BMC Genomics 2008, 9(Suppl 2):S20 http://www.biomedcentral.com/1471-2164/9/S2/S20 Table 3: Predicted functional modules of unclassified ORFs. ORF Physical/Genetic Associations (SGD) Functional Evidence Ribosomal RNA procesing (11.04.01) YBR271W YCR016W YDL063C YDL167C (NRP1) YDR361C (BCP1) YGR187C (HGH1) YIL064W Localizes to the cytoplasm YGL120C (PRP43) RNA helicase/maturation of rRNA, YPR135W (CTF4) Chromatin-associated protein YPL131W (RPL5-Protein of (60S) ribosomal subunit) Protein component of the large (60S) YDR188W (CCT6-Chaperonin Containing TCP-1) YIL096C YLR009W (RLP24) 60S ribosomal subunit biogenesis YIL110W YIL127C Localizes to the nucleolus YJR003C Detected in purified mitochondria YLR051C (FCF2) YLR196W (PWP) YPL131W (RPL5-Protein of (60S) ribosomal subunit), YDR188W (CCT6-Chaperonin Containing TCP-1) YLR287C YPR135W (CTF4) Chromatin-associated protein YOL022C YOR021C (TSR4) YOR154W (SLP1) YOR252W (TMA16) YLR009W (RLP24) 60S ribosomal subunit biogenesis, YGL120C (PRP43) RNA helicase/maturation of rRNA S-adenosylmethionine-dependent methyltransferase. GO ribosome biogenesis & assembly (RCA) GO ribosome biogenesis & assembly (RCA) GO ribosomal large subunit export from nucleus (IMP); Export of Mss4p lipid kinase GO ribosome biogenesis & assembly (RCA) GO ribosome biogenesis & assembly (RCA). S- adenosylmethionine-dependent methyltransferase GO ribosome biogenesis & assembly (RCA) Putative S-adenosylmethionine-dependent methyltransferase GO ribosome biogenesis & assembly (RCA) GO ribosome biogenesis & assembly (RCA) Essential nucleolar protein, 35S rRNA processing GO rRNA processing (IMP, ISS) Null mutant accumulates 20S pre-rRNA GO ribosome biogenesis & assembly (RCA) SUN like protein Negative regulation of transposition, RNA-mediated (IMP) YPL183C YBL112C YEL076C YER189W YHR219W YDR493W YKL137W YLR204W YLR218C YML030W YMR157C DNA Topology (10.01.02) Contained within telomere TEL02L, TEL02L-YP Contained within telomere TEL05L, TEL05L-YP, YEL076C-A Contained within telomere TEL05R, TEL05R-YP Putative protein of unknown function with similarity to helicases; Contained within telomere TEL08R, TEL08R-YP Mitochondrial (42.16) & Ribosomal Proteins (12.01.01) Null mutant displays decreased frequency of mitochondrial genome loss Mutation results in growth defect on a non-fermentable (respiratory) carbon source Mitochondrial inner membrane protein Localizes to mitochondria detected in purified mitochondria Growth defects on a non-fermentable carbon source Null mutant is viable & displays decreased frequency of mitochondrial genome loss Displays increased frequency of mitochondrial genome loss Predicted functional modules of unclassified ORFS. Genetic/Physical interaction and functional evidence supporting predicted functional modules. GO = Gene Ontology; RCA = Reviewed Computational Analysis. datasets is YDR493W, YKL137W, YLR204W, YLR218C, YML030W, YMR157C. These annotated biclusters were highly enriched in Mitochondrial (42.16) and Ribosomal Proteins (12.01.01) with significances of 2.48 × 10-53 & 5.88 × 10-40 and 1.23 × 10-36 & 4.23 × 10-34 for these func- tional categories in the Hughes and Gasch datasets respec- tively. The correlated expression of this group of unannotated ORFs can be seen in Figure 6 and additional supporting interaction and functional evidence is shown in Table 3. Discussion BALBOA represents a novel, systematic approach for ORF classification using expression data. BALBOA's novelty lies both in the use of biclustering for training and classi- fication and also in the subsequent 'ensemble-like' predic- tion strategy in which information provided by multiple biclusters is combined. Although such ensemble tech- niques are conceptually simple, resulting predictions tend to be more robust. In the first part of the Results section, cross validation showed that, on average, BALBOA Page 12 of 15 (page number not for citation purposes)