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)
EI24	2	0.040	-0.170				1.100	0.629
USP13	1	0.350	0.240	-1.142				0.643
USP13	1	0.350	0.240
USP5	1	0.450	-0.520	-1.142				0.643
ATG2B	1	-0.250	-0.100
RAB24	1	0.100	-0.060
ATG9A	1	-0.430	0.730					1.551
GABARAPL2	0	1.830	-0.990
PIK3CB	0	-1.390	2.350
PIK3CB	0	-0.710	1.450
VMP1	0	-1.240	2.060
PSEN1	0	0.930	-1.110
ABL1	0	0.670	-0.070
CHMP4A	0	-0.580	0.780
TM9SF1	0	-0.420	0.130
SUPT20H	0	-0.030	0.100					-0.029
USP10	0	-0.120	-0.210	0.958	0.948	0.289	-0.190	-0.313
ATG2A	0	-0.120	-0.210	-0.082
AMBRA1	0	1.670	-0.450	-1.226				-2.109
TFEB	0	0.270	0.450
DAP	0	0.240	-0.420
BNIP1	0	-0.940	0.840				0.333	0.290
EVA1A	0	-0.550	0.600
TMEM59	0	1.350	-0.820
PARK7	0	-0.660	0.930
STK11	0
ATG4C	0	1.830	-1.180
BECN1	0	0.080	-0.010
ATG4D	0	-1.190	1.270
PRKAA1	0	0.910	0.060
FNBP1L	0	0.890	-0.940
RAB15	0	0.710	-0.750		1.641	-1.484	0.560	0.491
RAB1A	0	0.980	-0.460				-0.532
RNF185	0	0.640	-0.360
NPC1	0	0.620	-0.700				0.275	0.103
S100A8	0	-0.880	1.550			-3.285		-4.740
ATG12	0	-0.150	1.370
VPS51	0	-0.170	0.340				0.542	-0.824
SQSTM1	0	-0.860	1.770	-2.165			-2.063	-1.741
SQSTM1	0	-0.440	0.530	-2.165			-2.063	-1.741
PRKAA2	0	-0.030	-0.350
PRKAA2	0	-0.030	-0.350
S100A9	0	-1.350	2.240					-4.360
IFI16	0	0.400	-0.680				0.620	0.590
GABARAP	0	-1.090	2.300
RAB33B	0	-1.210	1.500				0.261	-0.091
LAMP1	0	-0.830	0.960				0.121	0.196
LRRK2	0	0.530	-0.620	-0.240
ZKSCAN3	0	-0.120	0.260
TECPR2	0	1.230	-0.720
ATG7	0	-0.140	0.720	0.708

Gene name	PTM type	PTM site	UV	UV (MG132)	Sequence
ABL1	Phosphorylation	S1083	-1.131	-0.857	_GQGESDPLDHEPAVS(ph)PLLPR_
ABL1	Phosphorylation	S1134		0.293	_SSS(ph)FREMDGQPER_
ABL1	Phosphorylation	S1232	0.821	0.183	_SCS(ph)ASCVPHGAK_
AMBRA1	Ubiquitylation	K175	-0.373	0.447	_REPFAVVK(gl)TASEMER_
ATG12	Ubiquitylation	K116		0.431	_AVGDTPIMK(gl)TK_
ATG12	Ubiquitylation	K118		0.431	_AVGDTPIMK(gl)TK_
ATG2B	Phosphorylation	S239	-0.423	-0.513	_S(ph)SPVCSTAPVETEPK_
ATG2B	Phosphorylation	S240	-0.423	-0.513	_S(ph)SPVCSTAPVETEPK_
ATG2B	Phosphorylation	S497	1.523	0.570	_SVS(ph)VDESRPELIFR_
ATG2B	Phosphorylation	S1579	-0.595	0.128	_SYIS(ph)PHSSPSHTPTR_
ATG4C	Ubiquitylation	K403	0.208		_ASEEITK(gl)MLK_
ATG4D	Ubiquitylation	K241		-0.390	_LVELGQSSGK(gl)K_
ATG4D	Ubiquitylation	K242		-0.390	_LVELGQSSGK(gl)K_
ATG4D	Phosphorylation	S468	0.073	0.285	_AKRPSS(ph)EDFVFL_
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_
BNIP1	Ubiquitylation	K48	-0.830		_VK(gl)EKFQQLR_
BNIP1	Ubiquitylation	K178	0.158		_TILDANEEFK(gl)SMSGTIQLGR_
CHMP4A	Ubiquitylation	K115	-0.705		_TMELAAQSMKK(gl)_
DAP	Phosphorylation	S2	-0.404	1.136	_(ac)S(ph)SPPEGKLETK_
DAP	Phosphorylation	S3	-0.404	1.254	_(ac)SS(ph)PPEGKLETK_
DAP	Phosphorylation	S51	-0.968	0.151	_DKDDQEWESPS(ph)PPKPTVFISGVIAR_
EI24	Phosphorylation	S46	1.497	0.314	_RAS(ph)SVLAQR_
EI24	Phosphorylation	S330	3.730	2.164	_FPSPHPS(ph)PAK_
EVA1A	Phosphorylation	S114		0.039	_NVFTS(ph)AEELER_
FNBP1L	Phosphorylation	S295	0.730	0.489	_TIS(ph)DGTISASK_
FNBP1L	Phosphorylation	T496		-0.149	_HSSDINHLVT(ph)QGRESPEGSYTDDANQEVR_
FNBP1L	Phosphorylation	S501	-0.322	-0.235	_ES(ph)PEGSYTDDANQEVR_
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_
NPC1	Ubiquitylation	K1191		0.981	_AFTVSMK(gl)GSR_
PARK7	Ubiquitylation	K41	0.222	0.590	_VTVAGLAGK(gl)DPVQCSR_
PARK7	Ubiquitylation	K93	-0.291		_EILK(gl)EQENR_
PARK7	Ubiquitylation	K132	0.639		_VTTHPLAKDK(gl)_
PIK3CB	Ubiquitylation	K1044		0.990	_SEEEALKQFKQK(gl)_
PRKAA1	Ubiquitylation	K271		-0.536	_ATIK(gl)DIR_
PRKAA1	Ubiquitylation	K396		-0.419	_HTLDELNPQK(gl)SK_
PRKAA1	Ubiquitylation	K485	-1.326	-1.554	_SIDDEITEAK(gl)SGTATPQR_
PRKAA2	Ubiquitylation	K271		-0.536	_ATIK(gl)DIR_
PRKAA2	Phosphorylation	S377	-0.020		_MPPLIADS(ph)PK_
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_
RAB24	Ubiquitylation	K104	0.985	1.040	_FWVK(gl)ELR_
RAB24	Ubiquitylation	K156	1.852	-0.833	_AQLFETSSK(gl)TGQSVDELFQK_
RNF185	Ubiquitylation	K80	-0.439	0.423	_QVCPVCK(gl)AGISR_
RNF185	Ubiquitylation	K87	-0.438	0.332	_DK(gl)VIPLYGR_
RNF185	Ubiquitylation	K105	-2.577		_EK(gl)TPPRPQGQRPEPENR_
SQSTM1	Ubiquitylation	K13	0.150	0.302	_AYLLGK(gl)EDAAR_
SQSTM1	Phosphorylation	S28		-0.721	_RFSFCCS(ph)PEPEAEAEAAAGPGPCER_
SQSTM1	Ubiquitylation	K141	-0.915		_YK(gl)CSVCPDYDLCSVCEGK_
SQSTM1	Ubiquitylation	K157	-0.852	-0.677	_CSVCPDYDLCSVCEGK(gl)GLHR_
SQSTM1	Phosphorylation	T269	-0.681	-0.421	_LT(ph)PVS(ph)PESSSTEEK_
SQSTM1	Phosphorylation	S272	0.171	0.044	_LTPVS(ph)PESSSTEEK_
SQSTM1	Phosphorylation	S332		-0.007	_IALESEGRPEEQMESDNCS(ph)GGDDDWTHLSSK_
SQSTM1	Ubiquitylation	K420	-1.122	-0.061	_LLQTK(gl)NYDIGAALDTIQYSK_
SQSTM1	Ubiquitylation	K435	-1.352	-0.780	_NYDIGAALDTIQYSK(gl)HPPPL_
STK11	Phosphorylation	S31	0.437	0.073	_IDS(ph)TEVIYQPR_
STK11	Phosphorylation	T32	1.256	0.248	_IDS(ph)TEVIYQPR_
SUPT20H	Ubiquitylation	K226		-0.873	_LLYNK(gl)QK_
SUPT20H	Ubiquitylation	K294		-1.057	_AGNCVDMWK(gl)R_
SUPT20H	Phosphorylation	S378		0.675	_ADEESDS(ph)QMSPSHSSTDDHSNWFIIGSK_
SUPT20H	Phosphorylation	T494	-1.141	-1.685	_SPT(ph)PPPSSKPSSIPR_
TECPR2	Phosphorylation	S673		-0.027	_ADEGS(ph)PVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK_
TFEB	Phosphorylation	S541		-0.724	_KDLDLMLLDDSLLPLASDPLLSTMS(ph)PEASK_
TFEB	Phosphorylation	S555	0.499	0.811	_RSSFS(ph)MEEGDVL_
TM9SF1	Ubiquitylation	K115	-0.705		_TMELAAQSMKK(gl)_
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_
USP10	Phosphorylation	S76	0.220		_TPS(ph)YSISSTLNPQAPEFILGCTASK_
USP10	Phosphorylation	T208	-0.556	-0.706	_T(ph)CNSPQNSTDSVSDIVPDSPFPGALGSDTR_
USP10	Phosphorylation	S211		-0.454	_TCNS(ph)PQNSTDSVSDIVPDSPFPGALGSDTR_
USP10	Phosphorylation	S365	-0.539	-0.580	_YS(ph)PPAISPLVSEK_
USP10	Phosphorylation	S370	0.978	0.859	_YSPPAIS(ph)PLVSEK_
USP10	Ubiquitylation	K512	0.652		_LLTVNK(gl)SSLSEK_
USP10	Phosphorylation	S547	0.647	0.385	_LLS(ph)PSNEK_
USP10	Phosphorylation	S576	1.011	0.498	_NHSVNEEEQEEQGEGS(ph)EDEWEQVGPR_
USP10	Ubiquitylation	K662		-0.003	_ESVQGYTTK(gl)TK_
USP10	Ubiquitylation	K664	1.358		_TK(gl)QEVEISR_
USP10	Ubiquitylation	K780	0.763	0.364	_VINQYQVVK(gl)PTAER_
USP13	Ubiquitylation	K163	0.116	1.146	_K(gl)QEVQAWDGEVR_
USP13	Ubiquitylation	K184	-0.042	-0.044	_HAFSLK(gl)QLDNPAR_
USP13	Ubiquitylation	K328	0.320	0.109	_LK(gl)PMYGPGYTGLK_
USP13	Ubiquitylation	K353	1.225		_K(gl)YVDKLEK_
USP13	Ubiquitylation	K357	0.847		_YVDK(gl)LEK_
USP13	Ubiquitylation	K418	0.291	0.339	_MFK(gl)ALIGK_
USP13	Ubiquitylation	K423	0.440	-0.090	_ALIGK(gl)GHPEFSTNR_
USP13	Ubiquitylation	K430	0.505	0.308	_MFK(gl)AFVSK_
USP13	Ubiquitylation	K435	-0.932	-0.715	_AFVSK(gl)SHPEFSSNR_
USP13	Ubiquitylation	K468	0.433		_FLVEEK(gl)IK_
USP13	Ubiquitylation	K470	-0.606	0.287	_IK(gl)CLATEK_
USP13	Ubiquitylation	K478	0.243	0.990	_CLATEKVK(gl)_
USP13	Ubiquitylation	K558	0.626	0.552	_SVAVK(gl)TTR_
USP13	Phosphorylation	T623	1.685	0.623	_GTGLQPGEEELPDIAPPLVT(ph)PDEPK_
USP13	Ubiquitylation	K743	0.438	1.356	_DQALK(gl)ALR_
USP13	Ubiquitylation	K793	-0.216	0.033	_SAADSISESVPVGPK(gl)VR_
USP5	Ubiquitylation	K163	0.116	1.146	_K(gl)QEVQAWDGEVR_
USP5	Ubiquitylation	K184	-0.042	-0.044	_HAFSLK(gl)QLDNPAR_
USP5	Ubiquitylation	K353	1.225		_K(gl)YVDKLEK_
USP5	Ubiquitylation	K357	0.847		_YVDK(gl)LEK_
USP5	Ubiquitylation	K418	0.291	0.339	_MFK(gl)ALIGK_
USP5	Ubiquitylation	K423	0.440	-0.090	_ALIGK(gl)GHPEFSTNR_
USP5	Ubiquitylation	K468	0.433		_FLVEEK(gl)IK_
USP5	Ubiquitylation	K470	-0.606	0.287	_IK(gl)CLATEK_
USP5	Ubiquitylation	K478	0.243	0.990	_CLATEKVK(gl)_
USP5	Ubiquitylation	K558	0.626	0.552	_SVAVK(gl)TTR_
USP5	Phosphorylation	T623	1.685	0.623	_GTGLQPGEEELPDIAPPLVT(ph)PDEPK_
USP5	Ubiquitylation	K743	0.438	1.356	_DQALK(gl)ALR_
USP5	Ubiquitylation	K793	-0.216	0.033	_SAADSISESVPVGPK(gl)VR_
VMP1	Ubiquitylation	K245		0.854	_AK(gl)LAVQK_
VPS51	Phosphorylation	S18	-0.839		_(ac)AAAAAAGPSPGSGPGDS(ph)PEGPEGEAPER_
VPS51	Ubiquitylation	K189		0.062	_LTK(gl)CVELGAYGQAVR_
ZKSCAN3	Phosphorylation	S42		0.848	_VEEEEAGFPSSPDLGS(ph)EGSR_