.4. describes in detail theunderstanding and assignment of gene functions.3.3.1. Loading the Data in ClutrFree, Verifying Data Integrity,and Basic ClutrFree Window Organization1. ClutrFree is launched by the following command line wherein the path argumentis the root of the layout detailed in Subheading 3.2.1.$ java–jar clutrfree/home/ghbidaut/data/Rosetta_Dataset.The second possibility is to double-click on the ClutrFree icon (in MacOS X), thenuse the menus [File] [Import Data] and select the directory from the dialog. Again,the directory that must be selected is the layout root (Rosetta_Dataset). Once theinput directory is selected, ClutrFree displays a progress bar giving feedback onthe reading of the data.2. If everything is properly loaded, a dialog box with the following message isdisplayed:“ClutrFree has successfully loaded 16 experiments. The current displayed experimenthas five clusters of length 228.” This gives the general topology of the loadeddata, the number of experiments compared (here BD was performed with the numberof patterns varying between 5 and 20 giving 16 total experiments), and thenumber of conditions in each cluster (228 conditions from the original data set).This is consistent with the data size.3. Once the data is loaded, click “OK” on the dialog box. Two windows appearthen: the pattern graphics window (Titled ClutrFree: 1:5) and the pattern treewindow on top of it. If the pattern tree window is closed, it can be reopened bythe menu sequence [Window] [View The Pattern Tree]. The commands availablefrom this window are shown in Fig. 1. In addition to the loading data, the[File] menu permits data importation and exportation (graphics or tab-delimitedfiles). The [View] menu allows switching the display between stem-like graphicsor plot-like graphics (useful for temporal series), and the [window] menuallows the display of two other windows, the gene table window and the patterntree window.4. A gene window is opened by clicking on the [Gene List] button (as many windowscan be opened as the user wishes for ease of exploration and pattern comparison).This permits the comparison of a gene list for correlated patterns atdifferent tree levels.