Supplemental Table S3: GO term enrichment analysis of proteins carrying potential TORC1 and Atg1 regulated phosphosites. Enriched GO terms and associated genes are listed (see Figure 2C for visualization).

GOID	GOTerm	Ontology Source	Term PValue	Term PValue Corrected with Bonferroni step down	Group PValue	Group PValue Corrected with Bonferroni step down	GOLevels	GOGroups	% Associated Genes	Nr. Genes	Associated Genes Found
TORC1 regulated sites											
GO:0016310	phosphorylation	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	[5]	Group00	11.08	46.00	"[ALK1, ATG1, ATG13, BCK1, CDC19, DBF20, GAL83, GCN2, GLK1, HAL5, HOM6, HRK1, KCS1, KKQ8, KSP1, LCB5, LRE1, MSG5, NPR1, NUP42, PDA1, PFK1, PFK26, PGI1, PGK1, PRK1, PRS1, PSK1, PYK2, RCK2, SAK1, SCH9, SIP1, SKY1, SNT1, STE11, TDA1, TDH1, TDH2, TDH3, TPI1, URK1, UTR1, VAC7, YEF3, YPK3]"
GO:0071417	cellular response to organonitrogen compound	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.04	0.00	0.00	"[4, 5]"	Group01	27.27	6.00	"[DAL80, GAT1, GCN2, GLN3, GZF3, UME6]"
GO:0006468	protein phosphorylation	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.02	0.00	0.00	"[6, 7]"	Group02	10.83	26.00	"[ALK1, ATG1, ATG13, BCK1, DBF20, GAL83, GCN2, HAL5, HRK1, KKQ8, KSP1, LRE1, MSG5, NPR1, PRK1, PSK1, RCK2, SAK1, SCH9, SIP1, SKY1, SNT1, STE11, TDA1, YEF3, YPK3]"
GO:0006915	apoptotic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.02	0.00	0.00	[5]	Group03	23.53	8.00	"[BIR1, DRE2, MCA1, POR1, STM1, TDH2, TDH3, VAC7]"
GO:0007584	response to nutrient	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.05	0.00	0.00	"[3, 5]"	Group04	15.94	11.00	"[ADR1, BCK1, DAL80, GAT1, GLN3, GZF3, HAP1, MIG1, PDR3, STB3, UME6]"
GO:0048523	negative regulation of cellular process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[2, 3, 4]"	Group05	10.20	62.00	"[ADF1, ADR1, AFT1, AMN1, ASH1, BIR1, BNR1, CCR4, DAL80, DDC1, DOT6, DRE2, EAP1, FAR11, FPR3, FRA1, GCN2, GZF3, HAP1, HSF1, IFH1, IRA2, KSP1, LRE1, MAF1, MCM2, MED1, MIG1, MKS1, MPH1, MSG5, NGR1, NOT3, NPR1, NPR2, OPI1, PAT1, PPH21, PPH22, PSK1, REG1, ROM2, RPH1, RRM3, SAC7, SCP160, SET2, SIR4, SKO1, SNT1, SOD1, SPC105, SPT23, SPT5, SRS2, SSA1, SSA2, STM1, UME6, URA2, VAC7, YEF3]"
GO:0051049	regulation of transport	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[3, 4]"	Group06	15.93	18.00	"[AFT1, ALY2, BRE5, CCH1, GYP1, MSG5, NPR1, PEF1, PEP5, POR1, PRK1, RGC1, ROD1, ROM2, SKY1, UBR1, UPC2, VPS8]"
GO:0060627	regulation of vesicle-mediated transport	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.04	0.00	0.00	"[3, 4, 5]"	Group07	17.54	10.00	"[ALY2, BRE5, GYP1, NPR1, PEF1, PEP5, PRK1, ROD1, ROM2, VPS8]"
GO:0010447	response to acidic pH	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	[4]	Group08	42.86	6.00	"[BCK1, CUP2, GCN2, HAA1, MAC1, WAR1]"
GO:0071467	cellular response to pH	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	[4]	Group08	40.00	6.00	"[CUP2, FRT1, GCN2, HAA1, MAC1, WAR1]"
GO:0010646	regulation of cell communication	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.02	0.00	0.00	"[3, 4]"	Group09	13.14	18.00	"[BCK1, BIR1, FAR11, GCN2, GEA2, HSF1, IRA2, LST4, MSG5, MTC5, NPR2, ROD1, ROM2, RTC1, SAC7, SEA4, SNT1, STE11]"
GO:1902531	regulation of intracellular signal transduction	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[4, 5, 6]"	Group09	17.72	14.00	"[BCK1, GEA2, HSF1, IRA2, LST4, MSG5, MTC5, NPR2, ROM2, RTC1, SAC7, SEA4, SNT1, STE11]"
GO:0031929	TOR signaling	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.01	0.00	0.00	"[5, 6]"	Group10	23.08	9.00	"[HSF1, KSP1, LST4, MTC5, NPR2, RTC1, SEA4, STM1, TCO89]"
GO:0032006	regulation of TOR signaling	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.01	0.00	0.00	"[5, 6, 7]"	Group10	37.50	6.00	"[HSF1, LST4, MTC5, NPR2, RTC1, SEA4]"
GO:0007165	signal transduction	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[3, 4]"	Group11	11.72	43.00	"[ADF1, ALK1, BCK1, BIR1, BOI2, DBF20, FAR11, GAL83, GEA2, HAL5, HRK1, HSF1, IRA2, KKQ8, KSP1, LCB5, LST4, MKS1, MRS6, MSG5, MTC5, NPR1, NPR2, OPI1, RCK2, ROD1, ROM2, RTC1, RTG1, RTG3, SAC7, SCH9, SCP160, SEA4, SIP1, SNT1, STE11, STM1, SYG1, TCO89, VTC2, VTC3, YPK3]"
GO:0035556	intracellular signal transduction	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[4, 5]"	Group11	12.50	30.00	"[ALK1, BCK1, BOI2, DBF20, GEA2, HAL5, HRK1, HSF1, IRA2, KKQ8, KSP1, LCB5, LST4, MRS6, MSG5, MTC5, NPR1, NPR2, ROM2, RTC1, SAC7, SCH9, SEA4, SNT1, STE11, STM1, TCO89, VTC2, VTC3, YPK3]"
GO:0036464	cytoplasmic ribonucleoprotein granule	GO_CellularComponent-GOA_17.11.2016_10h53	0.00	0.01	0.00	0.00	"[4, 5, 6, 7, 8]"	Group12	13.43	18.00	"[BRE5, CCR4, EAP1, GIS2, GUS1, KSP1, LEU1, NGR1, NOT3, PAT1, PPH21, PRS1, PSP1, RPG1, SAM1, SAM2, SYH1, YEF3]"
GO:0010494	cytoplasmic stress granule	GO_CellularComponent-GOA_17.11.2016_10h53	0.00	0.05	0.00	0.00	"[5, 6, 7, 8, 9]"	Group12	14.29	13.00	"[EAP1, GIS2, GUS1, KSP1, LEU1, NGR1, PAT1, PPH21, PRS1, RPG1, SAM1, SAM2, YEF3]"
GO:0005773	vacuole	GO_CellularComponent-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[4, 5, 6, 7]"	Group13	11.11	34.00	"[ATG1, AVT1, AVT3, AVT4, GNP1, LST4, MAM3, MNR2, MTC5, NPR2, PEP5, PIB2, REG1, RTC1, SCH9, SEA4, SIP1, SSA1, SSA2, TAT1, TCO89, VAC17, VAC7, VHC1, VMA1, VTC2, VTC3, YCF1, YDL180W, YDR089W, YGR125W, YNL058C, YPK9, ZRT3]"
GO:0005774	vacuolar membrane	GO_CellularComponent-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[3, 4, 5, 6, 7, 8, 9]"	Group13	13.72	31.00	"[ATG1, AVT1, AVT3, AVT4, LST4, MAM3, MNR2, MTC5, NPR2, PEP5, PIB2, RTC1, SCH9, SEA4, SIP1, SSA1, SSA2, TCO89, VAC17, VAC7, VHC1, VMA1, VTC2, VTC3, YCF1, YDL180W, YDR089W, YGR125W, YNL058C, YPK9, ZRT3]"
GO:0000324	fungal-type vacuole	GO_CellularComponent-GOA_17.11.2016_10h53	0.00	0.02	0.00	0.00	"[6, 7, 8, 9]"	Group13	11.62	23.00	"[AVT1, AVT3, AVT4, MNR2, MTC5, NPR2, PEP5, RTC1, SCH9, SEA4, SIP1, SSA1, SSA2, TCO89, VAC17, VAC7, VMA1, VTC2, VTC3, YCF1, YDR089W, YPK9, ZRT3]"
GO:0048584	positive regulation of response to stimulus	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[2, 3, 4]"	Group14	21.05	12.00	"[BCK1, GCN2, LST4, MIG1, MTC5, NPR2, PDR3, RTC1, SEA4, SNT1, STE11, UPC2]"
GO:0010647	positive regulation of cell communication	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.02	0.00	0.00	"[3, 4, 5]"	Group14	20.45	9.00	"[BCK1, GCN2, LST4, MTC5, NPR2, RTC1, SEA4, SNT1, STE11]"
GO:1902533	positive regulation of intracellular signal transduction	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.04	0.00	0.00	"[4, 5, 6, 7]"	Group14	24.14	7.00	"[BCK1, LST4, MTC5, RTC1, SEA4, SNT1, STE11]"
KEGG:00010	Glycolysis / Gluconeogenesis	KEGG_18.11.2016	0.00	0.00	0.01	0.01	[-1]	Group15	22.41	13.00	"[ADH1, ADH2, CDC19, GLK1, PDA1, PFK1, PGI1, PGK1, PYK2, TDH1, TDH2, TDH3, TPI1]"
GO:0032787	monocarboxylic acid metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.04	0.01	0.01	"[6, 7]"	Group15	11.35	21.00	"[ACP1, ADH1, ADR1, ATG26, CDC19, CIT2, DAL7, FAS2, GLK1, OPI1, PDA1, PFK1, PGI1, PGK1, PYK2, SPT23, TDA9, TDH1, TDH2, TDH3, TPI1]"
GO:0009161	ribonucleoside monophosphate metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.04	0.01	0.01	"[6, 7, 8]"	Group15	12.18	19.00	"[ADH1, AMD1, ATP3, CDC19, GLK1, NUP42, PDA1, PFK1, PGI1, PGK1, PRS1, PYK2, TDH1, TDH2, TDH3, TPI1, URA2, URK1, VMA1]"
GO:0009199	ribonucleoside triphosphate metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.04	0.01	0.01	"[6, 7, 8]"	Group15	13.01	16.00	"[ADH1, ATP3, CDC19, GLK1, NUP42, PDA1, PFK1, PGI1, PGK1, PYK2, TDH1, TDH2, TDH3, TPI1, URK1, VMA1]"
GO:0006090	pyruvate metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.01	0.01	"[7, 8]"	Group15	22.64	12.00	"[ADH1, CDC19, GLK1, PDA1, PFK1, PGI1, PGK1, PYK2, TDH1, TDH2, TDH3, TPI1]"
GO:0046496	nicotinamide nucleotide metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.01	0.01	0.01	"[6, 7, 8, 9]"	Group15	15.73	14.00	"[ADH1, ADH2, CDC19, GLK1, PDA1, PFK1, PGI1, PGK1, PYK2, TDH1, TDH2, TDH3, TPI1, UTR1]"
GO:0046031	ADP metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.01	0.01	"[7, 8, 9, 10]"	Group15	27.91	12.00	"[ADH1, CDC19, GLK1, PDA1, PFK1, PGI1, PGK1, PYK2, TDH1, TDH2, TDH3, TPI1]"
GO:0010604	positive regulation of macromolecule metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[3, 4, 5]"	Group16	10.06	50.00	"[ADR1, AFT1, ASH1, ATG13, AZF1, BCK1, BUL1, CAF130, CCR4, CUP2, CWC2, EFT1, GAT1, GCN2, GIS2, GLN3, GZF3, HAA1, HAL1, HAP1, HSF1, IFH1, LYS14, MAC1, MBP1, MED1, MIG1, NAP1, NOT3, OPI1, PDR3, ROD1, RPH1, RTG1, RTG3, SCH9, SET2, SFP1, SIR4, SKO1, SNT1, SOD1, SPT23, SPT5, SRS2, STB3, STE11, UME6, UPC2, WAR1]"
GO:0031325	positive regulation of cellular metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[3, 4, 5]"	Group16	10.12	52.00	"[ADR1, AFT1, ASH1, ATG13, AZF1, BCK1, BUL1, CAF130, CCR4, CUP2, CWC2, EFT1, GAT1, GCN2, GIS2, GLN3, GZF3, HAA1, HAL1, HAP1, HSF1, IFH1, LYS14, MAC1, MBP1, MED1, MIG1, NAP1, NOT3, OPI1, OSH3, PDR3, ROD1, RPH1, RTG1, RTG3, SCH9, SET2, SFP1, SIR4, SKO1, SNT1, SOD1, SPT23, SPT5, SRS2, STB3, STE11, UME6, UPC2, VAC7, WAR1]"
GO:0051173	positive regulation of nitrogen compound metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[3, 4, 5]"	Group16	10.21	44.00	"[ADR1, AFT1, ASH1, AZF1, BUL1, CAF130, CCR4, CUP2, CWC2, EFT1, GAT1, GCN2, GIS2, GLN3, GZF3, HAA1, HAL1, HAP1, HSF1, IFH1, LYS14, MAC1, MBP1, MED1, MIG1, NAP1, NOT3, OPI1, PDR3, RPH1, RTG1, RTG3, SCH9, SFP1, SIR4, SKO1, SOD1, SPT23, SPT5, SRS2, STB3, UME6, UPC2, WAR1]"
GO:0010628	positive regulation of gene expression	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[4, 5, 6]"	Group16	10.80	43.00	"[ADR1, AFT1, ASH1, AZF1, BUL1, CAF130, CCR4, CUP2, CWC2, EFT1, GAT1, GCN2, GIS2, GLN3, GZF3, HAA1, HAL1, HAP1, HSF1, IFH1, LYS14, MAC1, MBP1, MED1, MIG1, NAP1, NOT3, OPI1, PDR3, RPH1, RTG1, RTG3, SCH9, SFP1, SIR4, SKO1, SOD1, SPT23, SPT5, STB3, UME6, UPC2, WAR1]"
GO:0031328	positive regulation of cellular biosynthetic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[4, 5, 6]"	Group16	10.31	43.00	"[ADR1, AFT1, ASH1, AZF1, BUL1, CAF130, CCR4, CUP2, EFT1, GAT1, GCN2, GIS2, GLN3, GZF3, HAA1, HAL1, HAP1, HSF1, IFH1, LYS14, MAC1, MBP1, MED1, MIG1, NAP1, NOT3, OPI1, PDR3, RPH1, RTG1, RTG3, SCH9, SFP1, SIR4, SKO1, SOD1, SPT23, SPT5, STB3, UME6, UPC2, VAC7, WAR1]"
GO:0045935	positive regulation of nucleobase-containing compound metabolic process	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[4, 5, 6]"	Group16	10.65	41.00	"[ADR1, AFT1, ASH1, AZF1, BUL1, CAF130, CCR4, CUP2, CWC2, GAT1, GLN3, GZF3, HAA1, HAL1, HAP1, HSF1, IFH1, LYS14, MAC1, MBP1, MED1, MIG1, NAP1, NOT3, OPI1, PDR3, RPH1, RTG1, RTG3, SCH9, SFP1, SIR4, SKO1, SOD1, SPT23, SPT5, SRS2, STB3, UME6, UPC2, WAR1]"
GO:0045893	"positive regulation of transcription, DNA-templated"	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[5, 6, 7, 8, 9, 10, 11]"	Group16	11.17	39.00	"[ADR1, AFT1, ASH1, AZF1, BUL1, CAF130, CCR4, CUP2, GAT1, GLN3, GZF3, HAA1, HAL1, HAP1, HSF1, IFH1, LYS14, MAC1, MBP1, MED1, MIG1, NAP1, NOT3, OPI1, PDR3, RPH1, RTG1, RTG3, SCH9, SFP1, SIR4, SKO1, SOD1, SPT23, SPT5, STB3, UME6, UPC2, WAR1]"
GO:0006357	regulation of transcription from RNA polymerase II promoter	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[6, 7, 8, 9, 10, 11]"	Group16	10.54	49.00	"[ADF1, ADR1, AFT1, ARP4, ASH1, AZF1, BUL1, CAF130, CCR4, CUP2, DAL80, DOT6, FRA1, GAT1, GLN3, GVP36, GZF3, HAA1, HAL1, HAP1, HSF1, IFH1, IKI3, LYS14, MAC1, MAF1, MBP1, MED1, MIG1, MKS1, NAP1, NOT3, OPI1, PDR3, REG1, RPH1, RTG1, RTG3, SCH9, SFP1, SKO1, SOD1, SPT23, SPT5, STB3, TOD6, UME6, UPC2, WAR1]"
											
Atg1 regulated sites											
GO:0043624	cellular protein complex disassembly	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	[6]	Group0	11.76	6.00	"[DBP5, ECM32, NUP2, SSA1, SUP35, YEF3]"
KEGG:04140	Autophagy	KEGG_18.11.2016	0.00	0.00	0.00	0.00	[-1]	Group1	41.18	7.00	"[ATG1, ATG11, ATG13, ATG16, VAC8, VPS30, VPS34]"
GO:0007033	vacuole organization	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	[4]	Group2	15.63	15.00	"[ATG1, ATG11, ATG13, ATG16, ATG2, ATG21, ATG23, ATG9, ENO1, IVY1, TPM1, VAC8, VPS30, VTC2, VTI1]"
GO:0034497	protein localization to pre-autophagosomal structure	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[5, 6, 7]"	Group3	55.56	5.00	"[ATG11, ATG13, ATG21, ATG23, ATG9]"
GO:0042144	"vacuole fusion, non-autophagic"	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[4, 5, 6]"	Group4	11.90	5.00	"[ENO1, IVY1, VAC8, VTC2, VTI1]"
GO:0042147	"retrograde transport, endosome to Golgi"	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[5, 6]"	Group5	18.92	7.00	"[ATG20, SNX41, VPS17, VPS30, VPS35, VTI1, YPT32]"
GO:1903008	organelle disassembly	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[4, 5]"	Group6	21.43	12.00	"[ATG1, ATG11, ATG13, ATG16, ATG2, ATG20, ATG21, ATG29, ATG33, ATG9, SSA1, WHI2]"
GO:0000422	mitophagy	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[3, 6, 7]"	Group6	30.56	11.00	"[ATG1, ATG11, ATG13, ATG16, ATG2, ATG20, ATG21, ATG29, ATG33, ATG9, WHI2]"
GO:0000045	autophagosome assembly	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[5, 6]"	Group7	32.14	9.00	"[ATG1, ATG11, ATG13, ATG16, ATG2, ATG21, ATG23, ATG9, VPS30]"
GO:0000407	pre-autophagosomal structure	GO_CellularComponent-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[4, 5, 6, 7]"	Group7	30.23	13.00	"[ATG1, ATG11, ATG13, ATG16, ATG2, ATG20, ATG21, ATG23, ATG29, ATG9, IRS4, VPS30, VPS34]"
GO:0034045	pre-autophagosomal structure membrane	GO_CellularComponent-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[3, 4, 5, 6, 7, 8]"	Group7	34.62	9.00	"[ATG1, ATG11, ATG16, ATG2, ATG20, ATG21, ATG23, ATG9, VPS30]"
GO:0006623	protein targeting to vacuole	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[5, 6, 7, 8]"	Group7	13.64	15.00	"[ATG1, ATG11, ATG13, ATG16, ATG2, ATG20, ATG21, ATG23, ATG9, HOM3, IRS4, VAC8, VPS13, VPS30, VTI1]"
GO:0032258	CVT pathway	GO_BiologicalProcess-GOA_17.11.2016_10h53	0.00	0.00	0.00	0.00	"[6, 7, 8, 9]"	Group7	23.53	12.00	"[ATG1, ATG11, ATG13, ATG16, ATG2, ATG20, ATG21, ATG23, ATG9, IRS4, VAC8, VPS30]"