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Gene Function Inference in Deletion Mutants 174. Notes1. BDrun has a distributed network mode wherein a series of nodes running a BDrunserver can be set up. A BDrun launched in client mode will send BD jobs toidle nodes on the network that run a BDrun server. This allows running BD on idlemachines and leaving the user machine resources free. The user can configure themachines he wishes to use by editing the following file provided with BDrun:/path_to_bdtools/BDservers.list.2. The pattern indices can be completely different if the analyses are run, because BDassigns patterns a random order number. Also, the values obtained for ontologicalenhancement may be slightly different than the one shown herein, owing to thegene amplitude values found by BD, and to the ongoing reannotation of the yeastgene ontologies in MIPS.3. ClutrFree offers the possibility to export pattern graphics (menu [File] [Export CurrentGraphics] from the ClutrFree main window) or tree graphics for further editing withpublishing tools (menu [File] [Export Current Tree] from one of the tree window).Supported formats include joint picture exchange (JPEG), tagged image file format(TIFF), portable network graphics (PNG), simple vector graphics (SVG), and dot fortree exportation. Tree exported in dot formats can be further displayed with theGraphViz package (AT&T Research, Florham Park, NJ, www.graphviz.org).4. In ClutrFree, trees can be rendered with more information if needed. It is possibleto include correlation value (menu [Display] [Correlation]), as well as displayingontological enrichment in each tree node (menu [Display] [Ontologies]). The displayparameters can be set at [Display] [Options].5. By following the procedure listed in Subheading 3.3.3., functions can be assigned topatterns 9 and 15. They are the two most enriched patterns for the ontology34.11.03.07: pheromone response, mating-type determination, and sex-specific proteins.To observe which genes are the highest contributors to pattern 9 and 15, theyare sorted by value in the upper gene table. For pattern 9, it is observed that 11 of thetop 15 genes are transposable elements, involved in filamentation. The hypothesis isthat the patterns 9 and 15 represent two reproductive modes in yeast; filamentationand the mating response (see ref. 14). To confirm this hypothesis, the contribution oftree mutants is examined in interest to those patterns; Ste12∆, Ste20∆, and Tec1∆. Inpattern 15, it is found that Ste12∆ is absent, whereas Ste20∆ and Tec1∆ have a strongsignal, which is in accordance with the mating pathway activated through Ste12 butwhich can bypass Ste20 through a G protein complex (14). In pattern 9, Ste12∆ is stillabsent, and Ste20∆ and Tec1∆ are showing weak signals. This measurement is inaccordance with the set of genes known to trigger filamentation, which includesSte12, Ste20, and Tec1. See ref. 5 for a detailed discussion of this issue.AcknowledgmentsThe author would like to thank Dr. Michael Ochs, for the development ofthe BD Method and contribution to ClutrFree, and Bill Speier, who is theauthor of BDrun.