PANDORA

Publication

Zhang KX and Ouellette BFF. Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence. Bioinformatics 2009 Dec 22

Many biological phenomena involve extensive interactions between many of the biological pathways present in cells. However, extraction of all the inherent biological pathways remains a major challenge in systems biology. With the advent of high-throughput functional genomic techniques, it is now possible to infer biological pathways and pathway organization in a systematic way by integrating disparate biological information. Here, we propose a novel integrated approach that uses network topology to predict biological pathways. We integrated four types of biological evidence (protein-protein interaction, genetic interaction, domain-domain interaction, and semantic similarity of GO terms) to generate a functionally associated network. This network was then used to develop a new pathway finding algorithm to predict biological pathways in yeast. Our approach discovered 195 biological pathways and 31 functionally redundant pathway pairs in yeast. By comparing our identified pathways to two public pathway databases (KEGG and Reactome), we observed that our approach achieves a positive prediction value of 12.8% and improves on other predictive approaches.

This study allows us to reconstruct biological pathways and delineates the cellular machinery in a systematic view.

The software is Open Source and is released under the GNU General Public License.

Contact information

BF Francis Ouellette and Kelvin Zhang

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Toronto, Ontario
M5G 0A3, Canada

francisoicr.on.ca

kelvin.zhangoicr.on.ca

Download information

The source code

The data set

If you use Pandora in your work, please cite the paper list above, published in Bioinformatics.

A list of discovered redundant pathway pairs in yeast. 31 pathway pairs in our study show they contain statistically more genetic interactions across them than expected at random. Pathway A and B in the table represents a pair of redundant pathway pair. Numbers of Genetic Interactions (No. of GIs) is the number of genetic interactions across a pair of redundant pathway pair. P-value for each pair was calculated using Z-test by comparing the actual number of GIs of each pair to its corresponding numbers in 100 randomized networks.

Pathway A	Pathway B	No. of GIs	P-value-order
35	157	6	7.10 x 10^-16
157	81	4	8.90 x 10^-16
35	153	15	8.90 x 10^-16
153	81	10	8.90 x 10^-16
127	118	14	8.90 x 10^-16
35	73	21	8.90 x 10^-16
23	201	4	4.40 x 10^-10
81	98	8	4.40 x 10^-10
153	182	15	4.40 x 10^-10
118	95	4	3.90 x 10^-9
118	201	4	3.90 x 10^-9
175	107	8	3.90 x 10^-9
157	153	10	3.90 x 10^-9
153	73	35	3.90 x 10^-9
153	189	10	3.90 x 10^-9
175	165	13	6.30 x 10^-8
153	47	55	6.30 x 10^-8
81	182	4	6.30 x 10^-8
98	189	5	6.30 x 10^-8
157	73	8	3.50 x 10^-7
118	157	2	1.20 x 10^-6
118	211	2	1.20 x 10^-6
118	116	3	1.20 x 10^-6
35	65	3	1.20 x 10^-6
157	63	2	1.20 x 10^-6
157	189	2	1.20 x 10^-6
197	153	5	1.20 x 10^-6
153	63	5	1.20 x 10^-6
153	177	5	1.20 x 10^-6
212	201	2	1.20 x 10^-6
63	201	2	1.20 x 10^-6

Pathway	No. of Proteins	Protein List	Annotation
0	407	YGR129W YPR165W YKL168C YMR197C YDL116W YIL143C YDR167W YLR052W YPR086W YBR279W YKR055W YNL025C YDR443C YGL092W YMR183C YER146W YPL140C YML049C YDR416W YDL108W YMR240C YPL115C YPL119C YLL019C YLR078C YML015C YER107C YPR054W YMR075W YDR088C YHR079C YGL120C YMR001C YBR055C YGR040W YGL210W YLR293C YOL115W YOR231W YPR168W YGR104C YPR057W YNL180C YDL101C YJL081C YNR031C YML010W YDR164C YDR283C YCR081W YJL176C YFR005C YFL013C YMR091C YBR065C YDL175C YOR267C YER031C YDR079C-A YNL286W YNL093W YKR022C YGL078C YHR102W YOR194C YKL095W YHR041C YHR086W YNL298W YHR165C YMR263W YOL113W YJR132W YDR192C YPR178W YER022W YKL006C-A YPL026C YLR262C YGL222C YDL030W YER112W YLR385C YKR029C YML031W YDL087C YLR335W YDR490C YHR099W YDL098C YML103C YMR104C YPL129W YJR059W YKL139W YPR082C YNL112W YDR389W YOR089C YJR022W YPR034W YIL126W YDR477W YBR188C YER114C YKL173W YFL005W YGR275W YOR244W YKL012W YAL041W YDR308C YFR037C YIL097W YNL216W YHL007C YJL050W YAR042W YIR009W YOR127W YGR116W YER164W YGR002C YHR082C YMR153W YDR498C YDR359C YAR018C YDL127W YGL238W YNR010W YLR321C YBR200W YGR091W YGL244W YGR005C YGL098W YDL209C YLR418C YDR247W YKR008W YHL031C YPR056W YOR185C YBR264C YLR116W YHR205W YBR135W YLR026C YDR507C YOL145C YOR290C YLR248W YKL126W YNL097C YML127W YBR095C YIL004C YKL203C YLR113W YFL024C YGL194C YMR135C YOR106W YMR236W YER172C YJL124C YOL051W YFL002C YLR424W YMR112C YGL212W YIL084C YNR023W YJR042W YGR074W YGL180W YPR101W YGL158W YGR186W YDL002C YDR190C YDL088C YNL161W YDR334W YLR071C YPL031C YBR059C YBR231C YDR379W YGR063C YDR189W YOR304W YOR233W YLL036C YOR123C YGL025C YDL005C YDL056W YJL165C YOL149W YCL032W YCR042C YJR082C YOR134W YIL115C YJL141C YCR038C YLR362W YGR278W YDR378C YNL307C YFL017W-A YDR311W YLR438C-A YNR011C YCR033W YKL048C YBR253W YBL016W YER009W YGL100W YCL039W YPL151C YBR289W YBR198C YHR058C YPL209C YDR364C YJL041W YKR062W YER136W YLR229C YGR075C YFL033C YMR005W YLR208W YBL026W YFL038C YEL018W YGL172W YMR290C YBL079W YDR460W YLR147C YIL061C YHL025W YGR056W YOL135C YGL195W YDR235W YNL289W YGR119C YPR106W YER013W YER029C YDR309C YNL236W YFR009W YOL004W YKL028W YAL011W YNL304W YHR056C YJL128C YFL047W YML098W YDR002W YBR260C YLR396C YML001W YIR005W YMR047C YLR276C YJL061W YBR193C YDL043C YJL203W YPL235W YBR119W YHR061C YLL008W YFR002W YPL122C YDR264C YBL093C YPL011C YPL082C YOR319W YDR422C YLR371W YDR303C YDR523C YOR204W YKL058W YPR023C YKL068W YMR235C YJL187C YDL019C YBR103W YLR298C YBR245C YDL028C YKR014C YLR093C YDR073W YFL029C YDL076C YMR227C YCL024W YML041C YPL153C YNL330C YGL095C YKL074C YOR308C YLR005W YBR160W YLR275W YPR025C YMR288W YOR327C YPR070W YPL232W YPR182W YNL245C YML046W YER035W YJL095W YER171W YOR098C YDR163W YLR268W YIL079C YOL018C YKL092C YIL063C YJL106W YGR006W YHR030C YNR038W YOR141C YDR473C YMR268C YGL150C YKL057C YGR152C YKR082W YMR129W YKR024C YPL204W YBR142W YOR159C YDL159W YCR052W YGL112C YPR031W YDR485C YNL136W YKR086W YPL181W YNL059C YLR033W YDR145W YLR085C YLR398C YNL090W YGR233C YIL112W YGR274C YML114C YDL031W YIL095W YER105C YER027C YLR096W YDR468C YDL240W YER155C YAL030W YPL016W YOR174W YER111C YNL118C YMR213W YBR152W YCR091W YLR357W YDR240C YNL299W YMR033W YGR092W YNL147W YKL196C YNL107W YGR013W YAR019C YLR182W YLR055C YJR050W YOR148C YOR036W YCR073C YDR255C YJR066W YPL139C	0000398: nuclear mRNA splicing, via spliceosome/mRNA splicing/pre-mRNA splicing
1	3	YPR156C YGR138C YLL028W	0000297: spermine transporter activity
2	65	YMR193W YML025C YDL202W YPL118W YBR122C YGR220C YNL081C YJR113C YDR322W YGR076C YDR494W YDR237W YBL038W YKL155C YIL093C YMR188C YOR150W YNL252C YKR085C YPL013C YDR175C YML009C YDR116C YLR439W YNL177C YJR101W YKL167C YPR166C YBR146W YHL004W YOR158W YGL129C YNL005C YDR462W YGL068W YGR084C YBR251W YDR347W YBR268W YMR024W YBR282W YPL173W YJL063C YDR337W YDR405W YNR037C YDR041W YNL185C YNL137C YMR158W YDL045W-A YER050C YCR003W YLR312W-A YNL306W YNL284C YKL003C YGR165W YCR046C YHR147C YGR215W YKR006C YCR071C Q0140 YBL090W	0005761: mitochondrial ribosome
3	25	YOR232W YGR082W YPL063W YNR017W YKL195W YMR203W YOR297C YEL020W-A YJL143W YJR135W-A YLR008C YNL131W YGR181W YKR065C YHR005C-A YPR133W-A YHR117W YNL328C YGR033C YDL217C YBR091C YIL022W YJL104W YJL054W YNL121C	0006626: protein-mitochondrial targeting/mitochondrial protein import
4	7	YER087C-B YLR292C YOR254C YBR171W YDR086C YPL094C YLR378C	0031205: Sec complex
5	16	YGR162W YMR146C YDR429C YPL237W YKR059W YOR361C YLR192C YNL244C YGL049C YER025W YJL138C YJR007W YMR260C YBR079C YMR309C YOL139C	0003743: translation initiation factor activity
6	56	YPL249C-A YLR075W YFR031C-A YDR012W YGL147C YLR406C YGR034W YIL018W YPL198W YLR029C YGL135W YEL054C YOR063W YFR032C-A YOL120C YDR382W YNL069C YKL180W YBR191W YBL027W YHR141C YML073C YPL143W YDL082W YPR102C YJL177W YDL136W YMR194W YBR031W YBR084C-A YLR325C YGL103W YBL092W YDR418W YGR085C YHL033C YOL039W YLR340W YNL301C YMR242C YHL001W YOR312C YPL220W YLL045C YGL076C YDL081C YDR471W YHR010W YLR448W YOL127W YOR234C YDL075W YLR344W YIL133C YPL131W YGL031C	0005842: cytosolic large ribosomal subunit (sensu Eukaryota)/60S ribosomal subunit/cytosolic large ribosomal subunit
7	2	YKL025C YGL094C	0004535: poly(A)-specific ribonuclease activity
8	22	YLR045C YBR233W-A YIR010W YCL029C YKR083C YGL061C YIL144W YER018C YGR113W YAL034W-A YDR201W YMR117C YJR112W YKR037C YDR320C-A YPL233W YDR016C YKL052C YKL138C-A YOL069W YBR211C YJR089W	0000777: condensed chromosome kinetochore
9	152	YDL111C YHR119W YNL232W YDL213C YDL167C YMR049C YKL214C YKR060W YBL008W YLL011W YDR195W YGR128C YOR206W YNL002C YJL122W YCR035C YHR196W YCR057C YOL010W YLR186W YER006W YJR041C YLR129W YOR272W YDR365C YHR148W YGR103W YKL021C YLR115W YGR156W YDR280W YMR229C YNL075W YHR089C YLR221C YJR140C YPL190C YHR197W YGR081C YDR398W YDR381W YDR101C YGR159C YBR258C YGR158C YNL110C YOR001W YPR144C YOL077C YNL317W YGR145W YOR078W YHR085W YNL308C YPL217C YNL207W YPL043W YLR196W YBL004W YDR449C YBR215W YOL021C YER126C YDR432W YER082C YFR021W YAR003W YPL093W YPL126W YLR222C YPL138C YNL016W YBR267W YKL193C YMR131C YNL251C YBR175W YDL148C YGR195W YER002W YPL012W YGR090W YHR066W YHR088W YLR435W YOL041C YLR197W YDR312W YGR095C YDR060W YNL004W YHR069C YPL211W YDR087C YDL060W YKL059C YPR143W YJL069C YAL025C YKL009W YGL029W YHR072W-A YNL132W YPR137W YKL172W YJR002W YIL019W YDR301W YNR053C YDR469W YOR038C YOR250C YCR072C YLR277C YMR061W YJR093C YOL123W YCL059C YML093W YER127W YCL011C YGL122C YMR128W YPR112C YNL182C YLR009W YOL142W YLR074C YBR212W YDR228C YBR247C YKL018W YNL175C YOR310C YOR294W YMR093W YLR015W YIR001C YDR324C YKR081C YJL109C YOL144W YGL111W YDL208W YAL043C YGL044C YNR054C YDL229W YNL197C YPR107C YLR409C YJL010C	0007028: cytoplasm organization and biogenesis
10	3	YPR018W YBR195C YML102W	0006334: nucleosome assembly
11	2	YEL009C YPL038W
12	2	YEL015W YBR094W
13	16	YDR329C YHR160C YJL210W YMR026C YLR191W YOL147C YDR244W YDR142C YDR265W YDL065C YOL044W YGL153W YNL214W YPL112C YAL055W YGR077C	0007031: peroxisome organization and biogenesis
15	3	YNL071W YER178W YBR221C	0045254: pyruvate dehydrogenase complex/pyruvate dehydrogenase complex (lipoamide)
16	3	YJL137C YFR015C YLR258W	0035251: UDP-glucosyltransferase activity
17	14	YMR256C YHR051W YDL067C Q0045 YLR395C Q0275 YNL052W Q0250 YPR191W YBL045C YFR033C YEL024W YGL187C YIL111W	0005746: mitochondrial electron transport chain/respiratory chain
18	7	YDL165W YNR052C YCR093W YAL021C YPR072W YIL038C YER068W	0000289: poly(A) tail shortening
19	2	YGR240C YMR205C	0003872: 6-phosphofructokinase activity
20	30	YGL070C YPR187W YPR110C YPR190C YOR340C YDR156W YDL140C YNR003C YOL005C YHR143W-A YDL150W YOR210W YKR025W YDR404C YNL248C YIL021W YNL113W YDR045C YBR154C YJR063W YJL011C YOR116C YJL148W YNL151C YKL144C YOR151C YOR207C YPR010C YOR224C YOR341W	0030880: RNA polymerase complex
21	2	YOR230W YOR229W	0003714: transcription corepressor activity/transcription co-repressor activity
23	2	YDR004W YER095W	0003714: transcription corepressor activity/transcription co-repressor activity
24	11	YBR155W YPR189W YMR186W YGR123C YDR168W YOR027W YPL240C YGL213C YCR060W YBL075C YAL005C	0006457: protein folding/chaperone activity
26	11	YCL008C YLR417W YLR119W YMR077C YPL065W YLR025W YPL002C YGR206W YKL002W YJR102C YKL041W	0043162: ubiquitin-dependent protein catabolism via the multivesicular body pathway/ubiquitin-dependent protein catabolism via the MVB pathway
27	35	YNL178W YPL090C YNL096C YML063W YGL123W YJR145C YOL040C YHL015W YGR214W YOR096W YML024W YLR441C YDR447C YLR287C-A YDR064W YML026C YIL069C YBR048W YJR123W YPL081W YDL083C YLR367W YGR027C YHR203C YDR450W YER102W YBR189W YER074W YCR031C YJL190C YBL072C YGR118W YBR181C YDR025W YMR230W	0005843: cytosolic small ribosomal subunit (sensu Eukaryota)/40S ribosomal subunit/cytosolic small ribosomal subunit
28	3	YHR206W YLR006C YIL147C	0042542: response to hydrogen peroxide
29	3	YMR080C YGR072W YHR077C	0000184: mRNA catabolism, nonsense-mediated decay/mRNA catabolism, nonsense-mediated/nonsense-mediated mRNA decay
30	4	YGR222W YMR257C YLR067C YNR045W	0045182: translation regulator activity
31	4	YDL095W YAL023C YOR321W YDL093W	0004169: dolichyl-phosphate-mannose-protein mannosyltransferase activity/O-glycoside mannosyltransferase/dolichyl-phosphate-mannose-protein O-mannosyltransferase activity/protein O-mannosyltransferase
32	2	YML075C YLR450W	0004420: hydroxymethylglutaryl-CoA reductase (NADPH) activity
33	11	YLR127C YDL008W YKL022C YDR118W YGL240W YOR249C YBL084C YLR102C YNL172W YFR036W YHR166C	0008054: cyclin catabolism/degradation of cyclin
34	3	YDR181C YMR127C YOR213C	0004406: H3/H4 histone acetyltransferase activity
35	3	YOR026W YJL030W YGL086W	0007094: mitotic spindle checkpoint
36	4	YIL035C YOR039W YOR061W YGL019W	0005956: protein kinase CK2 complex/casein kinase II complex
38	8	YGR047C YGR246C YAL001C YOR110W YNL039W YDR362C YPL007C YBR123C	0003709: RNA polymerase III transcription factor activity
39	10	YIL046W YFL009W YDR328C YDL132W YLR368W YDR054C YML088W YOL133W YJL204C YJR090C	0019005: SCF ubiquitin ligase complex/SCF complex/Skp1/Cul1/F-box protein complex/cullin complex
40	26	YBR210W YMR292W YDL145C YNL287W YIL076W YGR172C YAL042W YGL137W YOR016C YHR110W YNL044W YGL200C YAR002C-A YCL001W YGL002W YDL018C YML012W YML067C YAL007C YNL263C YER074W-A YFR051C YPL010W YGR284C YFL048C YDR238C	0045045: secretory pathway
41	6	YPR019W YLR274W YEL032W YBR202W YBL023C YGL201C	0042555: MCM complex/mini-chromosome maintenance complex
42	14	YNL126W YDR356W YAL047C YOR373W YPL255W YHR172W YKL042W YLR212C YGL075C YBL034C YGL093W YPL124W YOR257W YNL225C	0005200: structural constituent of cytoskeleton
43	8	YOR115C YDR472W YML077W YDR407C YDR246W YMR218C YBR254C YKR068C	0030008: TRAPP complex/transport protein particle
44	3	YDL220C YDR082W YLR010C	0016233: telomere capping
45	6	YDR179C YDL216C YIL071C YMR025W YOL117W YJR084W	0008180: signalosome complex/COP9 complex
46	2	YHR157W YMR133W	0000737: DNA catabolism, endonucleolytic/endonucleolytic degradation of DNA
47	15	YNL243W YLR337C YDL029W YBL007C YKL129C YCR088W YMR109W YJL020C YDR388W YNL084C YJR065C YCR009C YIR006C YHR114W YOR181W	0015629: actin cytoskeleton
48	2	YLR318W YIL009C-A	0003720: telomerase activity
49	3	YBR179C YDR470C YOR211C	0008053: mitochondrial fusion
50	2	YIL074C YER081W	0004617: phosphoglycerate dehydrogenase activity
51	6	YPR088C YKL122C YML105C YDL092W YPL210C YPL243W	0048500: signal recognition particle
52	3	YKL008C YHL003C YMR298W	0046513: ceramide biosynthesis
54	4	YAR008W YPL083C YMR059W YLR105C	0000214: tRNA-intron endonuclease complex
55	6	YAL003W YLR249W YDR385W YPR080W YOR133W YKL081W	0003746: translation elongation factor activity
56	2	YPL049C YDR480W	0008134: transcription factor binding/TF binding
57	10	YMR095C YNL333W YDR533C YPL280W YOR391C YNL334C YMR322C YMR096W YFL060C YFL059W	0042816: vitamin B6 metabolism
58	2	YKL007W YIL034C	0030834: regulation of actin filament depolymerization/regulation of actin depolymerization
59	5	YLR148W YDR080W YMR231W YPL045W YDL077C	0030897: HOPS complex
60	3	YNL021W YDR295C YPR179C	0006476: protein amino acid deacetylation
61	34	YML092C YGL004C YOR261C YER021W YPR103W YDL007W YMR314W YPR108W YOR259C YBL041W YGL011C YER012W YER094C YJL001W YHR200W YLR421C YOR117W YFR004W YGL048C YDR427W YKL145W YOR362C YDL147W YGR253C YGR135W YFR052W YGR232W YOR157C YIL075C YDR394W YOL038W YDL097C YFR050C YHR027C	0000502: proteasome complex (sensu Eukaryota)/26S proteasome
62	2	YJR103W YBL039C	0003883: CTP synthase activity
63	2	YML032C YDL059C	0000739: DNA strand annealing activity
64	2	YLR442C YDR227W	0030527: structural constituent of chromatin
65	2	YPR131C YOL076W	0017196: N-terminal peptidyl-methionine acetylation
66	11	YAL033W YGR030C YBR167C YHR062C YNL221C YNL282W YIR015W YLR145W YBL018C YDR478W YBR257W	0000172: ribonuclease MRP complex/RNase MRP complex/ribonuclease mitochondrial RNA processing complex
67	5	YGL087C YDR092W YCR066W YDL064W YLR032W	0008639: small protein conjugating enzyme activity
68	4	YBR126C YDR074W YML100W YMR261C	0005946: alpha,alpha-trehalose-phosphate synthase complex (UDP-forming)
69	3	YCR020C-A YPR051W YEL053C	0031365: N-terminal protein amino acid modification
70	2	YNL104C YOR108W	0003852: 2-isopropylmalate synthase activity
71	10	YMR224C YBL097W YFL008W YJL074C YDR325W YFR031C YLR272C YLR086W YNL250W YDR369C	0000799: nuclear condensin complex
72	11	YPR105C YNL258C YGL223C YGL005C YGL145W YER157W YLR440C YNL041C YGR120C YML071C YNL051W	0017119: Golgi transport complex
73	7	YGR179C YLR381W YDR254W YJR135C YPR046W YDR318W YPL018W	0000777: condensed chromosome kinetochore
74	8	YDR225W YBL003C YNL031C YBR009C YBR010W YDR224C YBL002W YNL030W	0000786: nucleosome
76	8	YDR176W YDR448W YPL254W YGL066W YBR081C YOR023C YGR252W YOL148C	0016573: histone acetylation
77	6	YPR162C YNL261W YLL004W YHR118C YBR060C YML065W	0005664: nuclear origin of replication recognition complex/eukaryotic ORC/nuclear ORC
78	6	YJL154C YOR132W YJL053W YOR069W YMR004W YHR012W	0030904: retromer complex
79	4	YNL139C YDR138W YML062C YHR167W	0000347: THO complex
80	2	YPL076W YDR437W
81	2	YMR294W YHR129C	0005869: dynactin complex
82	5	YLR170C YPR029C YHL019C YKL135C YPL259C	0030121: AP-1 adaptor complex/HA1
83	2	YNL283C YOL105C	0004888: transmembrane receptor activity
84	11	YOR332W YOR270C YPR036W YGR020C YBR127C YLR447C YDL185W YHR039C-A YMR054W YEL051W YKL080W	0046961: hydrogen-transporting ATPase activity, rotational mechanism
85	5	YDR097C YCR092C YMR167W YOL090W YNL082W	0005524: ATP binding
86	2	YNL288W YGR134W	0030014: CCR4-NOT complex
87	2	YHR094C YMR011W	0015578: mannose transporter activity
88	2	YFL003C YDL154W	0007131: meiotic recombination/female meiotic recombination/gene conversion with reciprocal crossover
89	4	YOR125C YLR201C YDR204W YGR255C	0006743: ubiquinone metabolism/coenzyme Q metabolism
91	3	YDR100W YMR071C YKR088C
92	7	YDL105W YLR383W YER038C YLR007W YDR288W YML023C YOL034W	0030915: Smc5-Smc6 complex
93	2	YGL051W YAR033W	0016050: vesicle organization and biogenesis
94	4	YJL099W YMR237W YKR027W YOR299W
95	2	YFR010W YOR124C	0004843: ubiquitin-specific protease activity/UBP/UCH2
96	5	YOR260W YLR291C YGR083C YKR026C YDR211W	0005851: eukaryotic translation initiation factor 2B complex/eIF-2B
97	2	YIR021W Q0115	0000376: RNA splicing, via transesterification reactions with guanosine as nucleophile
98	4	YER149C YLL021W YLR319C YNL271C	0005519: cytoskeletal regulatory protein binding
99	2	YAL051W YOR363C	0016563: transcriptional activator activity/transcription activating factor
100	4	YHR107C YCR002C YJR076C YLR314C	0005545: phosphatidylinositol binding
101	10	YDL232W YGL022W YJL002C YOR103C YEL002C YGL226C-A YMR149W YOR085W YPL227C YML019W	0008250: oligosaccharyl transferase complex/OST complex
102	2	YPL046C YNL230C	0008023: transcription elongation factor complex
103	3	YOL013C YLR207W YMR022W	0030433: ER-associated protein catabolism/ER-associated protein degradation/ERAD/endoplasmic reticulum-associated protein catabolism
104	5	YOL061W YKL181W YBL068W YER099C YHL011C	0004749: ribose-phosphate diphosphokinase activity/ribose-phosphate pyrophosphokinase activity
105	6	YOR326W YPR188C YHR023W YGL106W YAL029C YPL242C	0000146: microfilament motor activity
106	4	YGR261C YJL024C YBR288C YPL195W	0030123: AP-3 adaptor complex
107	4	YPL020C YDR510W YDR390C YPR180W	0016925: protein sumoylation/SUMO-protein conjugation/protein sumolation/small ubiquitin-related protein 1 conjugation/sumoylation
108	2	YGR010W YLR328W	0019674: NAD metabolism/NAD (oxidized) metabolism/nicotinamide adenine dinucleotide metabolism/oxidized NAD metabolism/oxidized nicotinamide adenine dinucleotide metabolism
109	4	YOR153W YGR281W YPL058C YDR011W	0042910: xenobiotic transporter activity
110	2	YMR255W YDL207W	0005643: nuclear pore/NPC/nuclear pore complex/nuclear pore membrane protein
111	2	YKL130C YBR130C	0008298: intracellular mRNA localization/intracellular mRNA positioning/mRNA localization, intracellular/mRNA positioning, intracellular
112	2	YNL291C YGR217W	0006816: calcium ion transport
113	3	YGR108W YLR079W YMR036C	0000079: regulation of cyclin dependent protein kinase activity/regulation of CDK activity
114	2	YHR026W YPL234C	0000220: hydrogen-transporting ATPase V0 domain
115	2	YJL089W YMR280C	0045722: positive regulation of gluconeogenesis
116	3	YOR253W YDL040C YHR013C	0004596: peptide alpha-N-acetyltransferase activity
117	3	YHR178W YBL005W YGL013C	0042221: response to chemical substance
118	2	YGL058W YDL074C	0016574: histone ubiquitination/histone ubiquitinylation/histone ubiquitylation
119	5	YPL218W YHR098C YPR181C YIL109C YNL049C	0030127: COPII vesicle coat
120	2	YBR037C YBR024W	0008379: thioredoxin peroxidase activity/peroxiredoxin activity
121	8	YJL008C YJR064W YJL111W YDR212W YDR188W YIL142W YJL014W YDL143W	0005832: chaperonin-containing T-complex/CCT particle/TriC
122	5	YML115C YER001W YPL050C YJL183W YEL036C	0000136: mannosyltransferase complex
123	4	YBR278W YNL262W YPR175W YDR121W	0008622: epsilon DNA polymerase complex
124	3	YLR433C YML057W YKL190W	0005955: calcineurin complex/calcium-dependent protein serine/threonine phosphatase complex
126	6	YKL010C YDL190C YPR093C YKL034W YDR059C YBR082C	0016567: protein ubiquitination/protein ubiquitinylation/protein ubiquitylation
127	7	YPL086C YLR384C YMR312W YGR200C YKL110C YHR187W YPL101W	0016944: RNA polymerase II transcription elongation factor activity/Pol II transcription elongation factor activity
128	2	YIR025W YDR260C	0030071: regulation of mitotic metaphase/anaphase transition
130	4	YOL146W YDR013W YJL072C YDR489W	0000811: GINS complex/Go, Ichi, Ni and San complex
131	6	YAL024C YNL098C YBR140C YLR310C YOR101W YOL081W	0007265: Ras protein signal transduction/Ras mediated signal transduction
133	2	YGR264C YGL245W	0017102: methionyl glutamyl tRNA synthetase complex
134	4	YBL037W YOL062C YJR058C YJR005W	0030128: clathrin coat of endocytic vesicle/clathrin coat of endocytotic vesicle
136	3	YIL065C YLL001W YJL112W	0048285: organelle fission
138	7	YLR141W YJL025W YML043C YBL014C YKL125W YBL025W YMR270C	0000120: RNA polymerase I transcription factor complex
139	2	YML013W YBR201W	0043161: proteasomal ubiquitin-dependent protein catabolism/proteasomal processing/proteasome pathway
140	2	YBR068C YPL265W	0015171: amino acid transporter activity
141	5	YBR052C YDR032C YOR086C YCR004C YML072C
142	4	YJL115W YPL001W YLL022C YEL056W	0000123: histone acetyltransferase complex/histone acetylase complex
143	2	YLR028C YMR120C	0003937: IMP cyclohydrolase activity/inosinicase
144	2	YIL125W YDR148C	0006103: 2-oxoglutarate metabolism/ketoglutarate metabolism
145	5	YJR068W YOL094C YBR087W YOR217W YNL290W	0005663: DNA replication factor C complex
146	3	YDR484W YJL029C YDR027C	0000938: GARP complex/Golgi associated retrograde protein complex/VFT tethering complex/Vps fifty three tethering complex
147	2	YEL037C YMR276W	0030433: ER-associated protein catabolism/ER-associated protein degradation/ERAD/endoplasmic reticulum-associated protein catabolism
148	6	YDL091C YBR273C YDL126C YJL048C YMR067C YDR330W	0019941: modification-dependent protein catabolism/protein-ligand-dependent protein catabolism
149	5	YCR039C YDR451C YMR043W YML027W YMR042W	0006357: regulation of transcription from RNA polymerase II promoter/regulation of transcription from Pol II promoter
150	3	YNL312W YAR007C YJL173C	0005662: DNA replication factor A complex
151	15	YPR020W YKL016C YBL099W Q0130 YBR039W Q0085 YPL078C YML081C-A YLR295C YJR121W YDL004W Q0080 YPL271W YDR377W YDR298C	0015986: ATP synthesis coupled proton transport
153	5	YGR078C YNL153C YML094W YEL003W YLR200W	0016272: prefoldin complex/GIM complex
154	4	YBL021C YGL237C YOR358W YKL109W	0016602: CCAAT-binding factor complex
155	2	YBR281C YFR044C
156	2	YOL130W YFL050C	0015693: magnesium ion transport
157	2	YMR198W YPR141C	0003777: microtubule motor activity/dynein/kinesin
158	5	YER110C YLR347C YGR218W YNL189W YMR308C	0008320: protein carrier activity
159	3	YIL132C YHL006C YLR376C	0045021: error-free DNA repair
160	2	YDR099W YER177W	0001402: signal transduction during filamentous growth
161	2	YLR432W YHR216W	0046039: GTP metabolism
162	2	YDL131W YDL182W	0004410: homocitrate synthase activity
163	2	YPL178W YMR125W	0005846: snRNA cap binding complex
164	7	YGL233W YLR166C YER008C YJL085W YDR166C YPR055W YIL068C	0000145: exocyst
165	7	YGR003W YLR234W YMR201C YJR052W YMR190C YER162C YBR114W	0000715: nucleotide-excision repair, DNA damage recognition
166	2	YMR108W YCL009C	0005948: acetolactate synthase complex
167	2	YLR181C YKR035W-A	0005770: late endosome/PVC/prevacuolar compartment
169	3	YMR094W YGR140W YMR168C	0019237: centromeric DNA binding
170	4	YER070W YJL026W YIL066C YGR180C	0004748: ribonucleoside-diphosphate reductase activity/ribonucleotide reductase
172	2	YGR121C YPR138C	0008519: ammonium transporter activity
173	3	YAL010C YOL009C YLL006W	0019867: outer membrane
174	3	YKL166C YPL203W YJL164C	0005952: cAMP-dependent protein kinase complex/PKA
175	2	YER116C YDL013W
176	2	YER044C-A YJR021C	0007131: meiotic recombination/female meiotic recombination/gene conversion with reciprocal crossover
177	2	YNR069C YLL049W
178	4	YGL170C YLR227C YOL091W YOR177C	0005816: spindle pole body
179	3	YBR112C YCR084C YKL213C	0016565: general transcriptional repressor activity
180	5	YGR192C YKL152C YCR012W YKL060C YJR009C	0006096: glycolysis
182	3	YML085C YML124C YFL037W	0045298: tubulin
183	3	YLR154C YDR279W YNL072W	0004523: ribonuclease H activity/RNase H activity/calf thymus ribonuclease H activity
184	3	YDR009W YML051W YPL248C	0006012: galactose metabolism
186	2	YHR007C YMR015C	0008204: ergosterol metabolism
188	2	YMR271C YML106W	0004588: orotate phosphoribosyltransferase activity
189	2	YOR269W YLR254C
190	2	YKL013C YLR370C	0005885: Arp2/3 protein complex
191	2	YNL048W YBR110W	0000030: mannosyltransferase activity
192	6	YHR150W YGR004W YDR479C YLR324W YMR204C YBR168W	0005778: peroxisomal membrane
193	2	YNL094W YHR016C	0030479: actin cortical patch/actin cortical patch (sensu Fungi)/actin cortical patch (sensu Saccharomyces)/actin patch
194	2	YDL245C YHR096C	0015578: mannose transporter activity
195	2	YHR064C YEL034W
196	5	YLR459W YHR188C YDR434W YLR088W YDR331W	0016255: attachment of GPI anchor to protein
197	2	YFR053C YGL253W	0004396: hexokinase activity
198	3	YDL192W YDR170C YDL137W	0005798: Golgi vesicle
200	2	YMR159C YPL149W	0006914: autophagy
201	2	YDR453C YML028W	0008379: thioredoxin peroxidase activity/peroxiredoxin activity
202	3	YDR093W YAL026C YER166W	0004012: phospholipid-translocating ATPase activity/aminophospholipid-transporting ATPase/flippase/magnesium-ATPase
203	2	YER159C YDR397C	0003714: transcription corepressor activity/transcription co-repressor activity
204	2	YGL161C YGL198W	0017137: Rab GTPase binding/Rab interactor activity
205	2	YNL238W YGL203C	0008236: serine-type peptidase activity/serine protease
206	2	YDR160W YFR029W	0007600: sensory perception
207	2	YGR238C YHR158C	0001100: negative regulation of exit from mitosis
208	2	YMR169C YMR170C	0019482: beta-alanine metabolism
209	2	YGL250W YLR082C
210	2	YJR159W YDL246C
211	2	YOR337W YDR207C
212	2	YLR320W YHR154W
213	2	YDR233C YDL204W