CELL CYCLE RESPONSE STRESS AVGPCC. YER179W DMC1 meiosis-specific protein unclear

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Kimberly Charles
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1 ORFNAME LOCUS DESCRIPTION DATE HUBS: ESSENTIAL k AVGPCC STRESS RESPONSE CELL CYCLE PHEROMONE TREATMENT UNFOLDED PROTEIN RESPONSE YER179W DMC1 meiosis-specific protein unclear SPORULATION Cv CATEGORY BIOLOGICAL PROCESS DNA recombination YDR246W TRS23 TRAPP subunit of 20 kda involved in targeting and fusion of ER to golgi transport vesicles adaptor cell traffic YLR313C SPH1 required for bipolar bud site selection regulator cell shape component of the Ada-Spt transcriptional YHR099W TRA1 regulatory complex regulator transcription YLL021W SPA2 involved in cell polarity regulator cell shape YGL025C PGD1 mediator complex subunit mediator transcription GDP/GTP exchange factor for Ras1p and YLR310C CDC25 Ras2p regulator cell signaling YBR200W BEM1 bud emergence mediator mediator cell division YLR362W STE11 ser/thr protein kinase of the MEKK family regulator cell cycle YOL004W SIN3 transcription regulatory protein regulator transcription YDR392W SPT3 general transcriptional adaptor or co-activator regulator transcription YMR117C SPC24 spindle pole body protein regulator cell cycle YBL016W FUS3 mitogen-activated protein kinase (MAP kinase) regulator cell signaling YIR006C PAN1 actin-cytoskeleton assembly protein regulator cell shape YJR093C FIP1 component of pre- polyadenylation factor PF I adaptor YIL061C SNP1 U1 small nuclear ribonucleoprotein adaptor splicing YLR319C BUD6 bud site selection protein adaptor cell division YOL148C SPT20 member of the TBP class of SPT proteins that alter transcription site selection regulator transcription YBR193C MED8 transcriptional regulation mediator regulator transcription YMR236W TAF17 TFIID and SAGA subunit regulator transcription YOL135C MED7 member of Polymerase II transcriptional regulation mediator complex mediator transcription YBL093C ROX3 transcription factor mediator transcription YML077W BET5 involved in targeting and fusion of ER to golgi transport vesicles adaptor cell traffic YBR109C CMD1 calmodulin mediator cell signaling YHR152W SPO12 sporulation protein regulator cell cycle YPL031C PHO85 cyclin-dependent protein kinase regulator cell cycle

2 YMR125W STO1 large subunit of the nuclear cap-binding protein complex CBC other YDR448W ADA2 general transcriptional adaptor or co-activator regulator transcription ser/thr phosphoprotein phosphatase 1, glycogen YER133W GLC7 catalytic chain regulator synthesis YLR055C SPT8 transcriptional adaptor or co-activator regulator transcription YML098W TAF19 TFIID subunit (TBP-associated factor), 19 kd regulator transcription YCR042C TSM1 component of TFIID complex regulator transcription YPR178W PRP4 U4/U6 snrnp 52 KD protein adaptor splicing YDR167W TAF25 TFIID and SAGA subunit regulator transcription YGR040W KSS1 ser/thr protein kinase of the MAP kinase family regulator cell signaling YAL040C CLN3 cyclin, G1/S-specific regulator cell cycle YOR212W STE4 GTP-binding protein beta subunit of the pheromone pathway regulator cell signaling YNL236W SIN4 global regulator protein mediator transcription YDR407C TRS120 TRAPP subunit of 120 kda involved in targeting and fusion of ER to golgi transport vesicles adaptor cell traffic YBR167C POP7 nuclear RNase P subunit complex t YBR045C GIP1 Glc7-interacting protein regulator glycogen synthesis YDL005C MED2 transcriptional regulation mediator mediator transcription YKR068C BET3 involved in targeting and fusion of ER to golgi transport vesicles adaptor cell traffic YDR328C SKP1 kinetochore protein complex CBF3, subunit D regulator cell cycle YJR022W LSM8 splicing factor complex Sm YBR289W SNF5 component of SWI/SNF transcription activator complex regulator transcription YGL112C TAF60 TFIID and SAGA subunit regulator transcription YER148W SPT15 the TATA-binding protein TBP regulator transcription YGR009C SEC9 protein transport protein regulator transcription YDL008W APC11 subunit of the anaphase promoting complex complex cell cycle YDR176W NGG1 general transcriptional adaptor or co-activator regulator transcription YGL240W DOC1 component of the anaphase promoting complex regulator cell cycle YOR174W MED4 transcription regulation mediator mediator transcription YDL140C RPO21 DNA-directed II, 215 KD subunit complex

3 YER022W SRB4 DNA-directed II holoenzyme and Kornberg's mediator (SRB) subcomplex subunit mediator transcription YBR055C PRP6 snrnp(u4/u6)-associated splicing factor adaptor splicing YBR253W SRB6 DNA-directed II suppressor protein mediator transcription YDR227W SIR4 silencing regulatory and DNA-repair protein regulator chromatin YLR229C CDC42 GTP-binding protein of RAS superfamily regulator cell cycle YGR252W GCN5 histone acetyltransferase regulator transcription YGR166W KRE11 beta-glucan synthesis-associated protein adaptor cell cycle YGR274C TAF145 TFIID subunit (TBP-associated factor), 145 kd regulator transcription YDR472W TRS31 TRAPP subunit of 31 kda involved in targeting and fusion of ER to golgi transport vesicles adaptor cell traffic YBR160W CDC28 cyclin-dependent protein kinase regulator cell cycle YBR081C SPT7 involved in alteration of transcription start site selection regulator transcription YDR378C LSM6 Sm-like (Lsm) protein complex Sm YIL106W MOB1 required for completion of mitosis and maintenance of ploidy regulator cell cycle YPR107C YTH1 protein of the 3' processing complex complex YAL041W CDC24 GTP/GDP exchange factor for Cdc42p regulator cell division YBR254C TRS20 TRAPP subunit of 20 kda involved in targeting and fusion of ER to golgi transport vesicles adaptor cell traffic YBR198C TAF90 TFIID and SAGA subunit regulator transcription YKR002W PAP1 poly(a) other YBL026W LSM2 Sm-like (Lsm) protein complex Sm YMR061W 14 component of pre- 3'-end processing factor CF I complex YOR115C TRS33 TRAPP subunit of 33 kda involved in targeting and fusion of ER to golgi transport vesicles adaptor cell traffic YPL254W HFI1 transcriptional coactivator regulator transcription YMR218C TRS130 TRAPP subunit of 130 kda involved in targeting and fusion of ER to golgi transport vesicles adaptor cell traffic YCR077C PAT1 topoisomerase II-associated protein unclear YDR404C RPB7 DNA-directed II, 19 KD subunit complex YDR108W GSG1 sporulation specific protein adaptor cell traffic YER165W PAB1 polyadenylate-binding protein regulator translation

4 YOL149W DCP1 decapping enzyme other H+- V0 domain 102 KD subunit, not YMR054W STV complex YFL039C ACT1 actin regulator cell shape YNL147W LSM7 Sm-like (Lsm) protein complex Sm YOR098C NUP1 nuclear pore protein complex cell traffic YER146W LSM5 Sm-like (Lsm) protein complex Sm YLR115W CFT2 cleavage and polyadenylation specificity factor, part of CF II complex YJL041W NSP1 nuclear pore protein complex nuclear pore YER112W LSM4 Sm-like (Lsm) protein complex Sm YLR293C GSP1 GTP-binding protein of the ras superfamily regulator cell cycle

5 PARTY HUBS: YDL132W CDC53 controls G1/S transition regulator cell cycle YNL172W APC1 (cyclosome) complex cell cycle YHR165C PRP8 U5 snrnp protein, pre- splicing factor complex spliceosome YOL018C TLG2 member of the syntaxin family of t-snares complex cell traffic YGL173C KEM1 multifunctional nuclease other YDR103W STE5 pheromone signal transduction pathway protein regulator scaffold YMR167W MLH1 DNA mismatch repair protein adaptor DNA YDR477W SNF1 carbon catabolite derepressing ser/thr protein kinase regulator YAL043C PTA1 pre-t processing protein / PF I subunit complex YLR026C SED5 syntaxin (T-SNARE) complex cell traffic YIL144W TID3 Dmc1p interacting protein complex centrosome YGR074W SMD1 sn-associated protein complex Sm YLR127C APC2 component of the anaphase promoting complex complex cell cycle YDR145W TAF61 TFIID and SAGA subunit regulator transcription YBL084C CDC27 (cyclosome) regulator cell cycle polyadenylation factor I subunit 2 required for 3'-end processing, bridges two 3' - YNL317W PFS2 end processing factors complex YFR036W CDC26 (cyclosome) regulator cell cycle YDR264C AKR1 ankyrin repeat-containing protein regulator cell shape YLR268W SEC22 synaptobrevin (V-SNARE) complex cell traffic YML065W ORC1 origin recognition complex, 104 KD subunit complex ori replication YDR301W CFT1 pre- 3'-end processing factor CF II complex v-snare: involved in Golgi retrograde protein YMR197C VTI1 traffic complex cell traffic YLR212C TUB4 gamma tubulin complex microtubule component of pre- polyadenylation YLR277C YSH1 factor PF I complex YDR388W RVS167 reduced viability upon starvation protein regulator cell shape YKL022C CDC16 (cyclosome) regulator cell cycle

6 YEL027W CUP5 H+- V0 domain 17 KD subunit, complex YLR102C APC9 subunit of the Anaphase Promoting Complex complex cell cycle YDR507C GIN4 ser/thr protein kinase regulator cell division YOR249C APC5 component of the anaphase-promoting complex complex cell cycle YHR166C CDC23 (cyclosome) regulator cell cycle YPL234C TFP3 H+- V0 domain 17 KD subunit, complex YLR347C KAP95 karyopherin-beta adaptor cell traffic YOR332W VMA4 H+- V1 domain 27 KD subunit, complex YBL050W SEC17 transport vesicle fusion protein adaptor cell traffic YIL021W RPB3 DNA-directed - II, 45 kda complex YLR208W SEC13 protein transport protein complex cell traffic YFR051C RET2 coatomer complex delta chain complex cell traffic YJL124C LSM1 Sm-like (Lsm) protein complex Sm YDR118W APC4 subunit of the anaphase promoting complex complex cell cycle YMR203W TOM40 forms the hydrophilic channel of the mitochondrial import pore for preproteins complex transport YGR020C VMA7 H+- V1 domain 14 kda subunit, complex YNL189W SRP1 karyopherin-alpha or importin adaptor cell traffic YPL240C HSP82 heat shock protein other chaperonin YPR181C SEC23 component of COPII coat of ER-golgi vesicles complex cell traffic YHR107C CDC12 septin complex septins YOR270C VPH1 H+- V0 domain 95K subunit, complex YOR210W RPB10 DNA-directed I, II, III 8.3 subunit complex YHR200W RPN10 26S proteasome regulatory subunit complex proteasome YFL008W SMC1 chromosome segregation protein complex cohesin YGL070C RPB9 DNA-directed II, 14.2 KD subunit complex YIL109C SEC24 component of COPII coat of ER-Golgi vesicles complex cell traffic YJR076C CDC11 septin complex septins YEL051W VMA8 H+-ATPsynthase V1 domain 32 KD subunit, complex YMR080C NAM7 nonsense-mediated decay protein regulator

7 YLR447C VMA6 H+- V0 domain 36 KD subunit, complex 3'->5' exoribonuclease required for 3' end YOL021C DIS3 formation of 5.8S r complex processosome YCR002C CDC10 cell division control protein complex septins YHR026W PPA1 H+- 23 KD subunit, complex coatomer complex alpha chain of secretory YDL145C COP1 pathway vesicles complex cell traffic YBR127C VMA2 H+- V1 domain 60 KD subunit, complex YDL029W ARP2 actin-like protein regulator cell shape YOR341W RPA190 DNA-directed I, 190 KD alpha subunit complex YGL137W SEC27 coatomer complex beta' chain (beta'-cop) of secretory pathway vesicles complex cell traffic YDL185W TFP1 H+- V1 domain 69 KD catalytic subunit, complex YOR116C RPO31 DNA-directed III, 160 KD subunit complex YNL113W RPC19 DNA-directed I,III 16 KD subunit complex YOR261C RPN8 26S proteasome regulatory subunit complex proteasome YFR004W RPN11 26S proteasome regulatory subunit complex proteasome YGL048C RPT6 26S proteasome regulatory subunit complex proteasome YGR095C RRP46 involved in r processing complex processosome YBR154C RPB5 DNA-directed I, II, III 25 KD subunit complex YOR117W RPT5 26S proteasome regulatory subunit complex proteasome YGR195W SKI6 3'->5' exoribonuclease required for 3' end formation of 5.8S r Complex processosome YDL147W RPN5 subunit of the regulatory particle of the proteasome complex proteasome YDR427W RPN9 subunit of the regulatory particle of the proteasome complex proteasome YCR035C RRP43 r processing protein complex processosome YDR394W RPT3 26S proteasome regulatory subunit complex proteasome YER012W PRE1 20S proteasome subunit C11(beta4) complex proteasome YPR010C RPA135 DNA-directed I, 135 KD subunit complex YDL097C RPN6 subunit of the regulatory particle of the proteasome complex proteasome YGL200C EMP24 component of the COPII-coated vesicles, 24 kda complex cell traffic YML092C PRE8 20S proteasome subunit Y7 (alpha2) complex proteasome

8 YGR162W TIF4631 cap-binding protein (eif4f), 150K subunit adaptor translation YOR207C RET1 DNA-directed III, 130 KD subunit complex YDR395W SXM1 putative beta-karyopherin adaptor cell traffic YOR259C RPT4 26S proteasome regulatory subunit complex proteasome YDR280W RRP45 r processing protein complex processosome YPR108W RPN7 subunit of the regulatory particle of the proteasome complex proteasome YNR003C RPC34 DNA-directed III, 34 KD subunit complex YER021W RPN3 26S proteasome regulatory subunit complex proteasome YHR069C RRP4 3'->5' exoribonuclease required for 3' end formation of 5.8S r complex processosome YDL111C RRP42 r processing protein complex processosome YOR224C RPB8 DNA-directed I, II, III 16 KD subunit complex YKL144C RPC25 DNA-direcred III, 25 KD subunit complex YDL007W RPT2 26S proteasome regulatory subunit complex proteasome YPR187W RPO26 DNA-directed I, II, III 18 KD subunit complex YGL011C SCL1 20S proteasome subunit YC7ALPHA/Y8 (alpha1) complex proteasome YKL145W RPT1 26S proteasome regulatory subunit complex proteasome YJR063W RPA12 DNA-directed I, 13.7 KD subunit complex YFR052W RPN12 26S proteasome regulatory subunit complex proteasome YOR361C PRT1 translation initiation factor eif3 subunit complex translation YBR039W ATP3 F1F0- complex, F1 gamma subunit complex mito. YPR110C RPC40 DNA-directed I, III 40 KD subunit complex YDL004W ATP16 F1F0- complex, F1 delta subunit complex mito. YJR121W ATP2 F1F0- complex, F1 beta subunit complex mito. YDR298C ATP5 F1F0- complex, OSCP subunit complex mito. YBL099W ATP1 F1F0- complex, F1 alpha subunit complex mito. DATE HUB PARTY HUB DATE % PARTY % Total % 100% Regulator % 12% Adaptor % 6% Mediator % 0%

9 Complex % 81% Other 3 2 3% 2% Unclear 2 0 2% 0%

Using graphs to relate expression data and protein-protein interaction data

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