Web supplement for:
Functional maps of protein complexes from quantitative genetic interaction data
 Sourav Bandyopadhyay, Ryan Kelley, Nevan Krogan, Trey Ideker
Contact: sourav @ bioeng.ucsd.edu

This is the web supplement for the paper in PLoS Computational Biology. Which describes a method for the discovery of protein complexes and their genetic relationships based on high throughput protein-protein interaction data (from TAP-MS data) and high thoughput genetic interaction screening (from E-MAP studies).

E-MAPs (Epistatic Mini Array Profiles) are formed by creating and quantifying high-density genetic interaction maps. With this method, observed double mutant colony sizes are compared to those that would be expected from a distribution of typical double mutant colonies of each strain. Each interaction is assigned a score, which indicates the magnitude of the difference from the expected value and the certainty of the score. Negative (or aggravating) scores (< -2.5) correspond to synthetic sick/lethal interactions while positive (or alleviating) scores (> +2.5) corresponds to epistatic or suppressor interactions.

For each module/complex, three types of data are shown:
Physical: Physical interactions from TAP-MS studies were used based on PE-scores assigned in Collins et al. Typically, PE-scores greater than 1 are considered viable interactions.
Score: The genetic interaction score from E-MAP screening (Collins et al).
Correlation: The correlation of the genetic interaction profiles for the members of the complex. This is also termed 'congruence' and is indiciative of proteins operating in the same pathway.


For each interaction between modules or complexes, relevant data is presented as follows:
# Ints: The number of genetic interactions that have been found to span between the two complexes.
Mean Score: The average S-score of these genetic interactions.
FDR: False Discovery Rate based on permutation of the edges. This indicates how likely it is to get such a strong link between two complexes at random.
Network: A network diagram of the two modules/complexes. Made in cytoscape.
Between Scores: A clustergram of the genetic interaction scores between two complexes


The data in this supplement can also be viewed in an experimental Cytoscape webstart plugin. Follow the instructions and click any link in the overview graph to view the details of the interaction.
Complex NumberMembers# Interactions
0 FKH1 0
347 POL30, HYS2, POL32 5
340 ESC1 0
341 TIM13 1
342 WHI4 0
343 NRD1 0
349 GON7 0
595 VPS21 2
719 RNH201, RNH202 0
718 HHT1 0
715 SPT21 3
714 OPY2 0
713 PCL5 0
712 PLM2 0
711 NTO1, YLR455W, SAS3 0
298 NAP1, HTZ1 2
299 SUB1 0
296 SEC28 2
294 SLX8 2
290 CKS1, SIC1, CLB3, CLN2, CLN1, CLB4 0
591 ENT5 0
590 GIS1 0
199 YFR038W 1
599 DDC1 1
197 RAD26 0
191 SLX1 0
270 UBP1 0
272 DSK2 0
274 ELP3, ELP6, ELP4, IKI3, ELP2, IKI1 13
275 ABF1 0
278 ARP4 0
279 MAG1 0
524 SGV1 0
527 PSP1 0
521 SAC1 1
528 MSH5 0
529 SET5 0
449 PAC11 1
443 UBP5 0
441 SKY1 0
447 ARP1 0
446 APN2 0
445 MUD1 0
444 RAD10, YAL027W, RAD1 0
108 UBP7 0
109 FAB1 0
102 UBP2, RSP5 0
101 EDC1 0
104 HHF2 0
39 VPS70 1
38 UNG1 0
33 SAE3 0
32 CST9 0
31 NUM1 1
36 LGE1, BRE1 10
35 CIN4 1
34 VPS8 1
641 TAF7, TAF6, TAF5, TAF4, TAF1, SPT8, UBP8, HFI1, SGF29, SGF73, TAF13, TAF12, TAF9, NGG1, SPT3, SGF11, GCN5 10
640 PZF1 0
642 MSL1 0
645 MON2 1
644 INO4 2
646 HAT1, HHT2, HAT2 0
436 JJJ1 0
437 MSH3 0
435 DEG1 0
432 YOR338W 0
433 DUN1 0
430 SOD1 0
431 CDC10, REV3 0
338 YDL162C 0
335 YTA7 2
334 NUP60 0
337 GET2 7
336 GCR2 1
331 RED1 0
333 HOP1 0
345 WHI2 0
98 RPN4 1
91 RVS161 2
92 UBC11 0
94 RPN2, POL4, RPN6, UBP6, GSG1, ECM29, RPN13, RPN10, HEX3, SEM1 10
97 RBL2 1
740 HCM1 2
741 CLB6 0
559 PDA1 1
558 YKL069W 0
555 CDC5 0
554 MEC3, RAD17 1
556 CLB5 0
550 TOP1 0
553 REB1 0
552 OPI3 3
238 RAD28 0
236 ORM2 0
152 UBC8 0
231 MET18, RAD3 3
232 TEC1 0
230 NTG2 0
1 SIS2 0
155 RGP1, RIC1 20
146 DIN7 0
147 UBC6 0
618 ARX1 0
619 BUB2 1
143 SPT2 1
140 HUR1 0
612 DBR1 0
613 FPR2 0
610 SRP40 2
611 SNT1, HST1, HOS4, HOS2, SET3, SIF2, CPR1 9
616 SSF1 1
617 ARD1 1
614 SPO11 0
149 UBC4, UBC5, UFD4 1
685 NEW1 0
684 PIL1 0
687 MIP1 0
681 ACT1 0
683 HSM3 0
682 PHO80 0
458 RAD24 0
622 SEC66 0
133 HHF1 1
498 CTF8, DCC1 5
135 PAT1, SNU66, LSM6, LSM7, LSM1, KEM1 17
134 REV1 0
495 CCS1 0
139 YBR094W 0
490 RAD2 0
493 RRM3 2
24 SER2 0
25 ASK10 1
26 TFP1 0
27 SER1 0
20 PSY4 0
21 KIP2 0
22 YML119W 1
23 LIF1 0
29 RIS1 0
407 YDR134C 1
406 TPA1 0
404 MAD3 0
401 IES3, IES5, IES4, NHP10, INO80, IES1, IES2, RVB2, RVB1, ARP8, TAF14 6
409 UFD2 0
408 BUD13, CWC21 0
378 TFA2 0
371 THR1 0
370 OGG1 0
373 ESC8 0
374 LHP1, BEM2 0
709 JIP4 0
705 TEL1, ECM5, DYN1, MAC1 0
700 PTI1, PTA1, SSU72 0
701 YCK3 0
702 SAP155 1
703 RPC40, RPC34, RPA14, RET1, RPA34, RPA43, RPC11, RPC25, RPC31, RPA190, RPA49, RPO26 1
393 SKI8, SKI3, SKI2, YKL023W 4
392 YJL181W 0
391 HDA1 0
89 UBC13, MMS2 0
396 BUG1 0
395 YHL039W 0
394 TMA22 0
82 RIF1 0
399 ATP11, CDC36 0
81 RIF2 0
586 KEX2 1
587 CDC26 0
584 SWE1 0
585 MSC1 0
582 YJR119C 0
583 HST2 0
581 IOC3, NHP6B, ISW2, ITC1 2
245 ASE1 0
244 CHL1 2
247 EST1 0
241 REV7 0
240 YPL113C 1
243 LEM3 0
242 AHC1, NUP84 4
249 MAD2, MAD1 10
248 YRM1 0
519 HRB1, RLR1, GBP2, TEX1, MFT1, THP2 2
518 UBA3 1
511 TOF1, CSM3 13
510 CSM1 0
512 SRC1 2
514 MEI5, SOY1 0
517 VPS64, HCS1 1
516 ERG3 0
623 RTT101, MMS1 2
459 HSL1 0
621 VID22, TBF1, YGR071C 4
620 REC102 0
627 CIK1 9
626 YKU80 0
625 SNF3 0
624 ELF1 2
450 CDC9 0
451 SAS5, SAS4, SAS2 1
452 RIM4 0
455 YBR255W 0
456 RPB4, RPB3, TFG2, TFG1, DST1, IWR1, RPO21, SPT4 4
457 IOC2, IOC4 0
179 YML090W 0
178 CPR6 0
177 SAE2 0
176 YKR077W 0
172 SHP1, DOA1 5
183 VPS75, RTT109 1
182 RPS11B 0
657 VPH2 0
654 YMR144W 0
655 RAD61 1
652 RAD16 0
653 SEC22 6
184 RTT106 0
651 FKH2 0
185 TRF5, YHP1 0
10 SIZ1 0
14 VID30, FYV10, VID28, GID8, RMD5, YDL176W 2
16 SDC1, SWD3, SPP1, SHG1, SWD2, BRE2, SWD1 10
103 ERG6 0
323 MEK1 0
320 RAD54 0
327 MUB1, RAD18, RAD6 2
325 SGO1 3
329 RAD5 0
201 YBR030W 0
200 RAD59 0
203 MSI1, RLF2, CAC2 2
202 DOT6 0
205 PFD1, PAC10, YKE2, GIM5, GIM4, GIM3, BUD27 53
207 RTT105 1
206 YNL224C 0
208 MOT2 0
77 YPT6 6
76 DOT5 0
74 CIN2 3
71 IRA2 2
70 BCK2 0
78 MMS22 0
668 PHO23, SAP30, RCO1, CTI6, UME1, UME6, RXT2, RXT3, SIN3, EAF3, DEP1, RPD3, SDS3 45
662 EDC2 0
660 PAC1 0
692 MUS81, MMS4 3
693 SLM3 0
690 ARO1, ILV1, GCN1, GCN20, SAM1, TUB3 1
691 YER030W 0
697 VID21, CIN8, YNG2, EAF5, EAF6, EAF7 2
694 MIH1 0
695 DNL4 0
698 REP1 0
699 MDM35 1
543 RAD7, ELC1 0
540 RTG2 0
541 CLB1 0
546 MGS1 0
547 TDP1 0
544 APQ12 4
545 HST3 0
549 GAL4 0
258 PEX22 0
120 TPP1 0
121 TSA1 2
122 UBP12 0
123 ALB1 0
126 RAD14 0
128 BUL2 0
129 UBI4 0
414 MLH3 0
415 FUN30 1
416 SAP190, SAP185 0
413 MRC1 2
418 BIM1 7
319 VAM3 2
318 REC8 0
312 RPH1 0
310 RDH54 0
317 YUH1 0
316 RNH1 0
314 HHO1 0
3 SSD1, RRD1, PSY2, PPH3 1
368 RAS2 0
369 HTL1, RSC58, RSC1, RSC2, RSC6, RSC8, RSC9, HTA1, RTT102 4
366 CLN3 0
367 EXO1 0
364 RUB1 0
365 VRP1, SLA1 3
362 ESC2 0
363 YML011C, YDR314C, RAD4, RAD23 0
360 SUS1 1
382 UBR2 1
383 HPR5 1
384 DMA1 0
385 LRP1, RRP6 4
386 UBR1 0
387 UBP15 0
388 TFB1, SSL1 0
389 TFB2 0
579 MSN5 0
578 REC107 0
573 RAD57 0
572 OAF1 1
571 ZRT1 0
577 SPN1 2
576 ACK1 0
60 YOR024W 0
62 GTR1 1
259 SIR1, DBF4 0
65 REI1 2
66 QRI8 0
67 STB5 0
68 SLK19 0
69 SPT23, RPN14 0
250 SWM1, MND2, APC9 0
251 MND1 0
256 BUL1 0
730 ASR1 0
733 ISC1 0
732 YPL150W 0
734 YBL036C 0
737 PSO2 0
736 CSF1 3
739 CTF3, MCM16, MCM21, CHL4, MCM22, CTF19, IML3 9
507 SET7 0
504 ERV46 0
505 CHK1 0
502 SET6 0
503 RNR3 0
500 AHA1 0
630 PSH1 0
631 HOP2 0
632 MON1 0
633 RAP1 1
634 PAC2, CIN1 3
637 DAL81 0
638 RAD51 0
639 RAD50 0
467 BLM10 0
466 HTA2 0
461 DPB4, DPB3 0
169 SPF1 2
164 CLB2 0
165 VIK1 1
166 RAD55 0
160 RMI1 1
161 RAI1, RTT103 1
163 YCR076C, PRE9, UMP1 3
439 MRE11, DMC1, XRS2 1
649 KAR3 4
356 NDJ1 0
355 SRO9 2
354 HPC2, HIR3, HIR2, HIR1, ASF1, RAD53 11
351 UBC12 0
359 SFP1 0
216 GET1 5
217 NHP6A 1
214 THI6 0
215 DOT1 0
211 SBA1 0
219 YLR247C 0
4 PSY3 0
281 THP1, SAC3 6
283 MGM101, RIM1, RFA1, MSH2, TOP3, SGS1, MPH1, MSH6, RAD52, RFA2 8
282 YJR087W 1
284 SLX4 0
286 YKU70 0
674 DPB11 1
676 HST4 0
677 BUB1, BUB3 8
670 MUM2 0
672 SCS7 1
673 CHD1, CKA1, CKA2, CDC73, PAF1, LEO1, CTR9, RTF1, CKB1, CKB2, POB3 12
260 RDI1 0
267 YLR218C 0
265 HOS1 0
268 HOS3 0
58 SAN1 0
55 IST3 0
57 CST6 0
51 PDC1 0
50 ZIP2 0
53 SAM37 0
52 TCO89 0
536 PHR1 0
535 HMT1 0
534 MSH1 0
533 MSH4 0
531 CLA4 1
530 BMH1 1
539 RTG3, RTG1 0
115 GAL11, MED4, SSN2, SSN3, SIN4, SOH1, SSN8, ROX3, MED2, MED11, MED1, NUT1, PGD1, CSE2, MED8, SRB2, SRB8 21
114 UBP9 0
117 APN1 0
116 UBP13 0
111 RAD27, DDR48 0
119 NOP6 0
429 PPH22, RTS1, RRD2, ZDS2, ZDS1, PPH21 0
428 SNF5, SNF11, SWI3 2
421 YHR151C 0
420 HUL4 0
425 MBP1, SWI4, SWI6 7
424 UBP3, BRE5 10
426 SWI5 1
308 YPL033C 0
309 MMR1 1
307 TOS2 0
568 PRP18 0
569 RTT107 0
561 HFM1 0
562 HTB2 0
563 RPL16A 0
564 ERG5 0
565 CAF130, CAF40 0
567 SWC7, SWC5, SWC3, YAF9, ARP6, VPS71, SWR1, VPS72 47
506 SET4 0
229 BFA1 1
738 NUP133 2
227 BDF2 0
226 RIM21 0
223 PBP4 0
222 URA5 0
220 NTG1 0
88 YNR048W 0
726 BIK1 0
727 ISW1 0
724 SNF4, SNF1, RAD30, GAL83 1
390 UBP11 0
722 FUS3 2
728 TAH1, PIH1 0
729 BRF1 0
150 REC114 0
606 PMS1, MLH2, MLH1 0
601 KAR9 0
603 YMR003W 0
156 NEJ1 0
159 PRI1 4
609 SRL2 1
608 MCK1, LTE1 0
48 CTF4 2
49 TOF2 0
47 CPR7 0
45 MKT1 0
40 YML030W 0
5 FPR3, FPR4 0
464 REC104 0
487 YLR278C 0
486 MNN11, MNN10 4
485 RAD9 0
483 YBL086C 1
482 TIM18 1
481 SET2 1
472 RFC5, RFC4, RFC1, RFC3, CTF18, ELG1 8
473 TMA20 0
471 SUR1 1
476 KIP3 0
474 COG8 1