RNAi screen result	RNAPII IP (MG132)	CSB IP	CSB IP (MG132)	Chrom.	Chrom. (MG132)	Ubi /Phospo	Ubi /Phospho (MG132)
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Gene name	MGoogle Score	RNAi high	RNAi low	RNAPII-IP (MG132)	CSB-IP	CSB-IP (MG132)	Chrom.	Chrom. (MG132)
WDR45B	1	2.620	-1.430
ATG9A	1	-0.430	0.730					1.551
RB1CC1	0	-0.320	0.680
RB1CC1	0	-0.320	0.680		-1.155	-0.488
GABARAPL2	0	1.830	-0.990
PIK3C3	0	-0.260	0.520
PSEN1	0	0.930	-1.110
ATG16L1	0	0.400	-0.280
RAB23	0	1.290	-1.270				-0.106	0.952
CTSD	0	0.580	-0.790	-0.768		-2.790	-0.655	-1.981
ATG101	0	-0.170	-0.710
ATG4C	0	1.830	-1.180
BECN1	0	0.080	-0.010
RAB15	0	0.710	-0.750		1.641	-1.484	0.560	0.491
RAB1A	0	0.980	-0.460				-0.532
ATG12	0	-0.150	1.370
WIPI2	0	0.250	-0.250
GABARAP	0	-1.090	2.300
ATG13	0	-0.790	0.540	-0.270	0.450	0.139
ULK1	0	0.740	-0.520

Gene name	PTM type	PTM site	UV	UV (MG132)	Sequence
ATG101	Ubiquitylation	K84		-0.706	_VVGEFK(gl)DALR_
ATG12	Ubiquitylation	K116		0.431	_AVGDTPIMK(gl)TK_
ATG12	Ubiquitylation	K118		0.431	_AVGDTPIMK(gl)TK_
ATG16L1	Phosphorylation	S304	-0.317	-1.220	_S(ph)VSSFPVPQDNVDTHPGSGK_
ATG4C	Ubiquitylation	K403	0.208		_ASEEITK(gl)MLK_
ATG9A	Phosphorylation	S18	0.284	0.175	_LEASYSDS(ph)PPGEEDLLVHVAEGSK_
ATG9A	Phosphorylation	S654	-0.181		_S(ph)FSPLQPGQAPTGR_
ATG9A	Phosphorylation	S656	-0.724	-0.246	_SFS(ph)PLQPGQAPTGR_
ATG9A	Phosphorylation	S828	-0.863	-0.673	_HPEPVPEEGS(ph)EDELPPQVHKV_
BECN1	Ubiquitylation	K237		-0.057	_EYSEFK(gl)R_
BECN1	Ubiquitylation	K324		0.066	_MGLK(gl)FQR_
GABARAP	Ubiquitylation	K13	-0.569		_FVYKEEHPFEK(gl)R_
GABARAPL2	Ubiquitylation	K20		-0.292	_CVESAK(gl)IR_
GABARAPL2	Ubiquitylation	K24	-0.237	-0.668	_AK(gl)YPDRVPVIVEK_
PIK3C3	Ubiquitylation	K29		0.271	_IGSLEGK(gl)R_
PIK3C3	Ubiquitylation	K158	-1.333		_VWPNVEADGSEPTK(gl)TPGR_
PIK3C3	Ubiquitylation	K209	-1.012		_EIEMINESEK(gl)R_
PIK3C3	Ubiquitylation	K287		-1.261	_SGPSDHDLK(gl)PNAATR_
PSEN1	Phosphorylation	S313		0.844	_VSKNS(ph)KYNAESTER_
PSEN1	Ubiquitylation	K314	0.016	0.414	_NSK(gl)YNAESTER_
PSEN1	Phosphorylation	S366	-0.340	0.055	_AAVQELSS(ph)SILAGEDPEER_
PSEN1	Phosphorylation	S367	0.005	0.066	_AAVQELSSS(ph)ILAGEDPEER_
RAB15	Ubiquitylation	K163		0.199	_LLLGNK(gl)CDMEAK_
RAB15	Ubiquitylation	K174	-0.188		_VQK(gl)EQADKLAR_
RAB15	Ubiquitylation	K213	-0.059	0.420	_DILLK(gl)SGGR_
RAB1A	Phosphorylation	S2	-0.429	0.634	_(ac)S(ph)SM(ox)NPEYDYLFK_
RAB1A	Phosphorylation	S3	-0.429	0.634	_(ac)S(ph)SM(ox)NPEYDYLFK_
RAB1A	Ubiquitylation	K58	-0.012	-0.593	_TIELDGK(gl)TIK_
RAB1A	Ubiquitylation	K61		-0.593	_TIELDGK(gl)TIK_
RAB1A	Ubiquitylation	K119	0.581	0.444	_YASENVNK(gl)LLVGNK_
RAB1A	Ubiquitylation	K131		0.790	_LLVGNKCDLTTK(gl)K_
RAB1A	Ubiquitylation	K132	-0.154		_LLVGNKCDLTTKK(gl)_
RAB1A	Ubiquitylation	K187	0.229	0.152	_MGPGATAGGAEK(gl)SNVK_
RAB1A	Ubiquitylation	K191	-0.108	0.036	_SNVK(gl)IQSTPVK_
RB1CC1	Phosphorylation	S222	0.084	0.562	_LDS(ph)LPEHEDSEK_
RB1CC1	Phosphorylation	S237	-0.464	-0.874	_S(ph)TELVLSPDM(ox)PR_
RB1CC1	Phosphorylation	T238	-0.376	-0.874	_S(ph)TELVLSPDM(ox)PR_
RB1CC1	Phosphorylation	S257	-0.819		_TTNESLLTS(ph)FPK_
RB1CC1	Phosphorylation	S266		0.766	_SVEHVS(ph)PDTADAESGK_
RB1CC1	Phosphorylation	S624	-0.685	-0.445	_AAQS(ph)LDEM(ox)SQTITDLLSEQK_
ULK1	Phosphorylation	S450	-0.237	-0.173	_NLQS(ph)PTQFQTPR_
ULK1	Phosphorylation	T468	-0.247	0.456	_SGST(ph)SPLGFAR_
ULK1	Phosphorylation	S469	0.035	0.470	_SGSTS(ph)PLGFAR_
ULK1	Phosphorylation	S623	-0.793	-0.874	_NPLPPILGS(ph)PTK_
ULK1	Phosphorylation	T625	-0.547	-0.776	_NPLPPILGSPT(ph)K_
ULK1	Phosphorylation	T636		0.087	_T(ph)PSSQNLLALLAR_
ULK1	Phosphorylation	S638	-0.154	0.598	_TPS(ph)SQNLLALLAR_
WDR45B	Ubiquitylation	K206	0.484		_IATASEK(gl)GTLIR_
WDR45B	Ubiquitylation	K266	-0.455		_NK(gl)QSSLASASFLPK_
WIPI2	Ubiquitylation	K223		-1.289	_LATASEK(gl)GTVIR_
WIPI2	Ubiquitylation	K341		-0.847	_NICSLATIQK(gl)IPR_
WIPI2	Phosphorylation	S413	0.225	0.402	_GTYVPSS(ph)PTR_
WIPI2	Phosphorylation	T415	0.157		_GTYVPSSPT(ph)R_