Cluster CG0001:
Q-value = 0.90 log10(P) = -15.09 log10(E) = -2.48 log10(Pevd) = -5.29
 YCR092C  MSH3 3 3 DNA mismatch repair protein
 YMR167W  MLH1 4 4 DNA mismatch repair protein
 YNL082W  PMS1 4 4 DNA mismatch repair protein
 YOL090W  MSH2 5 4 DNA mismatch repair protein
 YDR097C  MSH6 3 3 DNA mismatch repair protein
Cluster CG0003:
Q-value = 1.00 log10(P) = -9.22 log10(E) = -2.22 log10(Pevd) = -4.46
 YCL032W  STE50 8 3 pheromone response pathway protein
 YDR103W  STE5 12 3 pheromone signal transduction pathway protein
 YLR362W  STE11 16 3 ser/thr protein kinase of the MEKK family
 YOR212W  STE4 12 3 GTP-binding protein beta subunit of the pheromone pathway
Cluster CG0004:
Q-value = 0.90 log10(P) = -14.82 log10(E) = -3.65 log10(Pevd) = -5.29
 YGR082W  TOM20 7 4 mitochondrial outer membrane import receptor subunit, 20 kD
 YMR203W  TOM40 8 4 forms the hydrophilic channel of the mitochondrial import pore for preproteins
 YNL070W  TOM7 7 4 mitochondrial outer membrane import receptor subunit, 7 kD
 YNL131W  TOM22 4 3 mitochondrial outer membrane import receptor complex subunit
 YNL121C  TOM70 5 3 mitochondrial outer membrane specialized import receptor
Cluster CG0005:
Q-value = 0.80 log10(P) = -18.69 log10(E) = -7.51 log10(Pevd) = -5.77
 YGL161C  10 5 weak similarity to TRCDSEMBL:HS167A19_1 dJ167A19.1 human (Class IV)
 YGL198W  10 5 weak similarity to YIP1P (Class III)
 YGR172C  YIP1 16 5 golgi membrane protein
 YPL095C  4 3 strong similarity to YBR177C (Class IV)
 YDR425W  7 3 similarity to hypothetical protein YDL113C (Class IV)
 YDL226C  GCS1 15 3 ADP-ribosylation factor GTPase-activating protein (ARF-GAP)
Cluster CG0006:
Q-value = 1.00 log10(P) = -9.76 log10(E) = -0.54 log10(Pevd) = -4.46
 YDR244W  PEX5 4 3 peroxisomal targeting signal receptor
 YGL153W  PEX14 14 3 peroxisomal protein involved in protein import - peroxin
 YLR191W  PEX13 6 3 peroxisomal protein involved in protein import - peroxin
 YNL214W  PEX17 4 3 component of the peroxisomal protein translocation - peroxin
Cluster CG0007:
Q-value = 1.00 log10(P) = -10.22 log10(E) = 0.15 log10(Pevd) = -4.46
 YCR093W  CDC39 4 3 nuclear protein
 YER068W  MOT2 3 3 transcriptional repressor
 YIL038C  NOT3 3 3 general negative regulator of transcription, subunit 3
 YPR072W  NOT5 4 3 component of the NOT protein complex
Cluster CG0008:
Q-value = 1.00 log10(P) = -9.96 log10(E) = -1.97 log10(Pevd) = -4.46
 YBL050W  SEC17 11 3 transport vesicle fusion protein
 YDR468C  TLG1 7 3 member of the syntaxin family of t-SNAREs
 YMR197C  VTI1 8 3 v-SNARE: involved in Golgi retrograde protein traffic
 YOL018C  TLG2 10 3 member of the syntaxin family of t-SNAREs
Cluster CG0009:
Q-value = 0.80 log10(P) = -19.40 log10(E) = -5.57 log10(Pevd) = -5.77
 YFL059W  SNZ3 9 5 strong similarity to Para rubber tree ethylene-responsive protein1 (Class II)
 YMR095C  SNO1 3 3 similarity to M.leprae hisH protein (Class III)
 YMR096W  SNZ1 5 5 stationary phase protein
 YNL333W  SNZ2 8 5 putative pyridoxine (vitamin B6) biosynthetic enzyme
 YFL060C  SNO3 4 3 strong similarity to SNO1 and SNO2 (Class IV)
 YMR322C  4 3 strong similarity to YPL280W, YOR391C andYDR533C (Class IV)
Cluster CG0011:
Q-value = 0.90 log10(P) = -13.97 log10(E) = -4.35 log10(Pevd) = -5.29
 YDL132W  CDC53 13 4 controls G1/S transition
 YDR054C  CDC34 7 4 E2 ubiquitin-conjugating enzyme
 YDR328C  SKP1 17 4 kinetochore protein complex CBF3, subunit D
 YFL009W  CDC4 4 3 cell division control protein
 YIL046W  MET30 12 3 involved in regulation of sulfur assimilation genes and cell cycle progression
Cluster CG0012:
Q-value = 1.00 log10(P) = -8.59 log10(E) = 0.63 log10(Pevd) = -4.46
 YDR498C  SEC20 3 3 secretory pathway protein
 YGL145W  TIP20 7 3 required for ER to Golgi transport
 YLR268W  SEC22 10 3 synaptobrevin (V-SNARE)
 YOR075W  UFE1 5 3 syntaxin (T-SNARE) of the ER
Cluster CG0013:
Q-value = 1.00 log10(P) = -8.63 log10(E) = 0.13 log10(Pevd) = -4.46
 YDR016C  DAD1 6 3 hypothetical protein (Class V)
 YGL061C  DUO1 6 3 essential mitotic spindle protein
 YGR113W  DAM1 13 3 essential mitotic spindle pole protein
 YKR037C  SPC34 6 3 spindle pole body protein
Cluster CG0015:
Q-value = 1.00 log10(P) = -11.45 log10(E) = -1.71 log10(Pevd) = -4.46
 YAR008W  SEN34 5 3 tRNA splicing endonuclease gamma subunit
 YLR105C  SEN2 6 3 tRNA splicing endonuclease beta subunit
 YMR059W  SEN15 3 3 tRNA splicing endonuclease delta subunit
 YPL083C  SEN54 4 3 tRNA splicing endonuclease alpha subunit
Cluster CG0016:
Q-value = 1.00 log10(P) = -9.62 log10(E) = 0.13 log10(Pevd) = -4.46
 YHL031C  GOS1 4 3 SNARE protein of Golgi compartment
 YKL006C-A  SFT1 5 3 SNARE-like protein
 YKL196C  YKT6 4 3 SNARE protein for Endoplasmic Reticulum-Golgi transport
 YLR026C  SED5 8 3 syntaxin (T-SNARE)
Cluster CG0017:
Q-value = 1.00 log10(P) = -8.55 log10(E) = -0.83 log10(Pevd) = -4.46
 YAL041W  CDC24 11 3 GTP/GDP exchange factor for CDC42P
 YBR200W  BEM1 10 3 bud emergence mediator
 YJL157C  FAR1 6 3 cyclin-dependent kinase inhibitor (CKI)
 YLR229C  CDC42 13 3 GTP-binding protein of RAS superfamily
Cluster CG0020:
Q-value = 1.00 log10(P) = -7.43 log10(E) = -0.43 log10(Pevd) = -4.46
 YDL030W  PRP9 18 3 pre-mRNA splicing factor (snRNA-associated protein)
 YDL043C  PRP11 21 3 pre-mRNA splicing factor
 YJL203W  PRP21 14 3 pre-mRNA splicing factor
 YNR053C  6 3 strong similarity to human breast tumor associated autoantigen (Class II)
Cluster CG0021:
Q-value = 1.00 log10(P) = -9.22 log10(E) = -1.50 log10(Pevd) = -4.46
 YFR002W  NIC96 7 3 nuclear pore protein
 YGL172W  NUP49 9 3 nuclear pore protein
 YGR119C  NUP57 22 3 nuclear pore protein
 YJL041W  NSP1 7 3 nuclear pore protein
Cluster CG0023:
Q-value = 1.00 log10(P) = -9.74 log10(E) = 0.01 log10(Pevd) = -4.46
 YBL021C  HAP3 4 3 CCAAT-binding factor subunit
 YGL237C  HAP2 8 3 CCAAT-binding factor subunit
 YKL109W  HAP4 3 3 CCAAT-binding factor subunit
 YOR358W  HAP5 7 3 CCAAT-binding factor subunit
Cluster CG0024:
Q-value = 1.00 log10(P) = -10.21 log10(E) = 0.15 log10(Pevd) = -4.46
 YBR126C  TPS1 3 3 alpha,alpha-trehalose-phosphate synthase, 56 KD subunit
 YDR074W  TPS2 6 3 alpha,alpha-trehalose-phosphate synthase, 102 KD subunit
 YML100W  TSL1 3 3 alpha,alpha-trehalose-phosphate synthase, 123 KD subunit
 YMR261C  TPS3 3 3 alpha,alpha-trehalose-phosphate synthase, 115 KD subunit
Cluster CG0025:
Q-value = 1.00 log10(P) = -10.25 log10(E) = 0.12 log10(Pevd) = -4.46
 YLR148W  PEP3 3 3 vacuolar membrane protein
 YLR396C  VPS33 4 3 vacuolar sorting protein
 YMR231W  PEP5 4 3 vacuolar biogenesis protein
 YPL045W  VPS16 3 3 vacuolar sorting protein
Cluster CG0026:
Q-value = 1.00 log10(P) = -11.42 log10(E) = -1.68 log10(Pevd) = -4.46
 YAR007C  RFA1 4 3 DNA replication factor A, 69 KD subunit
 YJL173C  RFA3 5 3 DNA replication factor A, 13 KD subunit
 YML032C  RAD52 5 3 recombination and DNA repair protein
 YNL312W  RFA2 3 3 DNA replication factor A, 36 kDa subunit
Cluster CG0027:
Q-value = 1.00 log10(P) = -6.13 log10(E) = 0.87 log10(Pevd) = -4.46
 YDR228C  PCF11 9 3 component of pre-mRNA 3'-end processing factor CF I
 YER165W  PAB1 15 3 mRNA polyadenylate-binding protein
 YGL044C  RNA15 20 3 component of pre-mRNA 3'-end processing factor CF I
 YMR061W  RNA14 8 3 component of pre-mRNA 3'-end processing factor CF I
Cluster CG0029:
Q-value = 1.00 log10(P) = -15.87 log10(E) = -4.70 log10(Pevd) = -6.42
 YGL019W  CKB1 6 4 casein kinase II, beta subunit
 YIL035C  CKA1 4 4 casein kinase II, catalytic alpha chain
 YNL088W  TOP2 8 4 DNA topoisomerase II (ATP-hydrolysing)
 YOR039W  CKB2 9 4 casein kinase II beta' chain
 YOR061W  CKA2 4 4 casein kinase II alpha' chain
Cluster CG0030:
Q-value = 1.00 log10(P) = -16.44 log10(E) = -5.28 log10(Pevd) = -6.42
 YCR035C  RRP43 6 4 rRNA processing protein
 YDL111C  RRP42 5 4 rRNA processing protein
 YGR195W  SKI6 6 4 3'->5' exoribonuclease required for 3' end formation of 5.8S rRNA
 YHR069C  RRP4 4 4 3'->5' exoribonuclease required for 3' end formation of 5.8S rRNA
 YOL021C  DIS3 5 4 3'->5' exoribonuclease required for 3' end formation of 5.8S rRNA
Cluster CG0031:
Q-value = 0.95 log10(P) = -26.92 log10(E) = -15.55 log10(Pevd) = -9.74
 YBR193C  MED8 13 6 transcriptional regulation mediator
 YDL005C  MED2 7 6 transcriptional regulation mediator
 YGL025C  PGD1 8 6 mediator complex subunit
 YIL021W  RPB3 8 5 DNA-directed RNA-polymerase II, 45 kDa
 YOL135C  MED7 9 6 member of RNA Polymerase II transcriptional regulation mediator complex
 YOR174W  MED4 11 6 transcription regulation mediator
 YER022W  SRB4 101 5 DNA-directed RNA polymerase II holoenzyme and Kornberg's mediator (SRB) subcomplex subunit
Cluster CG0033:
Q-value = 1.00 log10(P) = -25.20 log10(E) = -12.17 log10(Pevd) = -8.43
 YEL003W  GIM4 5 5 Gim complex component
 YGR078C  PAC10 5 5 GIM4 - Gim complex component
 YLR200W  YKE2 10 5 Gim complex component
 YLR212C  TUB4 7 5 gamma tubulin
 YML094W  GIM5 5 5 Gim complex component
 YNL153C  GIM3 6 5 Gim complex component
Cluster CG0034:
Q-value = 1.00 log10(P) = -23.33 log10(E) = -10.30 log10(Pevd) = -8.43
 YCR002C  CDC10 6 5 cell division control protein
 YDL225W  SHS1 5 5 septin
 YDR507C  GIN4 6 5 ser/thr protein kinase
 YHR107C  CDC12 9 5 septin
 YJR076C  CDC11 6 5 septin
 YLR314C  CDC3 5 5 cell division control protein
Cluster CG0035:
Q-value = 1.00 log10(P) = -30.73 log10(E) = -18.06 log10(Pevd) = -10.47
 YAL043C  PTA1 8 6 pre-tRNA processing protein / PF I subunit
 YDR301W  CFT1 7 6 pre-mRNA 3'-end processing factor CF II
 YJR093C  FIP1 10 6 component of pre-mRNA polyadenylation factor PF I
 YKR002W  PAP1 10 6 poly(A) polymerase
 YLR115W  CFT2 6 6 cleavage and polyadenylation specificity factor, part of CF II
 YLR277C  YSH1 10 6 component of pre-mRNA polyadenylation factor PF I
 YPR107C  YTH1 8 6 protein of the 3' processing complex
Cluster CG0036:
Q-value = 0.98 log10(P) = -69.19 log10(E) = -53.07 log10(Pevd) = -15.95
 YBR254C  TRS20 11 9 TRAPP subunit of 20 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YDR246W  TRS23 9 9 TRAPP subunit of 20 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YDR407C  TRS120 9 9 TRAPP subunit of 120 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YDR472W  TRS31 9 9 TRAPP subunit of 31 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YGR166W  KRE11 10 8 beta-glucan synthesis-associated protein
 YKR068C  BET3 9 9 involved in targeting and fusion of ER to golgi transport vesicles
 YML077W  BET5 10 9 involved in targeting and fusion of ER to golgi transport vesicles
 YMR218C  TRS130 9 9 TRAPP subunit of 130 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YOR115C  TRS33 10 9 TRAPP subunit of 33 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YDR108W  GSG1 10 8 sporulation specific protein
Cluster CG0038:
Q-value = 0.98 log10(P) = -74.10 log10(E) = -59.60 log10(Pevd) = -99.00
 YBL026W  LSM2 15 10 Sm-like (Lsm) protein
 YCR077C  PAT1 20 10 topoisomerase II-associated protein
 YDR378C  LSM6 13 10 Sm-like (Lsm) protein
 YER112W  LSM4 14 10 Sm-like (Lsm) protein
 YER146W  LSM5 10 10 Sm-like (Lsm) protein
 YGL173C  KEM1 10 10 multifunctional nuclease
 YJR022W  LSM8 28 9 splicing factor
 YLR438C-A  LSM3 10 10 Sm-like (Lsm) protein
 YNL147W  LSM7 10 10 Sm-like (Lsm) protein
 YOL149W  DCP1 21 10 mRNA decapping enzyme
 YJL124C  LSM1 10 9 Sm-like (Lsm) protein
Cluster CG0040:
Q-value = 1.00 log10(P) = -82.33 log10(E) = -66.33 log10(Pevd) = -99.00
 YBL084C  CDC27 10 10 subunit of anaphase-promoting complex (cyclosome)
 YDL008W  APC11 10 10 subunit of the anaphase promoting complex
 YDR118W  APC4 10 10 subunit of the anaphase promoting complex
 YFR036W  CDC26 12 10 subunit of anaphase-promoting complex (cyclosome)
 YGL240W  DOC1 10 10 component of the anaphase promoting complex
 YHR166C  CDC23 15 10 subunit of anaphase-promoting complex (cyclosome)
 YKL022C  CDC16 10 10 subunit of anaphase-promoting complex (cyclosome)
 YLR102C  APC9 13 10 subunit of the Anaphase Promoting Complex
 YLR127C  APC2 12 10 component of the anaphase promoting complex
 YNL172W  APC1 10 10 subunit of anaphase-promoting complex (cyclosome)
 YOR249C  APC5 10 10 component of the anaphase-promoting complex
Cluster CG0041:
Q-value = 1.00 log10(P) = -122.34 log10(E) = -108.77 log10(Pevd) = -99.00
 YBR081C  SPT7 13 13 involved in alteration of transcription start site selection
 YBR198C  TAF90 16 13 TFIID and SAGA subunit
 YDR145W  TAF61 14 13 TFIID and SAGA subunit
 YDR167W  TAF25 22 13 TFIID and SAGA subunit
 YDR176W  NGG1 23 13 general transcriptional adaptor or co-activator
 YDR392W  SPT3 14 13 general transcriptional adaptor or co-activator
 YDR448W  ADA2 21 13 general transcriptional adaptor or co-activator
 YGL112C  TAF60 19 13 TFIID and SAGA subunit
 YGR252W  GCN5 16 13 histone acetyltransferase
 YHR099W  TRA1 15 13 component of the Ada-Spt transcriptional regulatory complex
 YLR055C  SPT8 13 13 transcriptional adaptor or co-activator
 YMR236W  TAF17 20 13 TFIID and SAGA subunit
 YOL148C  SPT20 15 13 member of the TBP class of SPT proteins that alter transcription site selection
 YPL254W  HFI1 13 13 transcriptional coactivator
Cluster SP0001:
Q-value = 0.80 log10(P) = -12.79 log10(E) = -0.18 log10(Pevd) = -4.16
 YBR009C  HHF1 3 3 histone H4
 YBR010W  HHT1 3 3 histone H3
 YGR116W  SPT6 4 4 transcription elongation protein
 YNL030W  HHF2 3 3 histone H4
 YNL031C  HHT2 3 3 histone H3
Cluster SP0010:
Q-value = 0.67 log10(P) = -8.26 log10(E) = 2.92 log10(Pevd) = -1.38
 YAL003W  EFB1 3 2 translation elongation factor eEF1beta
 YBR118W  TEF2 2 2 translation elongation factor eEF1 alpha-A chain, cytosolic
 YLR249W  YEF3 3 2 translation elongation factor eEF3
 YPR080W  TEF1 2 2 translation elongation factor eEF1 alpha-A chain, cytosolic
Cluster SP0011:
Q-value = 0.83 log10(P) = -10.32 log10(E) = 0.86 log10(Pevd) = -2.91
 YBR202W  CDC47 4 3 cell division control protein
 YEL032W  MCM3 2 2 replication initiation protein
 YLR103C  CDC45 3 2 required for minichromosome maintenance and initiation of chromosomal DNA replication
 YLR274W  CDC46 3 3 cell division control protein
Cluster SP0015:
Q-value = 0.90 log10(P) = -15.09 log10(E) = -2.48 log10(Pevd) = -5.29
 YCR092C  MSH3 3 3 DNA mismatch repair protein
 YDR097C  MSH6 3 3 DNA mismatch repair protein
 YMR167W  MLH1 4 4 DNA mismatch repair protein
 YNL082W  PMS1 4 4 DNA mismatch repair protein
 YOL090W  MSH2 5 4 DNA mismatch repair protein
Cluster SP0017:
Q-value = 1.00 log10(P) = -10.25 log10(E) = 0.12 log10(Pevd) = -4.46
 YLR148W  PEP3 3 3 vacuolar membrane protein
 YLR396C  VPS33 4 3 vacuolar sorting protein
 YMR231W  PEP5 4 3 vacuolar biogenesis protein
 YPL045W  VPS16 3 3 vacuolar sorting protein
Cluster SP0022:
Q-value = 1.00 log10(P) = -10.22 log10(E) = 0.15 log10(Pevd) = -4.46
 YCR093W  CDC39 4 3 nuclear protein
 YER068W  MOT2 3 3 transcriptional repressor
 YIL038C  NOT3 3 3 general negative regulator of transcription, subunit 3
 YPR072W  NOT5 4 3 component of the NOT protein complex
Cluster SP0025:
Q-value = 0.83 log10(P) = -9.56 log10(E) = 0.81 log10(Pevd) = -2.91
 YGL207W  SPT16 3 3 general chromatin factor
 YML069W  POB3 3 2 protein that binds to DNA polymerase I (PolI)
 YNL102W  POL1 4 3 DNA-directed DNA polymerase alpha, 180 KD subunit
 YPR135W  CTF4 3 2 DNA-directed DNA polymerase alpha-binding protein
Cluster SP0045:
Q-value = 0.83 log10(P) = -8.55 log10(E) = 1.81 log10(Pevd) = -2.91
 YCL019W  4 2
 YCL020W  4 2
 YDR261W-A  4 3
 YDR261W-B  3 3
Cluster SP0080:
Q-value = 1.00 log10(P) = -10.21 log10(E) = 0.15 log10(Pevd) = -4.46
 YBR126C  TPS1 3 3 alpha,alpha-trehalose-phosphate synthase, 56 KD subunit
 YDR074W  TPS2 6 3 alpha,alpha-trehalose-phosphate synthase, 102 KD subunit
 YML100W  TSL1 3 3 alpha,alpha-trehalose-phosphate synthase, 123 KD subunit
 YMR261C  TPS3 3 3 alpha,alpha-trehalose-phosphate synthase, 115 KD subunit
Cluster SP0127:
Q-value = 1.00 log10(P) = -23.33 log10(E) = -10.30 log10(Pevd) = -8.43
 YCR002C  CDC10 6 5 cell division control protein
 YDL225W  SHS1 5 5 septin
 YDR507C  GIN4 6 5 ser/thr protein kinase
 YHR107C  CDC12 9 5 septin
 YJR076C  CDC11 6 5 septin
 YLR314C  CDC3 5 5 cell division control protein
Cluster SP0167:
Q-value = 0.90 log10(P) = -14.82 log10(E) = -3.65 log10(Pevd) = -5.29
 YGR082W  TOM20 7 4 mitochondrial outer membrane import receptor subunit, 20 kD
 YMR203W  TOM40 8 4 forms the hydrophilic channel of the mitochondrial import pore for preproteins
 YNL070W  TOM7 7 4 mitochondrial outer membrane import receptor subunit, 7 kD
 YNL121C  TOM70 5 3 mitochondrial outer membrane specialized import receptor
 YNL131W  TOM22 4 3 mitochondrial outer membrane import receptor complex subunit
Cluster SP0168:
Q-value = 0.83 log10(P) = -8.77 log10(E) = 1.59 log10(Pevd) = -2.91
 YLL016W  SDC25 3 3 GDP/GTP exchange factor (GEF)
 YLR310C  CDC25 8 3 GDP/GTP exchange factor for RAS1P and RAS2P
 YNL098C  RAS2 3 2 GTP-binding protein
 YOR101W  RAS1 4 2 GTP-binding protein
Cluster SP0179:
Q-value = 0.60 log10(P) = -17.47 log10(E) = -3.64 log10(Pevd) = -3.10
 YDL195W  SEC31 4 3 component of the COPII coat of ER-golgi vesicles
 YGL200C  EMP24 4 2 component of the COPII-coated vesicles, 24 kDa
 YGR191W  HIP1 5 2 histidine permease
 YIL109C  SEC24 7 4 component of COPII coat of ER-Golgi vesicles
 YPL085W  SEC16 3 2 multidomain vesicle coat protein
 YPR181C  SEC23 9 5 component of COPII coat of ER-golgi vesicles
Cluster SP0213:
Q-value = 1.00 log10(P) = -25.20 log10(E) = -12.17 log10(Pevd) = -8.43
 YEL003W  GIM4 5 5 Gim complex component
 YGR078C  PAC10 5 5 GIM4 - Gim complex component
 YLR200W  YKE2 10 5 Gim complex component
 YLR212C  TUB4 7 5 gamma tubulin
 YML094W  GIM5 5 5 Gim complex component
 YNL153C  GIM3 6 5 Gim complex component
Cluster SP0236:
Q-value = 0.98 log10(P) = -69.19 log10(E) = -53.07 log10(Pevd) = -15.95
 YBR254C  TRS20 11 9 TRAPP subunit of 20 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YDR108W  GSG1 10 8 sporulation specific protein
 YDR246W  TRS23 9 9 TRAPP subunit of 20 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YDR407C  TRS120 9 9 TRAPP subunit of 120 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YDR472W  TRS31 9 9 TRAPP subunit of 31 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YGR166W  KRE11 10 8 beta-glucan synthesis-associated protein
 YKR068C  BET3 9 9 involved in targeting and fusion of ER to golgi transport vesicles
 YML077W  BET5 10 9 involved in targeting and fusion of ER to golgi transport vesicles
 YMR218C  TRS130 9 9 TRAPP subunit of 130 kDa involved in targeting and fusion of ER to golgi transport vesicles
 YOR115C  TRS33 10 9 TRAPP subunit of 33 kDa involved in targeting and fusion of ER to golgi transport vesicles
Cluster SP0287:
Q-value = 0.64 log10(P) = -50.36 log10(E) = -31.62 log10(Pevd) = -8.98
 YAL043C  PTA1 8 6 pre-tRNA processing protein / PF I subunit
 YDR301W  CFT1 7 7 pre-mRNA 3'-end processing factor CF II
 YDR390C  UBA2 3 2 E1-like (ubiquitin-activating) enzyme
 YGR048W  UFD1 5 2 ubiquitin fusion degradation protein
 YJR093C  FIP1 10 7 component of pre-mRNA polyadenylation factor PF I
 YKR002W  PAP1 10 9 poly(A) polymerase
 YLR115W  CFT2 6 6 cleavage and polyadenylation specificity factor, part of CF II
 YLR277C  YSH1 10 7 component of pre-mRNA polyadenylation factor PF I
 YNL317W  PFS2 6 5 polyadenylation factor I subunit 2 required for mRNA 3'-end processing, bridges two mRNA 3'-end processing factors
 YPR107C  YTH1 8 7 protein of the 3' processing complex
Cluster SP0288:
Q-value = 0.48 log10(P) = -20.04 log10(E) = -3.19 log10(Pevd) = -2.42
 YBR135W  CKS1 10 4 cyclin-dependent kinases regulatory subunit
 YBR160W  CDC28 14 6 cyclin-dependent protein kinase
 YGR108W  CLB1 3 2 cyclin, G2/M-specific
 YLR079W  SIC1 2 2 p40 inhibitor of CDC28P-Clb protein kinase complex
 YLR210W  CLB4 4 2 cyclin, G2/M-specific
 YPL256C  CLN2 3 2 cyclin, G1/S-specific
 YPR120C  CLB5 3 2 cyclin, B-type
Cluster SP0300:
Q-value = 0.67 log10(P) = -18.38 log10(E) = -5.34 log10(Pevd) = -3.99
 YAL041W  CDC24 11 4 GTP/GDP exchange factor for CDC42P
 YBR200W  BEM1 10 5 bud emergence mediator
 YGR152C  RSR1 3 2 GTP-binding protein
 YHL007C  STE20 3 2 ser/thr protein kinase of the pheromone pathway
 YJL157C  FAR1 6 3 cyclin-dependent kinase inhibitor (CKI)
 YLR229C  CDC42 13 4 GTP-binding protein of RAS superfamily
Cluster SP0309:
Q-value = 1.00 log10(P) = -9.62 log10(E) = 0.13 log10(Pevd) = -4.46
 YHL031C  GOS1 4 3 SNARE protein of Golgi compartment
 YKL006C-A  SFT1 5 3 SNARE-like protein
 YKL196C  YKT6 4 3 SNARE protein for Endoplasmic Reticulum-Golgi transport
 YLR026C  SED5 8 3 syntaxin (T-SNARE)
Cluster SP0397:
Q-value = 1.00 log10(P) = -82.33 log10(E) = -66.33 log10(Pevd) = -99.00
 YBL084C  CDC27 10 10 subunit of anaphase-promoting complex (cyclosome)
 YDL008W  APC11 10 10 subunit of the anaphase promoting complex
 YDR118W  APC4 10 10 subunit of the anaphase promoting complex
 YFR036W  CDC26 12 10 subunit of anaphase-promoting complex (cyclosome)
 YGL240W  DOC1 10 10 component of the anaphase promoting complex
 YHR166C  CDC23 15 10 subunit of anaphase-promoting complex (cyclosome)
 YKL022C  CDC16 10 10 subunit of anaphase-promoting complex (cyclosome)
 YLR102C  APC9 13 10 subunit of the Anaphase Promoting Complex
 YLR127C  APC2 12 10 component of the anaphase promoting complex
 YNL172W  APC1 10 10 subunit of anaphase-promoting complex (cyclosome)
 YOR249C  APC5 10 10 component of the anaphase-promoting complex
Cluster SP0405:
Q-value = 1.00 log10(P) = -8.48 log10(E) = -0.11 log10(Pevd) = -4.46
 YDL132W  CDC53 13 3 controls G1/S transition
 YDR054C  CDC34 7 3 E2 ubiquitin-conjugating enzyme
 YDR328C  SKP1 17 3 kinetochore protein complex CBF3, subunit D
 YFL009W  CDC4 4 3 cell division control protein
Cluster SP0423:
Q-value = 1.00 log10(P) = -9.76 log10(E) = -0.54 log10(Pevd) = -4.46
 YDR244W  PEX5 4 3 peroxisomal targeting signal receptor
 YGL153W  PEX14 14 3 peroxisomal protein involved in protein import - peroxin
 YLR191W  PEX13 6 3 peroxisomal protein involved in protein import - peroxin
 YNL214W  PEX17 4 3 component of the peroxisomal protein translocation - peroxin
Cluster SP0424:
Q-value = 1.00 log10(P) = -8.63 log10(E) = 0.13 log10(Pevd) = -4.46
 YDR016C  DAD1 6 3 hypothetical protein (Class V)
 YGL061C  DUO1 6 3 essential mitotic spindle protein
 YGR113W  DAM1 13 3 essential mitotic spindle pole protein
 YKR037C  SPC34 6 3 spindle pole body protein
Cluster SP0426:
Q-value = 0.67 log10(P) = -23.60 log10(E) = -7.85 log10(Pevd) = -5.34
 YFL059W  SNZ3 9 6 strong similarity to Para rubber tree ethylene-responsive protein1 (Class II)
 YFL060C  SNO3 4 3 strong similarity to SNO1 and SNO2 (Class IV)
 YMR095C  SNO1 3 3 similarity to M.leprae hisH protein (Class III)
 YMR096W  SNZ1 5 5 stationary phase protein
 YMR322C  4 3 strong similarity to YPL280W, YOR391C andYDR533C (Class IV)
 YNL333W  SNZ2 8 6 putative pyridoxine (vitamin B6) biosynthetic enzyme
 YNL334C  SNO2 5 2 strong similarity to hypothetical proteins YFL060C and YMR095C (Class IV)
Cluster SP0438:
Q-value = 0.57 log10(P) = -19.75 log10(E) = -5.73 log10(Pevd) = -3.88
 YFR002W  NIC96 7 3 nuclear pore protein
 YGL172W  NUP49 9 4 nuclear pore protein
 YGR119C  NUP57 22 6 nuclear pore protein
 YJL041W  NSP1 7 3 nuclear pore protein
 YMR294W  JNM1 12 4 mitosis protein, involved in nuclear migration
 YOL069W  NUF2 8 2 spindle pole body protein
 YPR083W  2 2 hypothetical protein (Class V)
Cluster SP0440:
Q-value = 0.81 log10(P) = -28.16 log10(E) = -14.81 log10(Pevd) = -7.54
 YBR193C  MED8 13 5 transcriptional regulation mediator
 YDL005C  MED2 7 5 transcriptional regulation mediator
 YDR308C  SRB7 4 2 DNA-directed RNA polymerase II holoenzyme and kornberg's mediator (SRB) subcomplex subunit
 YGL025C  PGD1 8 5 mediator complex subunit
 YIL021W  RPB3 8 5 DNA-directed RNA-polymerase II, 45 kDa
 YOL135C  MED7 9 6 member of RNA Polymerase II transcriptional regulation mediator complex
 YOR174W  MED4 11 6 transcription regulation mediator
Cluster SP0451:
Q-value = 0.73 log10(P) = -19.97 log10(E) = -8.21 log10(Pevd) = -4.88
 YDR100W  6 2 similarity to Dictyostelium development-specific membrane protein (Class III)
 YDR425W  7 3 similarity to hypothetical protein YDL113C (Class IV)
 YGL161C  10 5 weak similarity to TRCDSEMBL:HS167A19_1 dJ167A19.1 human (Class IV)
 YGL198W  10 4 weak similarity to YIP1P (Class III)
 YGR172C  YIP1 16 4 golgi membrane protein
 YPL095C  4 4 strong similarity to YBR177C (Class IV)
Cluster SP0559:
Q-value = 0.66 log10(P) = -139.42 log10(E) = -114.57 log10(Pevd) = -99.00
 YBR081C  SPT7 13 13 involved in alteration of transcription start site selection
 YBR198C  TAF90 16 13 TFIID and SAGA subunit
 YDR145W  TAF61 14 13 TFIID and SAGA subunit
 YDR167W  TAF25 22 15 TFIID and SAGA subunit
 YDR176W  NGG1 23 14 general transcriptional adaptor or co-activator
 YDR216W  ADR1 3 2 zinc-finger transcription factor
 YDR392W  SPT3 14 14 general transcriptional adaptor or co-activator
 YDR448W  ADA2 21 15 general transcriptional adaptor or co-activator
 YER148W  SPT15 10 5 the TATA-binding protein TBP
 YGL112C  TAF60 19 13 TFIID and SAGA subunit
 YGR252W  GCN5 16 14 histone acetyltransferase
 YGR274C  TAF145 2 2 TFIID subunit (TBP-associated factor), 145 kD
 YHR099W  TRA1 15 13 component of the Ada-Spt transcriptional regulatory complex
 YLR055C  SPT8 13 13 transcriptional adaptor or co-activator
 YMR236W  TAF17 20 13 TFIID and SAGA subunit
 YOL148C  SPT20 15 15 member of the TBP class of SPT proteins that alter transcription site selection
 YPL254W  HFI1 13 13 transcriptional coactivator
 YPR086W  SUA7 100 2 TFIIB subunit (transcription initiation factor), factor E
Cluster MC0876:
Q-value = 0.18 log10(P) = -113.65 log10(E) = -72.86 log10(Pevd) = -4.54
 YLR113W  HOG1 5 2 ser/thr protein kinase of MAP kinase (MAPK) family
 YDR103W  STE5 12 8 pheromone signal transduction pathway protein
 YCL032W  STE50 8 3 pheromone response pathway protein
 YLR362W  STE11 16 12 ser/thr protein kinase of the MEKK family
 YOR212W  STE4 12 8 GTP-binding protein beta subunit of the pheromone pathway
 YGR040W  KSS1 7 5 ser/thr protein kinase of the MAP kinase family
 YBL016W  FUS3 11 6 mitogen-activated protein kinase (MAP kinase)
 YDL159W  STE7 6 5 ser/thr/tyr protein kinase of MAP kinase kinase family
 YLR313C  SPH1 6 5 required for bipolar bud site selection
 YPL049C  DIG1 8 3 MAP kinase-associated protein, down-regulator of invasive growth and mating
 YDR264C  AKR1 10 4 ankyrin repeat-containing protein
 YDR480W  DIG2 6 3 MAP kinase-associated protein, down-regulator of invasive growth and mating
 YJR086W  STE18 5 3 GTP-binding protein gamma subunit of the pheromone pathway
 YHR005C  GPA1 3 2 GTP-binding protein alpha subunit of the pheromone pathway
 YJL128C  PBS2 4 2 tyrosine protein kinase of the MAP kinase kinase family
 YLL021W  SPA2 7 4 involved in cell polarity
 YLR319C  BUD6 9 3 bud site selection protein
 YPL140C  MKK2 5 2 protein kinase of the map kinase kinase (MEK) family
 YBR200W  BEM1 10 7 bud emergence mediator
 YLR229C  CDC42 13 5 GTP-binding protein of RAS superfamily
 YAL041W  CDC24 11 6 GTP/GDP exchange factor for CDC42P
 YJL157C  FAR1 6 4 cyclin-dependent kinase inhibitor (CKI)
 YGR152C  RSR1 3 2 GTP-binding protein
 YHL007C  STE20 3 2 ser/thr protein kinase of the pheromone pathway
 YBL085W  BOI1 2 2 BEM1 protein-binding protein
Cluster MC0877:
Q-value = 0.43 log10(P) = -69.72 log10(E) = -48.02 log10(Pevd) = -7.87
 YDR301W  CFT1 7 7 pre-mRNA 3'-end processing factor CF II
 YNL317W  PFS2 6 6 polyadenylation factor I subunit 2 required for mRNA 3'-end processing, bridges two mRNA 3'-end processing factors
 YJR093C  FIP1 10 9 component of pre-mRNA polyadenylation factor PF I
 YLR277C  YSH1 10 7 component of pre-mRNA polyadenylation factor PF I
 YKR002W  PAP1 10 8 poly(A) polymerase
 YPR107C  YTH1 8 7 protein of the 3' processing complex
 YLR115W  CFT2 6 6 cleavage and polyadenylation specificity factor, part of CF II
 YAL043C  PTA1 8 6 pre-tRNA processing protein / PF I subunit
 YMR061W  RNA14 8 6 component of pre-mRNA 3'-end processing factor CF I
 YER165W  PAB1 15 5 mRNA polyadenylate-binding protein
 YER032W  FIR1 9 2 interacts with the poly(A) polymerase in the two hybrid system
 YDR228C  PCF11 9 3 component of pre-mRNA 3'-end processing factor CF I
 YGL044C  RNA15 20 4 component of pre-mRNA 3'-end processing factor CF I
 YOL123W  HRP1 5 2 CF Ib (RNA3' Cleavage factor Ib)
Cluster MC0879:
Q-value = 0.23 log10(P) = -57.05 log10(E) = -33.18 log10(Pevd) = -3.28
 YJL041W  NSP1 7 4 nuclear pore protein
 YFR002W  NIC96 7 6 nuclear pore protein
 YMR153W  NUP53 25 3 component of the karyopherin docking complex of the nuclear pore complex
 YGL172W  NUP49 9 7 nuclear pore protein
 YBR017C  KAP104 10 4 beta-karyopherin
 YGR120C  SEC35 14 5 required for ER to golgi vesicle docking
 YGR119C  NUP57 22 8 nuclear pore protein
 YGL092W  NUP145 10 2 nuclear pore protein
 YMR294W  JNM1 12 4 mitosis protein, involved in nuclear migration
 YJL039C  NUP192 6 2 nucleoporin localize at the inner site of the nuclear membrane
 YDR311W  TFB1 24 3 TFIIH subunit (transcription initiation factor), 75 kD
 YNL041C  8 2 weak similarity to MLP1 (Class III)
 YNL086W  9 3 hypothetical protein (Class V)
 YOL069W  NUF2 8 3 spindle pole body protein
 YKL103C  LAP4 10 2 aminopeptidase yscI precursor, vacuolar
 YOR098C  NUP1 8 2 nuclear pore protein
 YDR395W  SXM1 11 2 putative beta-karyopherin
Cluster MC0912:
Q-value = 0.54 log10(P) = -25.84 log10(E) = -11.74 log10(Pevd) = -4.43
 YGL161C  10 5 weak similarity to TRCDSEMBL:HS167A19_1 dJ167A19.1 human (Class IV)
 YDR425W  7 3 similarity to hypothetical protein YDL113C (Class IV)
 YGR172C  YIP1 16 7 golgi membrane protein
 YGL198W  10 5 weak similarity to YIP1P (Class III)
 YDL226C  GCS1 15 3 ADP-ribosylation factor GTPase-activating protein (ARF-GAP)
 YPL095C  4 3 strong similarity to YBR177C (Class IV)
 YDR468C  TLG1 7 2 member of the syntaxin family of t-SNAREs
 YNL044W  YIP3 10 2 protein of unknown function
Cluster MC0916:
Q-value = 1.00 log10(P) = -15.44 log10(E) = -5.81 log10(Pevd) = -6.42
 YOL135C  MED7 9 4 member of RNA Polymerase II transcriptional regulation mediator complex
 YDL005C  MED2 7 4 transcriptional regulation mediator
 YBR193C  MED8 13 4 transcriptional regulation mediator
 YIL021W  RPB3 8 4 DNA-directed RNA-polymerase II, 45 kDa
 YGL025C  PGD1 8 4 mediator complex subunit
Cluster MC0921:
Q-value = 0.73 log10(P) = -18.49 log10(E) = -6.72 log10(Pevd) = -4.88
 YDR054C  CDC34 7 4 E2 ubiquitin-conjugating enzyme
 YDL132W  CDC53 13 5 controls G1/S transition
 YIL046W  MET30 12 3 involved in regulation of sulfur assimilation genes and cell cycle progression
 YDR328C  SKP1 17 5 kinetochore protein complex CBF3, subunit D
 YFL009W  CDC4 4 3 cell division control protein
 YJR090C  GRR1 5 2 required for glucose repression and for glucose and cation transport
Cluster MC3169:
Q-value = 0.79 log10(P) = -90.44 log10(E) = -74.19 log10(Pevd) = -99.00
 YJR022W  LSM8 28 11 splicing factor
 YNL147W  LSM7 10 10 Sm-like (Lsm) protein
 YGL173C  KEM1 10 10 multifunctional nuclease
 YOL149W  DCP1 21 12 mRNA decapping enzyme
 YLR438C-A  LSM3 10 10 Sm-like (Lsm) protein
 YDR378C  LSM6 13 10 Sm-like (Lsm) protein
 YER112W  LSM4 14 12 Sm-like (Lsm) protein
 YBL026W  LSM2 15 12 Sm-like (Lsm) protein
 YCR077C  PAT1 20 10 topoisomerase II-associated protein
 YER146W  LSM5 10 10 Sm-like (Lsm) protein
 YJL124C  LSM1 10 9 Sm-like (Lsm) protein
 YOR167C  RPS28A 14 4 40S small subunit ribosomal protein S28.e.c15
 YLR264W  RPS28B 7 4 40S small subunit ribosomal protein S28.e.c12
Cluster MC3355:
Q-value = 1.00 log10(P) = -82.33 log10(E) = -66.33 log10(Pevd) = -99.00
 YFR036W  CDC26 12 10 subunit of anaphase-promoting complex (cyclosome)
 YLR127C  APC2 12 10 component of the anaphase promoting complex
 YNL172W  APC1 10 10 subunit of anaphase-promoting complex (cyclosome)
 YGL240W  DOC1 10 10 component of the anaphase promoting complex
 YBL084C  CDC27 10 10 subunit of anaphase-promoting complex (cyclosome)
 YDR118W  APC4 10 10 subunit of the anaphase promoting complex
 YHR166C  CDC23 15 10 subunit of anaphase-promoting complex (cyclosome)
 YKL022C  CDC16 10 10 subunit of anaphase-promoting complex (cyclosome)
 YLR102C  APC9 13 10 subunit of the Anaphase Promoting Complex
 YDL008W  APC11 10 10 subunit of the anaphase promoting complex
 YOR249C  APC5 10 10 component of the anaphase-promoting complex
Cluster MC3934:
Q-value = 0.73 log10(P) = -146.97 log10(E) = -123.10 log10(Pevd) = -99.00
 YDR176W  NGG1 23 13 general transcriptional adaptor or co-activator
 YDR392W  SPT3 14 14 general transcriptional adaptor or co-activator
 YPL254W  HFI1 13 13 transcriptional coactivator
 YMR236W  TAF17 20 13 TFIID and SAGA subunit
 YGR252W  GCN5 16 14 histone acetyltransferase
 YBR081C  SPT7 13 13 involved in alteration of transcription start site selection
 YOL148C  SPT20 15 14 member of the TBP class of SPT proteins that alter transcription site selection
 YDR145W  TAF61 14 13 TFIID and SAGA subunit
 YHR099W  TRA1 15 13 component of the Ada-Spt transcriptional regulatory complex
 YGL112C  TAF60 19 13 TFIID and SAGA subunit
 YDR167W  TAF25 22 15 TFIID and SAGA subunit
 YDR448W  ADA2 21 15 general transcriptional adaptor or co-activator
 YLR055C  SPT8 13 13 transcriptional adaptor or co-activator
 YBR198C  TAF90 16 13 TFIID and SAGA subunit
 YER148W  SPT15 10 5 the TATA-binding protein TBP
 YGR274C  TAF145 2 2 TFIID subunit (TBP-associated factor), 145 kD
 YDR216W  ADR1 3 2 zinc-finger transcription factor
Cluster NN0501:
 YDR311W  TFB1 24 6 TFIIH subunit (transcription initiation factor), 75 kD
 YHR113W  4 2 similarity to vacuolar aminopeptidase Ape1p (Class III)
 YKL103C  LAP4 10 5 aminopeptidase yscI precursor, vacuolar
 YOL082W  CVT19 18 4 similarity to YOL083W (Class IV)
 YOR302W  JUNP 7 2 CPA1 leader peptide
 YAL034W-A  MTW1 4 3 determining metaphase spindle length
 YGL172W  NUP49 9 5 nuclear pore protein
 YGR119C  NUP57 22 7 nuclear pore protein
 YGR120C  SEC35 14 5 required for ER to golgi vesicle docking
 YIL144W  TID3 17 4 DMC1P interacting protein
 YMR294W  JNM1 12 6 mitosis protein, involved in nuclear migration
 YNL041C  8 3 weak similarity to MLP1 (Class III)
 YNL086W  9 4 hypothetical protein (Class V)
 YOL069W  NUF2 8 4 spindle pole body protein
 YPR083W  2 2 hypothetical protein (Class V)
 YPL174C  NIP100 8 2 component of the dynactin complex
 YKL061W  7 2 hypothetical protein (Class V)
Cluster NN0504:
 YGL206C  CHC1 3 3 clathrin heavy chain
 YGR167W  CLC1 5 3 clathrin light chain
 YGR241C  YAP1802 8 3 Yeast Adaptor Protein, member of AP180 protein family
 YHR161C  YAP1801 4 3 Yeast Adaptor Protein, member of AP180 protein family
 YIR006C  PAN1 8 2 actin-cytoskeleton assembly protein
Cluster NN0510:
 YAL047C  SPC72 6 2 STU2P Interactant
 YDR356W  NUF1 4 2 spindle pole body component
 YHR172W  SPC97 6 4 spindle pole body component
 YLR212C  TUB4 7 2 gamma tubulin
 YNL126W  SPC98 5 4 spindle pole body component
Cluster NN0514:
 YBR270C  20 2 strong similarity to hypothetical protein YJL058C (Class IV)
 YIL105C  8 4 weak similarity to probable transcription factor ASK10P (Class III)
 YMR068W  4 2 weak similarity to mouse transcription factor NF-kappa B (Class III)
 YNL047C  9 4 similarity to probable transcription factor ASK10P and hypothetical protein YPR115W, and strong similarity to hypothetical protein YIL105C (Class III)
 YPL059W  GRX5 5 2 member of the subfamily of yeast glutaredoxins (Grx3, GRX4, and Grx5)
Cluster NN0516:
 YCR088W  ABP1 4 3 actin-binding protein
 YDR388W  RVS167 9 3 reduced viability upon starvation protein
 YFL039C  ACT1 22 4 actin
 YNL138W  SRV2 3 2 adenylate cyclase-associated protein, 70kDa
 YOR181W  LAS17 6 2 component of actin cortical patches
Cluster NN0518:
 YDR422C  SIP1 7 2 multicopy suppressor of SNF1
 YDR477W  SNF1 10 4 carbon catabolite derepressing ser/thr protein kinase
 YER027C  GAL83 3 2 glucose repression protein
 YGL115W  SNF4 10 4 nuclear regulatory protein
 YGL208W  SIP2 2 2 dominant suppressor of some ts mutations in RPO21 and PRP4
Cluster NN0519:
 YDR120C  TRM1 4 2 N2,N2-dimethylguanine tRNA methyltransferase
 YEL017W  12 4 hypothetical protein (Class V)
 YGR121C  MEP1 2 2 ammonia permease of high capacity and moderate affinity
 YHR123W  EPT1 3 2 sn-1,2-diacylglycerol ethanolamine- and cholinephosphotransferase
 YIR038C  GTT1 23 4 glutathione S-transferase
Cluster NN0522:
 YBR009C  HHF1 3 3 histone H4
 YBR010W  HHT1 3 3 histone H3
 YGR116W  SPT6 4 4 transcription elongation protein
 YNL030W  HHF2 3 3 histone H4
 YNL031C  HHT2 3 3 histone H3
Cluster NN0623:
 YAL021C  CCR4 2 2 transcriptional regulator
 YDL160C  DHH1 13 6 putative RNA helicase of the DEAD box family
 YGR092W  DBF2 7 4 ser/thr protein kinase related to DBF20P
 YIL106W  MOB1 9 3 required for completion of mitosis and maintenance of ploidy
 YJR122W  CAF17 3 2 CCR4 associated factor
 YNR052C  POP2 8 4 required for glucose derepression
 YBL026W  LSM2 15 7 Sm-like (Lsm) protein
 YBR094W  3 3 weak similarity to pig tubulin-tyrosine ligase (Class III)
 YEL015W  12 6 weak similarity to SPA2P (Class III)
 YJR022W  LSM8 28 9 splicing factor
 YLR264W  RPS28B 7 6 40S small subunit ribosomal protein S28.e.c12
 YNL118C  DCP2 5 3 suppressor protein of a yeast pet mutant
 YOL149W  DCP1 21 9 mRNA decapping enzyme
 YOR167C  RPS28A 14 6 40S small subunit ribosomal protein S28.e.c15
 YER112W  LSM4 14 6 Sm-like (Lsm) protein
 YGR158C  MTR3 5 2 involved in mRNA transport
 YLR269C  3 2 questionable ORF (Class VI)
Cluster NN0626:
 YBR045C  GIP1 8 5 GLC7-interacting protein
 YER133W  GLC7 17 4 ser/thr phosphoprotein phosphatase 1, catalytic chain
 YIL045W  PIG2 5 2 Protein Interacting with GSY2P
 YLR263W  RED1 5 2 meiosis-specific protein
 YOR178C  GAC1 5 3 ser/thr phosphoprotein phosphatase 1, regulatory chain
 YOR329C  SCD5 5 2 suppressor of clathrin deficiency
Cluster NN0628:
 YDL043C  PRP11 21 2 pre-mRNA splicing factor
 YER165W  PAB1 15 3 mRNA polyadenylate-binding protein
 YGL049C  TIF4632 3 3 mRNA cap-binding protein (eIF4F), 130K subunit
 YGR162W  TIF4631 6 4 mRNA cap-binding protein (eIF4F), 150K subunit
 YOL139C  CDC33 5 4 translation initiation factor eIF4E
 YOR276W  CAF20 3 2 mRNA CAP-binding protein (eIF4F), 20K subunit
Cluster NN0631:
 YBR172C  SMY2 2 2 kinesin-related protein
 YKL074C  MUD2 8 5 pre-mRNA splicing factor
 YLR116W  MSL5 18 5 branch point bridging protein
 YML046W  PRP39 2 2 pre-mRNA splicing factor
 YPL016W  SWI1 6 2 component of SWI/SNF global transcription activator complex
 YPL105C  5 2 similarity to SMY2P (Class III)
Cluster NN0635:
 YDL135C  RDI1 4 3 rho GDP dissociation inhibitor with activity toward RHO1P
 YKR055W  RHO4 5 3 GTP-binding protein of the rho family
 YLR229C  CDC42 13 3 GTP-binding protein of RAS superfamily
 YNL271C  BNI1 8 3 regulator of budding
 YPL161C  BEM4 7 3 bud emergence protein
 YPR165W  RHO1 8 3 GTP-binding protein of the rho subfamily of ras-like proteins
Cluster NN0637:
 YBL078C  AUT7 4 2 essential for autophagy
 YBR217W  APG12 11 4 component of the autophagic system
 YHR171W  APG7 5 4 component of the autophagic system
 YMR159C  APG16 11 2 coiled-coil protein required for autophagy
 YNR007C  AUT1 5 3 essential for autophagocytosis
 YPL149W  APG5 4 3 involved in autophagy and nutrient starvation
Cluster NN0852:
 YBR135W  CKS1 10 6 cyclin-dependent kinases regulatory subunit
 YBR160W  CDC28 14 6 cyclin-dependent protein kinase
 YDL155W  CLB3 5 3 cyclin, G2/M-specific
 YGR108W  CLB1 3 3 cyclin, G2/M-specific
 YLR210W  CLB4 4 2 cyclin, G2/M-specific
 YPL124W  NIP29 14 2 nuclear import protein
 YPL256C  CLN2 3 2 cyclin, G1/S-specific
 YPR119W  CLB2 12 2 cyclin, G2/M-specific
Cluster NN0857:
 YBR079C  RPG1 2 2 translation initiation factor eIF3 (p110 subunit)
 YDR429C  TIF35 6 3 translation initiation factor eIF3 (p33 subunit)
 YMR146C  TIF34 4 4 translation initiation factor eIF3, p39 subunit
 YMR309C  NIP1 7 5 associated with 40s ribosomal subunit
 YNL244C  SUI1 3 2 translation initiation factor 3 (eIF3)
 YOR361C  PRT1 7 6 translation initiation factor eIF3 subunit
 YPL105C  5 2 similarity to SMY2P (Class III)
 YPR041W  TIF5 3 2 translation initiation factor eIF5
Cluster NN1072:
 YDL195W  SEC31 4 3 component of the COPII coat of ER-golgi vesicles
 YGL200C  EMP24 4 3 component of the COPII-coated vesicles, 24 kDa
 YGR191W  HIP1 5 4 histidine permease
 YIL004C  BET1 4 2 protein transport protein
 YIL109C  SEC24 7 6 component of COPII coat of ER-Golgi vesicles
 YLR268W  SEC22 10 4 synaptobrevin (V-SNARE)
 YPL085W  SEC16 3 2 multidomain vesicle coat protein
 YPL218W  SAR1 4 3 GTP-binding protein of the ARF family
 YPR181C  SEC23 9 7 component of COPII coat of ER-golgi vesicles
 YIR038C  GTT1 23 2 glutathione S-transferase
 YLR026C  SED5 8 2 syntaxin (T-SNARE)
Cluster NN1284:
 YBL016W  FUS3 11 7 mitogen-activated protein kinase (MAP kinase)
 YDL159W  STE7 6 5 ser/thr/tyr protein kinase of MAP kinase kinase family
 YDR103W  STE5 12 4 pheromone signal transduction pathway protein
 YDR480W  DIG2 6 3 MAP kinase-associated protein, down-regulator of invasive growth and mating
 YGR040W  KSS1 7 6 ser/thr protein kinase of the MAP kinase family
 YLL021W  SPA2 7 5 involved in cell polarity
 YLR313C  SPH1 6 6 required for bipolar bud site selection
 YLR319C  BUD6 9 4 bud site selection protein
 YLR362W  STE11 16 7 ser/thr protein kinase of the MEKK family
 YOR231W  MKK1 6 2 ser/thr protein kinase
 YPL049C  DIG1 8 3 MAP kinase-associated protein, down-regulator of invasive growth and mating
 YPL140C  MKK2 5 2 protein kinase of the map kinase kinase (MEK) family
 YGL178W  MPT5 4 2 multicopy suppressor of POP2
 YMR186W  HSC82 5 2 heat shock protein
Cluster NN1310:
 YBL026W  LSM2 15 8 Sm-like (Lsm) protein
 YBR094W  3 3 weak similarity to pig tubulin-tyrosine ligase (Class III)
 YDL160C  DHH1 13 7 putative RNA helicase of the DEAD box family
 YEL015W  12 8 weak similarity to SPA2P (Class III)
 YER112W  LSM4 14 7 Sm-like (Lsm) protein
 YGR158C  MTR3 5 2 involved in mRNA transport
 YJR022W  LSM8 28 13 splicing factor
 YLR264W  RPS28B 7 6 40S small subunit ribosomal protein S28.e.c12
 YLR269C  3 2 questionable ORF (Class VI)
 YNL118C  DCP2 5 4 suppressor protein of a yeast pet mutant
 YOL149W  DCP1 21 11 mRNA decapping enzyme
 YOR167C  RPS28A 14 6 40S small subunit ribosomal protein S28.e.c15
 YGL096W  TOS8 4 2 similarity to copper homeostasis protein CUP9P (Class III)
 YOR319W  HSH49 7 3 essential yeast splicing factor
 YBR103W  SIF2 8 2 SIR4P interacting protein
 YCR077C  PAT1 20 7 topoisomerase II-associated protein
 YBR143C  SUP45 4 2 translational release factor
 YDR172W  SUP35 5 2 eukaryotic peptide chain release factor GTP-binding subunit
 YMR080C  NAM7 9 3 nonsense-mediated mRNA decay protein
 YDR206W  EBS1 5 2 similarity to EST1 protein (Class III)
 YER105C  NUP157 4 2 nuclear pore protein
 YJL030W  MAD2 8 2 spindle-assembly checkpoint protein
 YAL021C  CCR4 2 2 transcriptional regulator
 YGR092W  DBF2 7 5 ser/thr protein kinase related to DBF20P
 YIL106W  MOB1 9 3 required for completion of mitosis and maintenance of ploidy
 YJR122W  CAF17 3 2 CCR4 associated factor
 YNR052C  POP2 8 4 required for glucose derepression
 YBR270C  20 3 strong similarity to hypothetical protein YJL058C (Class IV)
 YDR228C  PCF11 9 2 component of pre-mRNA 3'-end processing factor CF I
 YIL046W  MET30 12 2 involved in regulation of sulfur assimilation genes and cell cycle progression
 YLR424W  12 3 weak similarity to STU1P (Class III)
Cluster NN1460:
 YBR205W  KTR3 4 3 alpha-1,2-mannosyltransferase
 YDR100W  6 2 similarity to Dictyostelium development-specific membrane protein (Class III)
 YDR468C  TLG1 7 4 member of the syntaxin family of t-SNAREs
 YER031C  YPT31 7 3 GTP-binding protein of the rab family
 YFL038C  YPT1 10 6 GTP-binding protein of the rab family
 YGL161C  10 6 weak similarity to TRCDSEMBL:HS167A19_1 dJ167A19.1 human (Class IV)
 YGL212W  VAM7 15 7 vacuolar morphogenesis protein
 YGR172C  YIP1 16 7 golgi membrane protein
 YHR105W  5 4 weak similarity to MVP1P (Class III)
 YNL044W  YIP3 10 4 protein of unknown function
 YNL263C  YIF1 6 5 SLH1P Interacting Factor
 YOR036W  PEP12 11 6 syntaxin (T-SNARE), vacuolar
 YPL246C  3 3 weak similarity to mouse proteinase activated receptor 2 (Class IV)
 YPR017C  DSS4 4 2 GDP/GTP exchange factor for SEC4P
 YBL050W  SEC17 11 5 transport vesicle fusion protein
 YLR026C  SED5 8 2 syntaxin (T-SNARE)
 YLR093C  NYV1 2 2 v-SNARE, vacuolar
 YMR197C  VTI1 8 5 v-SNARE: involved in Golgi retrograde protein traffic
 YOR106W  VAM3 5 4 syntaxin (t-SNARE)
 YDR084C  9 2 similarity to hypothetical C.elegans protein (Class IV)
 YGL044C  RNA15 20 4 component of pre-mRNA 3'-end processing factor CF I
 YGL104C  2 2 similarity to glucose transport proteins (Class III)
 YGR004W  3 3 strong similarity to hypothetical protein YLR324W (Class IV)
 YLR324W  9 4 strong similarity to YGR004W (Class IV)
 YMR153W  NUP53 25 4 component of the karyopherin docking complex of the nuclear pore complex
 YOL129W  4 2 similarity to hypothetical S. pombe protein (Class IV)
 YPR028W  YIP2 4 3 Ypt-interacting protein
Cluster NN1467:
 YBR017C  KAP104 10 2 beta-karyopherin
 YDR311W  TFB1 24 6 TFIIH subunit (transcription initiation factor), 75 kD
 YGL172W  NUP49 9 6 nuclear pore protein
 YGR119C  NUP57 22 8 nuclear pore protein
 YGR120C  SEC35 14 8 required for ER to golgi vesicle docking
 YHR129C  ARP1 6 2 centractin
 YIL144W  TID3 17 5 DMC1P interacting protein
 YMR294W  JNM1 12 7 mitosis protein, involved in nuclear migration
 YNL041C  8 3 weak similarity to MLP1 (Class III)
 YNL086W  9 6 hypothetical protein (Class V)
 YOL069W  NUF2 8 4 spindle pole body protein
 YPL174C  NIP100 8 3 component of the dynactin complex
 YPR083W  2 2 hypothetical protein (Class V)
 YPR105C  11 2 similarity to hypothetical protein SPCC338.13 S. pombe (Class IV)
 YAL034W-A  MTW1 4 3 determining metaphase spindle length
 YKL061W  7 3 hypothetical protein (Class V)
 YKL103C  LAP4 10 5 aminopeptidase yscI precursor, vacuolar
 YPR185W  APG13 6 3 protein required for the autophagic process
 YEL013W  VAC8 8 3 required for vacuole inheritance and protein targeting from the cytoplasm to vacuole
 YOL082W  CVT19 18 5 similarity to YOL083W (Class IV)
 YOR302W  JUNP 7 2 CPA1 leader peptide
 YHR113W  4 2 similarity to vacuolar aminopeptidase Ape1p (Class III)
 YOR353C  3 2 weak similarity to adenylate cyclases (Class III)
 YEL005C  VAB2 6 2 VAC8P binding protein of 31 kDa
Cluster NN1625:
 YBL016W  FUS3 11 7 mitogen-activated protein kinase (MAP kinase)
 YCL027W  FUS1 3 2 cell fusion protein
 YDL159W  STE7 6 6 ser/thr/tyr protein kinase of MAP kinase kinase family
 YDR103W  STE5 12 7 pheromone signal transduction pathway protein
 YDR480W  DIG2 6 4 MAP kinase-associated protein, down-regulator of invasive growth and mating
 YFL039C  ACT1 22 11 actin
 YGL178W  MPT5 4 2 multicopy suppressor of POP2
 YGR040W  KSS1 7 7 ser/thr protein kinase of the MAP kinase family
 YLL021W  SPA2 7 6 involved in cell polarity
 YLR313C  SPH1 6 6 required for bipolar bud site selection
 YLR319C  BUD6 9 6 bud site selection protein
 YLR362W  STE11 16 10 ser/thr protein kinase of the MEKK family
 YMR186W  HSC82 5 2 heat shock protein
 YNL271C  BNI1 8 3 regulator of budding
 YOR122C  PFY1 4 2 profilin
 YPL049C  DIG1 8 4 MAP kinase-associated protein, down-regulator of invasive growth and mating
 YBR200W  BEM1 10 4 bud emergence mediator
 YDL178W  AIP2 2 2 actin interacting protein 2
 YOR231W  MKK1 6 4 ser/thr protein kinase
 YPL140C  MKK2 5 4 protein kinase of the map kinase kinase (MEK) family
 YJL095W  BCK1 2 2 ser/thr protein kinase of the MEKK family
 YEL048C  5 2 weak similarity to trp-asp repeat protein - S. pombe (Class IV)
 YHR030C  SLT2 11 4 ser/thr protein kinase of MAP kinase family
 YLR147C  SMD3 16 2 spliceosomal snRNA-associated Sm core protein required for pre-mRNA splicing
 YHR084W  STE12 2 2 transcriptional activator
 YCR088W  ABP1 4 3 actin-binding protein
 YDR388W  RVS167 9 3 reduced viability upon starvation protein
 YNL138W  SRV2 3 2 adenylate cyclase-associated protein, 70kDa
 YOR181W  LAS17 6 2 component of actin cortical patches
 YAL041W  CDC24 11 3 GTP/GDP exchange factor for CDC42P
 YDR264C  AKR1 10 5 ankyrin repeat-containing protein
 YHR005C  GPA1 3 2 GTP-binding protein alpha subunit of the pheromone pathway
 YJR086W  STE18 5 3 GTP-binding protein gamma subunit of the pheromone pathway
 YOR212W  STE4 12 6 GTP-binding protein beta subunit of the pheromone pathway
 YPL242C  IQG1 4 2 involved in cytokinesis, has similarity to mammalian IQGAP proteins