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Classification results and annotation for 62 novel predicted nucleolar/ribosome-associated proteins |
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| Gene |
ORF |
Hs |
At |
Ue |
It |
Kr |
Ga |
Ho |
log(O) |
Description |
|
|
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| SUA7 |
YPR086W |
1 |
0 |
1 |
0 |
1 |
0 |
o |
0.665 |
TFIIB subunit (transcription initiation factor) factor E |
| HTA1 |
YDR225W |
1 |
0 |
1 |
0 |
0 |
1 |
0 |
0.612 |
Histone H2A |
| HSC82 |
YMR186W |
1 |
1 |
0 |
0 |
1 |
0 |
0 |
0.697 |
Heat shock protein |
| TIF1 |
YKR059W |
1 |
1 |
0 |
0 |
1 |
0 |
0 |
0.699 |
Translation initiation factor 4A |
| PRP4 |
YPR178W |
1 |
0 |
0 |
0 |
1 |
0 |
1 |
0.703 |
U4/U6 snRNP 52 kDa protein |
| KAR2 |
YJL034W |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.684 |
Component of ER translocon |
| HTA2 |
YBL003C |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0.724 |
Histone H2A.2 |
| AAC3 |
YBR085W |
1 |
1 |
0 |
0 |
0 |
1 |
0 |
0.686 |
Mitochondrial ADP/ATP carrier - member of the mitochondrial carrier (MCF) family |
| RFC2 |
YJR068W |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.686 |
DNA replication factor C 41 kDa subunit |
| TEF1 |
YPR080W |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.686 |
Translation elongation factor eEF1 alpha-A chain cytosolic |
| SMX2 |
YFL017W-A |
1 |
1 |
0 |
0 |
1 |
0 |
0 |
0.696 |
snRNP G protein (the homologue of the human Sm-G) |
| BCP1 |
YDR361C |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.686 |
Similarity to hypothetical protein S. pombe |
| LEA1 |
YPL213W |
1 |
1 |
0 |
0 |
1 |
0 |
0 |
0.704 |
U2 A snRNP protein |
| HSP82 |
YPL240C |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.686 |
Heat shock protein |
| SMD3 |
YLR147C |
1 |
1 |
0 |
0 |
1 |
0 |
0 |
0.699 |
Spliceosomal snRNA-associated Sm core protein required for pre-mRNA splicing |
| TIF2 |
YJL138C |
1 |
1 |
0 |
0 |
0 |
1 |
0 |
0.686 |
Translation initiation factor eIF4A |
| None |
YBR025C |
1 |
0 |
1 |
0 |
0 |
1 |
0 |
0.610 |
Strong similarity to Ylf1p |
| SPT16 |
YGL207W |
1 |
1 |
0 |
0 |
1 |
1 |
0 |
0.705 |
General chromatin factor |
| SUI2 |
YJR007W |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0.720 |
Translation initiation factor eIF2 alpha chain |
| HSH49 |
YOR319W |
0 |
1 |
0 |
1 |
0 |
1 |
0 |
0.702 |
Essential yeast splicing factor |
| DED1 |
YOR204W |
0 |
1 |
0 |
0 |
0 |
0 |
1 |
0.716 |
ATP-dependent RNA helicase |
| HTB1 |
YDR224C |
1 |
1 |
1 |
0 |
0 |
1 |
0 |
0.709 |
Histone H2B |
| HRR25* |
YPL204W |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0.718 |
Casein kinase I Ser/Thr/Tyr protein kinase |
| SSA2 |
YLL024C |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.686 |
Heat shock protein of HSP70 family cytosolic |
| SRP1 |
YNL189W |
0 |
1 |
1 |
0 |
1 |
1 |
1 |
0.696 |
Karyopherin-alpha or importin |
| SUB2 |
YDL084W |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.686 |
Probably involved in pre-mRNA splicing |
| CKA1 |
YIL035C |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0.698 |
Casein kinase II catalytic alpha chain |
| PRP43* |
YGL120C |
1 |
1 |
1 |
0 |
1 |
1 |
0 |
0.695 |
Involved in spliceosome disassembly |
| SUI3 |
YPL237W |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0.721 |
Translation initiation factor eIF2 beta subunit |
| DST1 |
YGL043W |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0.692 |
TFIIS (transcription elongation factor) |
| PRP8 |
YHR165C |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0.721 |
U5 snRNP protein pre-mRNA splicing factor |
| PRP9 |
YDL030W |
1 |
0 |
1 |
0 |
1 |
0 |
0 |
0.667 |
Pre-mRNA splicing factor (snRNA-associated protein) |
| SUP45 |
YBR143C |
1 |
0 |
1 |
0 |
1 |
1 |
0 |
0.704 |
Translational release factor |
| ASC1 |
YMR116C |
1 |
1 |
0 |
0 |
1 |
0 |
0 |
0.698 |
40S small subunit ribosomal protein |
| DBP2* |
YNL112W |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0.719 |
ATP-dependent RNA helicase of DEAD box family |
| CKB2 |
YOR039W |
1 |
0 |
0 |
1 |
1 |
1 |
0 |
0.710 |
Casein kinase II beta chain |
| YRA1 |
YDR381W |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0.720 |
RNA annealing protein |
| GCD11 |
YER025W |
1 |
0 |
1 |
0 |
0 |
1 |
0 |
0.609 |
Translation initiation factor eIF2 gamma chain |
| TFG2 |
YGR005C |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0.695 |
TFIIF subunit (transcription initiation factor) 54 kDa |
| TOP1* |
YOL006C |
1 |
0 |
1 |
1 |
1 |
0 |
0 |
0.693 |
DNA topoisomerase I |
| BRR2 |
YER172C |
1 |
1 |
0 |
0 |
0 |
0 |
1 |
0.708 |
RNA helicase-related protein |
| RVB1 |
YDR190C |
1 |
1 |
1 |
0 |
0 |
1 |
0 |
0.709 |
RUVB-like protein |
| MLP1 |
YKR095W |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.686 |
Myosin-like protein related to Uso1p |
| HTZ1 |
YOL012C |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.685 |
Evolutionarily conserved member of the histone H2A F/Z family of histone variants |
| ATP2 |
YJR121W |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.685 |
F1F0-ATPase complex F1 beta subunit |
| SMD2 |
YLR275W |
1 |
1 |
0 |
1 |
1 |
0 |
0 |
0.688 |
U1 snRNP protein of the Sm class |
| PRP3 |
YDR473C |
1 |
0 |
0 |
0 |
1 |
0 |
1 |
0.704 |
Essential splicing factor |
| EFT1 |
YOR133W |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0.682 |
Translation elongation factor eEF2 |
| HTB2 |
YBL002W |
1 |
1 |
0 |
0 |
0 |
1 |
0 |
0.690 |
Histone H2B.2 |
| TEF4 |
YKL081W |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0.718 |
Translation elongation factor eEF1 gamma chain |
| HHF2 |
YNL030W |
1 |
1 |
0 |
0 |
1 |
0 |
0 |
0.695 |
Histone H4 |
| Predictions based solely on protein interactions |
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| RPO21 |
YDL140C |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0.728 |
DNA-directed RNA polymerase II 215 kDa subunit |
| DHH1 |
YDL160C |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0.714 |
Putative RNA helicase of the DEAD box family |
| CFT1 |
YDR301W |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0.731 |
Pre-mRNA 3-end processing factor CF II |
| KAP95 |
YLR347C |
0 |
0 |
1 |
0 |
1 |
1 |
1 |
0.689 |
Karyopherin-beta |
| SPT5 |
YML010W |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0.732 |
Transcription elongation protein |
| TAF14 |
YPL129W |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0.733 |
TFIIF subunit (transcription initiation factor) 30 kDa |
| RPB3 |
YIL021W |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0.728 |
DNA-directed RNA-polymerase II 45 kDa |
| RPO31 |
YOR116C |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0.729 |
DNA-directed RNA polymerase III 160 kDa subunit |
| TIF4631 |
YGR162W |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0.734 |
mRNA cap-binding protein (eIF4F) 150K subunit |
| PRP24 |
YMR268C |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0.734 |
Pre-mRNA splicing factor |
| RET1 |
YOR207C |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0.731 |
DNA-directed RNA polymerase III 130 kDa subunit |
|
The data used for classification and the detailed prediction results are listed for all 62 proteins that passed our threshold of Opost > 0.4. These proteins had not been annotated as associated with nucleolar or ribosomal components before, but were classified as such in our analysis. A literature survey for the predicted proteins revealed that for four proteins a role in the nucleolus and ribosome biogenesis had already been established (see Note added in proof). The lower part of the table lists 11 proteins that were predicted as NRCA proteins solely on the basis of shared participation in complexes or interactions. For these proteins, we do not necessarily predict a nucleolar localization, but direct interaction with nucleolar/ribosomal components at least under one specific cellular condition at an unspecified locus within the cell. *Four proteins for which recent articles have confirmed a role in ribosome biogenesis or the nucleolus. The results are supplemented by a concise annotation for each protein from the Comprehensive Yeast Genome Database (CYGD) [72]. The header line contains abbreviations describing the column content: Gene, gene symbol of yeast gene; ORF, yeast open reading frame ID; Hs, orthology to human nucleolar protein; At, orthology to mouse-ear cress nucleolar protein; It, link to nucleolar protein via Y2H interaction in Ito dataset; Ue, link to nucleolar protein via Y2H interaction in Uetz dataset; Ga, link to nucleolar protein via participation in a complex in Gavin data set; Ho, link to nucleolar protein via participation in a complex in Ho data set; Kr, link to nucleolar protein via participation in a complex in Krogan data set; log(O), average posterior odds ratio from all prediction runs in which the protein was not used for training; Description, concise description of protein function. | ||||||||||
Staub et al. Genome Biology 2006 7:R98 doi:10.1186/gb-2006-7-10-r98 |
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