Supplementary material for "A Plasma Membrane E-MAP Reveals Links Between the Eisosome, Sphingolipid Metabolism and Endosomal Trafficking"

Supplemenatry material for "A Plasma Membrane E-MAP Reveals Links Between the Eisosome, Sphingolipid Metabolism and Endosomal Trafficking"

Pablo S. Aguilar^1,#, Florian Fröhlich^2,#, Michael Rehman^2,#, Mike Shales^3,#, Igor Ulitsky⁵, Agustina Olivera-Couto¹, Ron Shamir⁵, Peter Walter⁷, Matthias Mann⁴, Christer S. Ejsing⁶, Nevan J. Krogan^3, Tobias C. Walther^2
¹ Institut Pasteur de Montevideo, Uruguay
² Max Planck Institute of Biochemistry, Organelle Architecture and Dynamics, Martinsried, Germany
³ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
⁴ Max Planck Institute of Biochemistry, Proteomics and Signal Transduction, Martinsried, Germany
⁵ The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
⁶ University of Southern Denmark, Department of Biochemistry and Molecular Biology, Odense, Denmark
⁷ Department of Biochemistry and Biophysics, University of California and Howard Hughes Medical Institute, San Francisco, CA, USA
# These authors contributed equally
* Correspondence to:
Nevan Krogan
Department of Cellular and Molecular Pharmacology
University of California, San Francisco
krogan@cmp.ucsf.edu or
Tobias C. Walther
Max Planck Institute of Biochemistry
Organelle Dynamics and Architecture
Germany
twalther@biochem.mpg.de

Modules obtained using the PPI network (click module name for details):

Module	Genes	Average S-score profile correlation	Density of protein-protein interactions
Module 1	PEX1, PEX15, PEX6	0.584	0.667
Module 2	CAP1, SLA1, BCK1, ARC18, BEM3, EDE1, RVS167, CLA4, SMY1, SYP1, ABP1, BBC1, BNR1, CAP2, MYO5, TWF1, BZZ1, SLT2	0.241	0.124
Module 3	YGL079W, YLR408C, YKL061W	0.254	1.000
Module 4	YPT53, VPS21, YPT52	0.273	1.000
Module 5	RTG1, RTG3	0.583	1.000
Module 6	SNC1, SRO7, SYN8	0.205	0.667
Module 7	PEP5, VPS8, CCZ1, VPS41, YPT7	0.257	0.400
Module 8	SRN2, MVB12	0.557	1.000
Module 9	CDC50, DRS2	0.526	1.000
Module 10	ERG2, ERG3, ERG6, ERG5	0.265	0.500
Module 11	HOG1, PBS2, SSK1, SSK22	0.305	0.500
Module 12	TCB3, TCB2	0.489	1.000
Module 13	MON2, ARL1	0.517	1.000
Module 14	ARL3, SYS1	0.862	1.000
Module 15	APL5, APM3	0.703	1.000
Module 16	VPS5, VPS35, PEP8, VPS17, VPS29	0.534	1.000
Module 17	ARF1, TLG2, SNC2, YPT31	0.288	0.500
Module 18	COG6, COG8, COG7, COG5	0.873	1.000
Module 19	LAC1, SUR2, LAG1, DPL1, LCB3, FEN1, SUR4, LCB4	0.259	0.536

Modules obtained without using the PPI network (click module name for details):

Module	Genes	Average correlation	Density of protein-protein interactions
Module 1	GUP1, SLA1, BEM3, SKN7, EDE1, SMY1, VPS64, SYP1, BNR1, CHS6, VPS9, AKR1, PEX15, PEX6, CAP1, ERG4, VPS27, ARC18, BSP1, PEX1, ADH1, CLA4, FPS1, HKR1, ECM33	0.274	0.030
Module 2	CHS1, ISC1, SCH9, BRO1	0.225	0.000
Module 3	RVS161, SAC6, PMP3, RVS167	0.336	0.167
Module 4	TAT2, YOL019W, PLB3, PDR5	0.191	0.000
Module 5	SUR7, MSB3, YGL079W, PRM8, JSN1, GIM4, GGA1, ABP1, BBC1, CAP2, MYO5, YPT35, TWF1, AIP1, YLR408C, BZZ1	0.235	0.033
Module 6	GPA2, MDG1, CCH1, GSC2, LRO1, CMP2, PDR12, MID2, YBP2, CIS3, YKL061W, BUL1	0.218	0.000
Module 7	ARN2, BRE4, MRH1, DUR3, RAD1, SIP2, GPB2, CHC1, MID1, JJJ1, PBS2, ARN1, VPS33	0.236	0.000
Module 8	VPS5, MKS1, RTG1, BCH2, PEP12, VAC8, RTG3, RTG2, KEM1, ALP1, COG1	0.260	0.036
Module 9	SIT1, HAC1, ERG2, ATG18	0.182	0.000
Module 10	RAS1, YPT53, ENT3, VPS21, CCZ1, SYN8, YMR031C, YPT7, MVB12, TAT1, SRN2, ARF3, YPT52	0.286	0.064
Module 11	PIL1, INP51, EMP70, COS10, YSR3, ERG6	0.255	0.000
Module 12	SNC1, SNQ2, GCS1	0.256	0.000
Module 13	YCK3, ELM1, RGD1, WHI2	0.218	0.000
Module 14	ARK1, SPO14, KIN2, EXG1, WSC4, SHO1, BOI1	0.228	0.048
Module 15	GPB1, SVL3, SSU1, GAP1, YTA6	0.205	0.000
Module 16	GPG1, SKM1, GPR1	0.219	0.000
Module 17	YNL086W, IPT1, HOG1, ENT4, SKN1, SSK1, ERP1, CRZ1, ATO3, RAS2, SUR1, LCB4	0.245	0.000
Module 18	LCB5, TCB3, TCB2, WSC3, SIW14, ROM1	0.200	0.067
Module 19	GOT1, ENT5, ARL1, SWA2, VPS17, RIC1, SYS1, VPS13, TLG2, SCS7, SAC1, GET3, VPS29, MON2, VPS8, SNC2, GET1, VPS35, TPM1, ARL3, PEP8, YPT31, APL5, APM3, SFT2	0.381	0.040
Module 20	CDC50, ARF1, COG6, COG8, INP53, DRS2, COG7, PIB2, COG5, PER1, ERG3, GYL1	0.288	0.106
Module 21	SES1, HSE1, STV1, YBR108W	0.355	0.000
Module 22	PRM9, GYP5, DAL5	0.269	0.000
Module 23	KIN1, MTL1, ENB1, SLI1, UBC5	0.185	0.000
Module 24	PSR2, HOR7, YPS3, FUI1, YBR016W	0.217	0.000
Module 25	QDR3, ASK10, HXT2, CRN1, GAL2, ATG8, STD1, ASG7, RSR1, TOR1, TGS1, YHL044W	0.205	0.000
Module 26	TRE1, NCR1, PMA2, NHA1, SST2, MKK2	0.225	0.000
Module 27	LSB5, ROD1, AKR2, RSB1	0.275	0.000
Module 28	ERS1, HXT10, BIO5	0.240	0.000
Module 29	TSC10, FAT1, LAG1, DPL1, VPS4	0.232	0.100
Module 30	SEM1, PKH3, SUR2, LCB3, LEM3, FEN1, SUR4, ROM2, ERG5, FKS1	0.272	0.067
Module 31	CSG2, SRO7, YAP1801, ALR2	0.173	0.000
Module 32	YAP1802, IMH1, SPS22	0.222	0.000
Module 33	THI7, QDR1, CNA1, YLR073C	0.186	0.000
Module 34	YGR266W, YOR1, YIR044C, ENT2	0.277	0.000
Module 35	YEH2, EHD3, GEF1, AIF1, OSH2, YDL012C	0.263	0.000
Module 36	PEX11, SMF1, FTR1, SSK22	0.200	0.000