ORF YJR154W Metabolism: Amino Acid (01.01) YDL072C (YET3) Energy: Respiration (02.13) YGR149W YCR072C (RSA4) Energy: Respiration (02.13) Transcription: rRNA (11.04.01) YDL167C (NRP1) Transcription: rRNA (11.04.01) YMR259C YNL022C YDR361C (BCP1) YJL122W (ALB 1) YJR003C Transcription: rRNA (11.04.01)/ Transport Routes (20.09) Transcription: rRNA (11.04.01) Transcription (11)/Ribosomal Proteins (12.01.01) Transcription (11)/Ribosomal Proteins (12.01.01) Transcription: rRNA (11.04.01)/ Transport Routes (20.09) YLR196W (PWP1) Ribosomal Proteins (12.01.01)/ Transcription (11) YER049W (TPA1) Ribosomal Proteins (12.01.01)/ Cellular Transport (20) YDR282C YGR266W YIL039W YOR175C YPL105C YIL060W YJR030C YIL157C YML030W Transported Compounds(20.01)/ Tansposable Elements (38) Transport Routes (20.09) Transport Routes (20.09) Transport Routes (20.09) Transport Routes (20.09)/ Transcription (11) Tansposable Elements (38) Tansposable Elements (38) Biogenesis of Cellular Components: Mitochondrion (42.16) Biogenesis of Cellular Components: Mitochondrion (42.16) BMC Genomics 2008, 9(Suppl 2):S20 http://www.biomedcentral.com/1471-2164/9/S2/S20 gories, were consistent across 2 or more datasets. We will now focus on these consistent annotations, presented in Table 2. We can see from this table that some of BALBOA's putative functional annotations seem to be well sup- ported given the external experimental and sequence information. One case which stands out in particular is that of YCR072C. This ORF was unclassified by MIPS when we labelled the data. However this ORF has subse- quently been labelled by MIPS as being involved in tran- scription of ribosomal RNA (rRNA) and assigned category rRNA processing (11.04.01). This functional label agrees with our predicted function. In fact six of the seven ORFs assigned to the Transcription (11) functional category seem to have good supporting external evidence. This includes YDL167C and YJR003 both of which are sup- ported by previous computational evidence defined as Table 2: BALBOA annotation of unclassified ORFs that are consistent over two or more datasets. Predicted Function Experimental Evidence (SGD) Protein Sequence Unclassified ORFs consistently annotated over two or more datasets, additional labels in italics are from one dataset only. GFP = Green Fluorescent Protein; Rca = Reviewed Computational Analysis. Putative protein, unknown function. GFP- fusion protein localizes to cytoplasm. Null mutant has decreased level of secreted invertase (enables respiration of sucrose). Putative protein, unknown function Recently verified by MIPS – ribosomal biogenesis. Role in ribosome biogenesis and assembly (RCA). Putative protein, unknown function; GFP- fusion protein localizes to the cytoplasm. Putative protein of unknown function. GFP- fusion protein localizes to a single spot in the nucleus. Associated with RPL23a & PL23b (Ribosomal sub-units) in Affinity Capture Expts. Shuttling pre-60S factor; involved in the biogenesis of ribosomal large subunit. Putative protein. Detected in purified mitochondria. Role in ribosome biogenesis and assembly (RCA). Protein with WD-40 repeats involved in rRNA processing. Interacts with Sup45p (eRF1) and Sup35p (eRF3) and Pab1p; role in translation termination efficiency. Putative protein of unknown function. Protein of unknown function. Localizes to mitochondrial outer membrane and plasma membrane GFP-fusion localizes to the ER. Deletion confers sensitivity to GSAO (angiogenesis inhibitor drug). Protein of unknown function. Co-purification with Ribosomes. Protein of unknown function. Co-purification with both Ribosomes & mitochondria. Putative protein of unknown function. Mutant accumulates less glycogen than does wild type. Putative protein of unknown function. Expression repressed in carbon limited cultures Detected in Co-purified mitochondria. Null mutant is defective in cytochrome oxidase. Putative protein of unknown function; GFP- fusion protein localizes to mitochondria. Similarity (p = 2.8e-5) to cytosolic L- asparaginase (YDR321W). Human BAP31 homolog. Predicted integral membrane protein. Similarity (p = 1.2e-18) to YNL061W involved in rRNA processing. Similarity (p = 2.2e-21) to YDL001W required for sporulation. Predicted to have single trans- membrane domain. Member of MBOAT putative membrane bound O-acyltransferases. Similarity (p = 4.2e-06) to TyA & TyB Retrotransposons. Similar to YJL181w (cell cyle regulator) & MBP-1 binding site (cell cycle). Page 9 of 15 (page number not for citation purposes)