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Table 1 Classification results and annotation for 62 novel predicted nucleolar/ribosome-associated proteins

From: An inventory of yeast proteins associated with nucleolar and ribosomal components

Gene

ORF

Hs

At

Ue

It

Kr

Ga

Ho

log(O)

Description

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

          

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

  1. The data used for classification and the detailed prediction results are listed for all 62 proteins that passed our threshold of O post > 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.