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. 2009 Oct 6;7(10):e1000213. doi: 10.1371/journal.pbio.1000213

Table 1. Summary of the evidence from this study for the involvement of known and new proteins in ribosome biogenesis.

ORF Genea Human Orthologb Number of Links to Seed Genes Network Evidencec Mutant Growth Polysome Profile Defect Co-sedimentationd Pre-rRNA Processing Defect Ribosome Export Defect
YGR162W TIF4631 EIF4G1, EIF4G, EIF4G3 22 MS, CX, LC Slow 60S Across gradient 35S, 27S, 7S, 20S 60S
YOR308C SNU66 SART1 8 MS, CC, LC Slow at 20°C 60S 40S 35S, 27S, 5S No
YDL063C — — 5 MS, CC, YH, CX Slow 60S Free 35S, 27S No
YDR412W RRP17 ?NOL12 14 CX, MS, YH Essential 60S Free 35S, 7S 60S
YPR169W JIP5 ?AAC69625 19 CX, MS Essential 60S Free, 60S 35S, 27S No
YOL006C TOP1 TOP1 7 CC, MS, LC, CX Slow 60S Across gradient 35S, 27S No
YNL132W KRE33 [10] NAT10 77 MS, CX, LC Essential 40S — 35S 40S
YDR496C PUF6 [21] KIAA0020 94 CX, MS, LC Slow at 20°C 60S 60S 35S, 27S, 7S 60S
YLR336C SGD1 NOM1 31 CX, MS Essential 40S 40S, 60S, 80S 35S 40S
YLR397C AFG2 [52] SPATA5 7 CX, MS, CC Essential 60S — 35S, 7S 60S
YDR361C BCP1 BCCIP 19 CX Essential 60S Free, 60S 35S 60S
YJL010C NOP9 [40] C14orf21 56 CX, LC Essential 40S 40S, Polysome 35S 40S
YOR287C — C6orf153 40 CX, MS Essential 40S — 35S No
YDR339C FCF1 [41] CN111_HUMAN 13 CX Essential 40S — 35S 40S
YMR014W BUD22 — 37 CX, MS Slow 40S 80/90S, Polysome 35S 40S
YCR047C BUD23 [68] WBSCR22 7 MS, CX Slow 40S 40S 35S, 20S 40S
YLR051C FCF2 [41] DNTTIP2 13 CX Essential 40S — 35S —
YGR145W ENP2 NOL10 91 CX, MS, LC, RS Essential 40S — 35S 40S
YDR299W BFR2 AATF 71 CX, MS, LC Essential 40S 40S, 80/90S 35S 40S
YIL091C — DEF 12 CX, MS Essential 40S 40S 35S No
YOL022C TSR4 ?PDCD2L 30 CX Essential 40S Free 20S No
YOR006C TSR3 C16orf42 2 CX Slow at 20°C and 30°C 40S Free 20S No
YGR081C SLX9 [43] — 14 MS, CX, GT Slow at 30°C 40S 40S 20S 40S
YDR159W SAC3 MCM3AP 1 LC Slow 40S 40S, 80/90S 35S No
YPL226W NEW1 ?ABCF1 8 CX, MS Slow at 20°C and 30°C 40S Across gradient 35S No
YJR074W MOG1 RANGRF 3 CC, GT, MS, LC, YH Slow Minor Free 35S, 27S, 20S No
YAL035W FUN12 EIF5B 40 MS, GN, CX Slow 40S Polysome 20S No
YPR178W PRP4 PRPF4 11 MS, LC, CC, YH Essential Minor Free, 40S 35S No
YDR378C LSM6 [44] LSM6 7 MS, LC, CC, YH, TS Slow Minor — 35S, 20S 50% cells 60S
YNL147W LSM7 [44] LSM7 7 MS, LC, CC, YH, TS Slow Minor Polysome 35S, 20S 50% cells 60S
a

Citations indicate prior evidence for roles in ribosome biogenesis. Note that all genes listed have at least some prior evidence (e.g., protein interactions, expression patterns, or localization, as indicated in the network evidence column), as this forms the basis of the computational predictions; only studies reporting detailed characterization are indicated here.

b

Human orthologs were identified using INPARANOID. For genes without clear orthologs, the best BLASTP hits are indicated by a question mark (?).

c

CC, co-citation; CX, co-expression; GN, gene neighbor; GT, genetic interaction; LC, literature-curated protein-protein interaction; MS, mass spectrometry analysis of purified complex; PG, phylogenetic profile; RS, Rosetta Stone protein (gene fusion); TS, protein tertiary structure inferred protein-protein interaction; YH, high-throughput yeast two hybrid.

d

Free represents the low density fractions.