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)
VTI1B	1	0.710	-0.320
CHMP4B	1	0.110	0.340
VPS33A	1	1.740	-0.870					0.283
ARL8A	1	-1.930	3.380
LAMTOR1	1	0.700	-0.850	0.343			0.382
CHMP4C	1	-1.280	1.910
VPS33B	1	0.750	-0.120
ATG9A	1	-0.430	0.730					1.551
LAMP2	0	-0.040	0.180				0.379	0.711
LAMP2	0	-0.040	0.180	0.164
STARD3NL	0	-0.110	0.450					-0.395
TSG101	0	0.060	-0.480
PLD1	0	-0.150	-0.140
RNF13	0	-0.590	0.720
RNF13	0	0.180	-0.460
CHMP2B	0	-0.500	1.180
MICALL1	0	1.820	-1.320				0.010	-0.796
VPS18	0	-0.130	-0.260				-0.775	-0.482
TMEM106B	0	-0.240	-0.310
PIKFYVE	0	-0.230	0.410
TMEM59	0	1.350	-0.820
TMEM9	0	-0.200	0.950					-0.690
OSBPL9	0	-0.180	-0.250	0.139			0.339	-0.315
VAMP8	0	0.400	-0.770
VPS4B	0	-0.670	1.580
VAMP7	0	0.400	0.320				0.660	-0.175
CHMP2A	0
VPS4A	0			-1.530				-0.566
ARL8B	0	0.400	-0.100	0.105			0.781	-0.457
TMEM165	0	-1.210	2.320
CD63	0	-1.190	1.800				1.412	0.887
NPC1	0	0.620	-0.700				0.275	0.103
MVB12A	0	0.740	-0.730
RHOB	0	0.130	-0.210
OSBPL11	0	-0.210	-0.470	0.222			-0.178	-0.416
VPS37A	0	0.440	-0.560
SNF8	0	1.120	-0.560
TMEM55B	0	-1.160	2.060
VPS37C	0	0.110	-0.130
STX8	0						0.283	0.633
VPS16	0	0.140	0.080				-0.408	-0.029
TICAM2	0						0.641	1.449
CHMP1B	0	0.350	0.050

Gene name	PTM type	PTM site	UV	UV (MG132)	Sequence
ARL8A	Ubiquitylation	K141	-0.106	-0.468	_DLPGALDEK(gl)ELIEK_
ARL8B	Ubiquitylation	K114	-0.375		_KVTK(gl)GNVTIK_
ARL8B	Ubiquitylation	K193	0.027	-0.061	_DLPNALDEK(gl)QLIEK_
ARL8B	Ubiquitylation	K198	0.185		_QLIEK(gl)MNLSAIQDR_
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_
CHMP1B	Ubiquitylation	K6	0.892		_(ac)SNMEK(gl)HLFNLK_
CHMP1B	Ubiquitylation	K42	0.359		_AIQK(gl)GNMEVAR_
CHMP1B	Ubiquitylation	K87	1.236		_VQTAVTM(ox)GK(gl)VTK_
CHMP1B	Ubiquitylation	K104	1.243		_SMDATLK(gl)TMNLEK_
CHMP2A	Ubiquitylation	K52	0.105		_MAK(gl)QGQMDAVR_
CHMP2A	Ubiquitylation	K94	0.439	0.611	_IQTLK(gl)SNNSMAQAMK_
CHMP2A	Ubiquitylation	K108	0.133		_GVTK(gl)AMGTMNR_
CHMP2B	Ubiquitylation	K195	-0.063		_SLPSASTSK(gl)ATISDEEIER_
CHMP2B	Phosphorylation	S199	0.711	0.812	_ATIS(ph)DEEIER_
CHMP4B	Ubiquitylation	K6	0.858		_(ac)SVFGK(gl)LFGAGGGK_
CHMP4B	Ubiquitylation	K17	-0.147	0.040	_AGK(gl)GGPTPQEAIQR_
CHMP4B	Ubiquitylation	K39	0.591		_LRDTEEMLSKK(gl)_
CHMP4B	Ubiquitylation	K45	1.027		_KQEFLEK(gl)K_
CHMP4B	Ubiquitylation	K56	0.362		_KIEQELTAAKK(gl)_
CHMP4B	Ubiquitylation	K70	2.554		_AALQALK(gl)R_
CHMP4B	Ubiquitylation	K107	0.634		_EALENANTNTEVLK(gl)NMGYAAK_
CHMP4B	Ubiquitylation	K114	0.459		_NMGYAAK(gl)AMK_
CHMP4C	Ubiquitylation	K70	2.554		_AALQALK(gl)R_
LAMP2	Ubiquitylation	K355	0.979		_RK(gl)SYAGYQTL_
LAMTOR1	Ubiquitylation	K20	-0.365	-0.474	_K(gl)LLLDPSSPPTK_
LAMTOR1	Phosphorylation	S27	-0.440	-0.557	_KLLLDPSS(ph)PPTK_
LAMTOR1	Ubiquitylation	K31	-1.467		_KLLLDPSSPPTK(gl)ALNGAEPNYHSLPSAR_
MICALL1	Phosphorylation	S273		-0.960	_AS(ph)PEARPQIPTKPR_
MICALL1	Phosphorylation	S295	-0.855	-0.714	_LQELAS(ph)PPAGRPTPAPR_
MICALL1	Phosphorylation	S391	-1.476	-2.088	_KKPAPLPPSSS(ph)PGPPSQDSR_
MICALL1	Phosphorylation	S486	-0.513	-0.540	_APSAS(ph)PLALHASR_
MICALL1	Phosphorylation	S578	-0.453	-0.351	_VEQM(ox)PQAS(ph)PGLAPR_
MICALL1	Phosphorylation	S619		-0.921	_SPVPSPGS(ph)SSPQLQVK_
MICALL1	Phosphorylation	S620		-0.870	_SPVPSPGSS(ph)SPQLQVK_
MICALL1	Phosphorylation	S621	-0.800	-0.798	_SPVPSPGSSS(ph)PQLQVK_
MVB12A	Ubiquitylation	K44		0.519	_GFSAISCTVEGAPASFGK(gl)SFAQK_
MVB12A	Phosphorylation	S170	0.061	-0.233	_DMQGLS(ph)LDAASQPSK_
NPC1	Ubiquitylation	K1191		0.981	_AFTVSMK(gl)GSR_
OSBPL11	Phosphorylation	S179		0.034	_SFSLASSS(ph)NSPISQR_
OSBPL11	Phosphorylation	S181	-0.143	-0.159	_SFSLASSSNS(ph)PISQR_
OSBPL11	Phosphorylation	S189	0.718	0.168	_RPS(ph)QNAISFFNVGHSK_
OSBPL9	Phosphorylation	S342		1.042	_RLIDSSGSASVLTHSSS(ph)GNSLK_
OSBPL9	Ubiquitylation	K631		0.099	_ITAEIFSPNDK(gl)K_
OSBPL9	Ubiquitylation	K632	-0.516	0.099	_ITAEIFSPNDKK(gl)_
PIKFYVE	Phosphorylation	S307	0.463	0.429	_SAS(ph)ITNLSLDR_
PIKFYVE	Phosphorylation	S1714		-0.557	_SSS(ph)PIRLPEMSGGQTNR_
PIKFYVE	Phosphorylation	S1754	-0.097	0.057	_GTAGKS(ph)PDLSSQK_
PLD1	Ubiquitylation	K501		-0.155	_LTDVGSVK(gl)R_
PLD1	Ubiquitylation	K547	0.453	1.120	_SIDDVDSK(gl)LK_
PLD1	Ubiquitylation	K549		1.120	_SIDDVDSK(gl)LK_
PLD1	Ubiquitylation	K1000	-0.600		_NATIYDK(gl)VFR_
RHOB	Ubiquitylation	K135	0.050	-0.281	_MK(gl)QEPVRTDDGR_
RNF13	Ubiquitylation	K273	1.281		_CVDPWLTK(gl)TK_
SNF8	Ubiquitylation	K14		-1.326	_GVGAGAIAKK(gl)_
SNF8	Ubiquitylation	K134	0.597		_GK(gl)FAQDVSQDDLIR_
STX8	Ubiquitylation	K98	-0.839	-0.064	_LLLASFK(gl)NEGAEPDLIR_
STX8	Ubiquitylation	K117	0.144	1.154	_SSLMSEEAK(gl)R_
TMEM106B	Ubiquitylation	K164		0.965	_SIDVK(gl)YIGVK_
TMEM106B	Ubiquitylation	K179		0.875	_SAYVSYDVQK(gl)R_
TMEM165	Ubiquitylation	K198	-1.517		_MSPDEGQEELEEVQAELK(gl)K_
TMEM165	Ubiquitylation	K199	-1.102		_MSPDEGQEELEEVQAELK(gl)K_
TMEM165	Ubiquitylation	K208	-1.496	-0.854	_TK(gl)LLNGPGDVETGTSITVPQKK_
TMEM165	Ubiquitylation	K227		-0.650	_LLNGPGDVETGTSITVPQK(gl)K_
TMEM165	Ubiquitylation	K228	-0.843	-0.650	_LLNGPGDVETGTSITVPQKK(gl)_
TMEM55B	Ubiquitylation	K148	-0.935	-0.827	_IACPRPYCK(gl)R_
TMEM59	Ubiquitylation	K206		-0.063	_ESSLSK(gl)MSYLQMR_
TMEM59	Ubiquitylation	K302	-2.229	-0.900	_SK(gl)TEDHEEAGPLPTK(gl)VNLAHSEI_
TMEM59	Ubiquitylation	K315	-1.591	-0.691	_TEDHEEAGPLPTK(gl)VNLAHSEI_
TMEM9	Ubiquitylation	K190	0.152	0.487	_WK(gl)LQVQEQR_
TSG101	Ubiquitylation	K237	-1.467	0.252	_ASLISAVSDK(gl)LR_
TSG101	Ubiquitylation	K257	0.192	0.329	_AQAELNALK(gl)R_
VAMP7	Ubiquitylation	K125	0.653	1.311	_GLDK(gl)VMETQAQVDELK_
VAMP7	Ubiquitylation	K137	0.694	1.092	_VMETQAQVDELK(gl)GIMVR_
VAMP7	Ubiquitylation	K172	0.306		_TENLVDSSVTFK(gl)TTSR_
VAMP8	Ubiquitylation	K47	0.262	0.420	_NK(gl)TEDLEATSEHFK_
VAMP8	Phosphorylation	S55	0.753	0.547	_NKTEDLEATS(ph)EHFK_
VAMP8	Ubiquitylation	K59	-0.052		_NKTEDLEATSEHFK(gl)TTSQK_
VPS16	Ubiquitylation	K510	-0.970	-1.022	_AINQK(gl)LGDTPGVSYSDIAAR_
VPS18	Ubiquitylation	K46		-1.029	_EVPIFTK(gl)QR_
VPS33A	Ubiquitylation	K67		7.613	_MFTLK(gl)GNR_
VPS33A	Ubiquitylation	K313		-1.029	_DKNFNAVGSVLSK(gl)K_
VPS33A	Ubiquitylation	K314		-1.029	_DKNFNAVGSVLSK(gl)K_
VPS33B	Ubiquitylation	K321		1.641	_GMDIK(gl)QMK_
VPS33B	Ubiquitylation	K480	-0.791		_ITDAFSSLAK(gl)R_
VPS33B	Ubiquitylation	K504	-0.823	-0.779	_VDGEYDLK(gl)VPR_
VPS37A	Ubiquitylation	K29		-0.751	_SASSSAAGSPGGLTSLQQQK(gl)QR_
VPS37C	Ubiquitylation	K5	0.354		_(ac)METLK(gl)DK_
VPS4B	Phosphorylation	S102	-0.658	-0.952	_EGQPSPADEKGNDS(ph)DGEGESDDPEK_
VTI1B	Ubiquitylation	K13	0.008	1.711	_(ac)ASSAASSEHFEK(gl)LHEIFR_