SiDeS on Yeast |
The following table lists the 73 sets of S. Cerevisiae proteins that induce
significantly dense subgraphs in the yeast PPI network obtained from
BIND and DIP
, which are identified by
SiDeS.
The dense subgraphs are sorted according to their p-value, which is defined
as the probability of existence of such a large set of proteins that would induce such a dense
subgraph in the network, according to a reference graph model.
For each dense subgraph, the most significant 10 GO terms that are found to be significantly
enriched in the corresponding set of proteins, as identified by the
Ontologizer,
are also listed. For each annotation, if there are P proteins in the subgraph, C of which are attached to the
corresponding term, and the term is attached to T proteins in total, then sensitivity is defined as
C/T, whereas specificity is defined as P/T. The reported p-value for the annotation is the one assigned
by the Ontologizer.
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|
Rank | Size (#Prot, #Int) | p-value | Proteins |
|
1 | 22, 145 | 2e-234 | SPT7 TAF90 TSM1 TAF61 TAF10 NGG1 ADR1 SPT3 ADA2 GCN4 TBP1 TAF6 GCN5 TAF1 TRA1 SPT8 TAF19 TAF40 TAF4 TAF17 ADA5 HFI1 |
| |
|
2 | 21, 123 | 3e-181 | LSM2 DHH1 LSM8 PAT1 LSM8 LSM6 EDC3 LSM4 LSM5 KEM1 PAT1 PRP31 LSM1 SNU114 SMD2 LSM3 PRP24 LSM7 DCP2 DCP1 PRP4 |
| |
|
3 | 20, 114 | 1e-169 | DBP10 YDR060W NUG1 NSA2 NSA1 NOP7 CIC1 SSF1 RPF1 CKA1 YKR081C ERB1 HAS1 NOP2 BRX1 DNL4 YTM1 NOP4 TIF6 MAK5 |
| |
|
4 | 20, 112 | 4e-163 | REF2 PCF11 CFT1 GLC7 RNA15 PTI1 FIP1 RSM7 MPE1 PAP1 CFT2 YSH1 RNA14 PFS2 SSU72 CLP1 YTH1 HCA4 SWD2 PTA1 |
| |
|
5 | 18, 94 | 5e-138 | PRE7 PPH22 RPN5 PRE4 PRE1 PUP3 SCL1 PRE9 PUP2 RPN10 PRE3 PRE8 PRE5 PRE6 PUP1 RPN8 PRE10 PRE2 |
| |
|
6 | 12, 62 | 2e-134 | CDC27 DOC1 APC11 APC4 CDC26 DOC1 CDC23 CDC16 APC9 APC2 APC1 APC5 |
| |
|
7 | 17, 82 | 2e-114 | ROX3 MED8 MED22 MED2 SRB4 SRB5 MED20 MED6 MED14 SIN4 MED9 MED7 GAL11 MED4 GAL4 SRB10 MED1 |
| |
|
8 | 15, 64 | 6e-85 | MUD1 LUC7 SNU56 PRP3 SNU71 SMD1 NAM8 SNP1 PRP42 PRP40 SMD3 PRP39 STO1 SAE1 YHC1 |
| |
|
9 | 14, 55 | 5e-69 | RRP42 RRP45 RRP43 MTR3 SKI6 RRP4 LRP1 MAS1 RRP40 DIS3 RRP6 SKI7 CSL4 RRP46 |
| |
|
10 | 10, 38 | 1e-66 | OST4 OST2 WBP1 OST5 STT3 OST2 OST5 OST1 SWP1 OST3 |
| |
|
11 | 13, 48 | 5e-59 | APG12 RPN6 RPN11 RPN12 RPN9 RAD23 RPN3 RPN1 RPT1 RPT4 ECM29 18 UBP6 |
| |
|
12 | 13, 48 | 5e-59 | TRS20 GSG1 TRS23 TRS120 TRS31 TRS65 GYP6 BET3 BET5 3 TRS130 ALF1 TRS33 |
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|
13 | 10, 35 | 7e-54 | ARF1 RET1 RET2 SEC26 GLO3 SEC28 BET1 BOS1 SEC22 SEC21 |
| |
|
14 | 12, 42 | 1e-51 | VMA2 RAV2 TFP1 RAV1 SKP1 VMA8 VMA7 VMA10 VMA5 STV1 VPH1 VMA4 |
| |
|
15 | 9, 30 | 8e-49 | GCD6 GCD2 SUI3 FKH1 SUI2 GCN3 GCD7 GCD1 IST1 |
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16 | 10, 32 | 4e-42 | NOT4 NOT1 DBF2 CAF130 NOT3 CAF40 POP2 CAF4 NOT5 CCR4 |
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17 | 11, 33 | 3e-33 | SLA1 ABP1 RVS167 YSC84 BZZ1 MYO3 MYO5 APP1 BEE1 BSP1 BBC1 |
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|
18 | 9, 26 | 2e-32 | CWC2 SYF1 PRP45 ISY1 YJU2 PRP19 CEF1 PRP46 SNT309 |
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19 | 10, 29 | 4e-31 | ATP5 ATP17 ATP1 ATP11 ATP18 ATP6 ATP7 ATP2 ATP4 ATP20 |
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|
20 | 8, 22 | 2e-29 | YBR175W YDR469W RAD6 SET1 BRE2 YPL138C SHG1 YAR003W |
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21 | 10, 27 | 4e-24 | RPO21 RPB1 RPB7 RPB9 TFG2 TFG1 RPB3 RPB11 RPB2 ANC1 |
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22 | 7, 17 | 1e-21 | POL12 RFC5 POL30 ECO1 RFC2 RFC3 RFC4 |
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23 | 8, 20 | 2e-21 | VAM6 VPS41 MON1 PEP3 VPS33 PEP5 VPS16 VPS8 |
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24 | 9, 23 | 3e-21 | TOM20 YHR003C TIM17 TOM40 TOM22 TOM70 TOM7 TOM6 TOM5 |
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25 | 9, 22 | 1e-17 | BRE1 SMC1 SMC2 SPC19 YEL043W TID3 SMC3 SPC24 NUF2 |
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26 | 9, 22 | 1e-17 | MRS5 TIM22 TIM9 TIM13 TIM10 TIM54 TIM23 TIM18 TIM8 |
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27 | 8, 19 | 1e-17 | GCS1 YPT1 YPT31 YIP5 YIP1 YHR105W PEP12 YIP4 |
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28 | 8, 19 | 1e-17 | GBP2 SUB2 HPR1 THO1 THP2 MFT1 RLR1 RLR1 |
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29 | 7, 16 | 2e-17 | SEC17 SLY1 TLG1 VPS45 YKT6 VTI1 TLG2 |
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30 | 6, 13 | 1e-16 | ELP2 IKI1 KTI12 ELP6 ELP4 ELP3 |
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31 | 7, 15 | 3e-13 | EXO84 SEC5 SEC3 SEC15 SEC6 SEC10 SEC8 |
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32 | 7, 15 | 3e-13 | BEM1 BOI2 CDC24 RSR1 STE20 BEM4 CDC24 |
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33 | 7, 15 | 3e-13 | FUS3 STE50 STE5 GPA1 STE11 STE4 STE11 |
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34 | 6, 12 | 4e-12 | TSC11 TOR2 AVO2 LST8 AVO1 TOR2 |
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35 | 6, 12 | 4e-12 | GIC2 GIC1 CDC42 ZDS2 CLA4 RGA1 |
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36 | 8, 17 | 2e-10 | RPB5 RPA12 RPC25 RPC34 RPB10 RPB8 RPA190 RPO26 |
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37 | 5, 9 | 3e-10 | DAD1 DAM1 DAM1 DUO1 SPC34 |
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38 | 7, 14 | 2e-09 | HTB2 REB1 ISW1 MOT1 VPS1 NPL6 NHP6B |
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39 | 7, 14 | 2e-09 | RPG1 ARC40 TIF35 HCR1 NIP1 TIF5 TFIIB |
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40 | 7, 14 | 2e-09 | NUP84 PSE1 SEH1 NUP145 NUP57 NUP120 NUP85 |
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41 | 7, 14 | 2e-09 | ACTIN PEA2 FUS1 BNR1 BUD6 FUS2 BNI1 |
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42 | 7, 14 | 2e-09 | SEC31 EMP24 SEC24 SEC13 ERV25 ERP2 ERP1 |
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43 | 6, 11 | 7e-08 | ENP1 PWP2 NOP1 CBF5 SIK1 YMR093W |
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44 | 6, 11 | 7e-08 | CNS1 RVB1 PGK1 HSC82 UBP10 SSA1 |
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45 | 6, 11 | 7e-08 | NUP42 MSN5 PAB1 NUP49 NUP133 NUP2 |
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46 | 7, 13 | 9e-06 | SSZ1 AHA1 PPT1 TDH3 SSA2 YPT6 SSE1 |
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47 | 7, 13 | 9e-06 | FYV14 YDR449C KRR1 YGR090W ENP2 UTP20 KRE33 |
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48 | 7, 13 | 9e-06 | PRP11 PRP9 SMB1 PRP21 YNR053C SNU66 SMX2 |
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49 | 7, 13 | 9e-06 | QCR7 RIP1 COB QCR9 QCR8 CYT1 UBIQUINOL-CYTOCHROME |
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50 | 5, 8 | 2e-05 | MNN10 MNN11 ANP1 HOC1 MNN9 |
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51 | 6, 10 | 7e-04 | SEC35 COG2 SEC34 SED5 YPR105C MTW1 |
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52 | 6, 10 | 7e-04 | MCM7 MCM3 MCM2 CDC45 CDC46 GLT1 |
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53 | 6, 10 | 7e-04 | IML3 AME1 MCM21 CBF2 OKP1 CTF19 |
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54 | 6, 10 | 7e-04 | VPS25 VPS37 VPS36 VPS20 VPS28 VPS22 |
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55 | 4, 5 | 1e-01 | RAD3 RAD26 ACO1 MDH1 |
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56 | 4, 5 | 1e-01 | YDL239C BBP1 NIP29 YPL070W |
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57 | 4, 5 | 1e-01 | CYC8 TUP1 RPD3 SIN3 |
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58 | 4, 5 | 1e-01 | GSP1 KAP95 RNA1 GSP2 |
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59 | 4, 5 | 1e-01 | YDR013W YJL072C YLR320W CTF4 |
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60 | 4, 5 | 1e-01 | YDR078C SHU1 YLR376C SHU1 |
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61 | 5, 7 | 4e-01 | CDC53 GRR1 HRT1 CLN2 POR1 |
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62 | 5, 7 | 4e-01 | SIP2 ARC15 ARC19 ARC18 ARC35 |
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63 | 5, 7 | 4e-01 | MSH5 RAD57 PGD1 MRE11 CST9 |
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64 | 5, 7 | 4e-01 | MRPL16 MRPL10 MRPL3 MRPL28 MRPL35 |
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65 | 5, 7 | 4e-01 | ZUO1 SCP160 ASC1 YAR014C KIN3 |
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66 | 5, 7 | 4e-01 | VPS32 VTA1 RIM20 VPS31 VPS4 |
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67 | 5, 7 | 4e-01 | YBL049W YCL039W YDR255C FYV10 DCR1 |
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68 | 5, 7 | 4e-01 | KAP104 SXM1 NUP100 NUP116 NUP1 |
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69 | 5, 7 | 4e-01 | SEC4 GDI1 21 YPT7 YIF1 |
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70 | 5, 7 | 4e-01 | PRP6 SPP381 SME1 LEA1 SMX3 |
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71 | 5, 7 | 4e-01 | PRP8 CLF1 RSE1 CUS1 HSH155 |
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72 | 5, 7 | 4e-01 | VPS5 VPS29 VPS35 PEP8 PEP8 |
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73 | 5, 7 | 4e-01 | RPP1B RPP1A RPP2B RPL12B RPP0 |
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