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)
CAT	2	2.260	-1.180				1.895	-0.238
LRBA	2	-0.630	0.460	0.507
LRBA	2	-0.630	0.460					-0.806
RAB7A	1	1.540	-0.590	0.299	1.971	-0.775	0.288	-0.293
VPS36	1	1.310	-0.830
BCL10	1	0.000	0.200
LAMTOR1	1	0.700	-0.850	0.343			0.382
VPS33B	1	0.750	-0.120
AP3M1	1	2.120	-1.010	-0.529			-0.213	-0.553
LAMP2	0	-0.040	0.180				0.379	0.711
LAMP2	0	-0.040	0.180	0.164
RRAGD	0	-0.870	0.980
RRAGD	0	-0.870	0.980
HEXB	0	-0.370	0.060				0.103
CTSA	0	0.050	0.530				0.264
FGFR3	0	-1.120	1.390
RRAGB	0	1.330	-0.980	0.176
HPS4	0	0.980	-0.680
LGMN	0	-0.120	0.250				0.435	0.710
ASAH1	0	-0.300	0.340
MAN2B1	0	-0.130	-0.550
ANKRD27	0	-0.140	0.170
PON2	0	-0.260	0.150				-0.822	0.003
NAGLU	0	-0.400	0.020
WDR48	0	0.940	-0.610	0.277			-0.306	-0.478
PCYOX1	0	0.530	-0.170				1.292	0.660
TMEM59	0	1.350	-0.820
TMEM9	0	-0.200	0.950					-0.690
RRAGC	0	-0.530	0.100
RRAGC	0	-0.530	0.100
VAMP4	0	0.540	-0.460
PRDX6	0	0.680	-0.490	0.508	0.694	-1.150	0.703	0.179
CTSD	0	0.580	-0.790	-0.768		-2.790	-0.655	-1.981
TNFAIP3	0	0.760	-0.500
RAB14	0	0.630	-0.150				0.314	0.321
VPS4B	0	-0.670	1.580
SLC17A5	0	0.440	-0.600
GOT1	0	-0.320	0.110
CXCR4	0	0.640	-0.440
RAB9A	0	1.450	-0.760				0.793	0.935
TRIP10	0	0.140	-0.170
LDLR	0	0.610	-0.680					-0.328
PPT1	0	1.320	-0.730
ACP2	0	1.070	-0.530				0.434	0.627
CD63	0	-1.190	1.800				1.412	0.887
ITM2C	0	-0.570	0.530
CCDC115	0	-1.060	1.960
PRCP	0	0.190	0.050				1.040
GGH	0	-0.450	-0.130		-0.144	-0.184	0.145
SCARB2	0	0.220	0.470				0.565	0.756
TOM1L1	0	-0.380	0.180
NPC1	0	0.620	-0.700				0.275	0.103
RPTOR	0	0.520	-1.030				0.623	0.466
ANK3	0	0.110	-0.340
ANK3	0	0.110	-0.340	-0.060			1.268	0.717
TIAL1	0	-0.540	0.100
TIAL1	0	-0.540	0.100	-0.721	-0.259	-0.319	-0.332	-0.199
GJA1	0	-0.410	0.430
RRAGA	0	-0.490	0.890	0.176
ATP13A2	0	-0.050	0.320
SQSTM1	0	-0.860	1.770	-2.165			-2.063	-1.741
SQSTM1	0	-0.440	0.530	-2.165			-2.063	-1.741
TPCN2	0	0.360	0.190
FYCO1	0	0.970	-1.080				-1.408	0.596
PLEKHF1	0	0.780	-0.300
TPP1	0	-0.540	0.760	0.431			1.429	1.399
GLB1	0	-1.310	1.460				0.469	0.688
GABARAP	0	-1.090	2.300
CHID1	0	1.840	-1.250				0.533	0.542
LAMP1	0	-0.830	0.960				0.121	0.196
FNBP1	0	0.860	-0.550
LAMTOR4	0	-0.850	2.120
LAMTOR4	0	-0.650	1.640
NBR1	0	0.470	-0.040	-2.408
GM2A	0	1.660	-0.700
ADA	0	0.340	-0.830
SRC	0	0.050	0.470	-0.031
MTOR	0	-0.680	0.150	0.757			0.074	0.101
NAGA	0	0.830	0.170
RAB12	0	0.390	0.030
SLC35F6	0	0.580	-0.580

Gene name	PTM type	PTM site	UV	UV (MG132)	Sequence
ACP2	Ubiquitylation	K153		-2.937	_LLK(gl)FPLGPCPR_
ADA	Ubiquitylation	K312		0.123	_STLDTDYQMTK(gl)R_
ANK3	Phosphorylation	S1405	0.434	0.363	_IRDTS(ph)QEPCGR_
ANK3	Phosphorylation	S1459	0.743	0.188	_RQS(ph)FASLALR_
ANK3	Phosphorylation	S1462		0.189	_RYS(ph)YLTEPGMSPQSPCER_
ANK3	Phosphorylation	S4298	0.236	0.621	_IHGSGHVEEPAS(ph)PLAAYQK_
ANKRD27	Ubiquitylation	K241	1.291		_YVGTMEASEDAAFNK(gl)ITR_
ANKRD27	Phosphorylation	T1023	-0.229	-0.481	_RHT(ph)VEDAVVSQGPEAAGPLSTPQEVSASR_
ANKRD27	Phosphorylation	S1030	0.129		_RHTVEDAVVS(ph)QGPEAAGPLSTPQEVSASR_
AP3M1	Ubiquitylation	K283	-0.147		_HSISFK(gl)ENSSCGR_
AP3M1	Ubiquitylation	K413	-0.636	-0.807	_AGK(gl)FQVR_
ASAH1	Ubiquitylation	K461		0.139	_ESLDVYELDAK(gl)QGR_
ATP13A2	Ubiquitylation	K150	0.643	0.021	_DTAQLHK(gl)SEEAVSVGQK_
ATP13A2	Ubiquitylation	K160		-0.674	_SEEAVSVGQK(gl)R_
ATP13A2	Ubiquitylation	K213		-1.661	_K(gl)AIYGPNVISIPVK_
ATP13A2	Ubiquitylation	K290		0.174	_DMVK(gl)LSMR_
ATP13A2	Ubiquitylation	K693		-2.381	_VVALASK(gl)PLPTVPSLEAAQQLTR_
BCL10	Phosphorylation	S138	1.515	1.393	_SNS(ph)DESNFSEK_
CCDC115	Ubiquitylation	K173	-0.116		_LK(gl)QLEPGAA_
CXCR4	Phosphorylation	S319	0.861	-0.615	_TSAQHALTS(ph)VSR_
CXCR4	Ubiquitylation	K327	0.978	0.329	_GSSLK(gl)ILSK_
FGFR3	Ubiquitylation	K205		-0.115	_IGGIK(gl)LR_
FNBP1	Phosphorylation	S296	0.887	1.145	_TVS(ph)DNSLSNSR_
FYCO1	Ubiquitylation	K416	0.606	0.803	_TK(gl)VEEVNR_
GABARAP	Ubiquitylation	K13	-0.569		_FVYKEEHPFEK(gl)R_
GGH	Ubiquitylation	K109		0.582	_SDYAK(gl)VAK_
GJA1	Ubiquitylation	K109	0.099		_LNKK(gl)EEELK_
GJA1	Ubiquitylation	K128	0.209	1.057	_VAQTDGVNVDMHLK(gl)QIEIK_
GJA1	Ubiquitylation	K136	-0.888		_FK(gl)YGIEEHGK_
GJA1	Ubiquitylation	K243	0.152	0.237	_GK(gl)SDPYHATSGALSPAK_
GJA1	Ubiquitylation	K258	-0.280	0.063	_SDPYHATSGALSPAK(gl)DCGSQK_
GJA1	Ubiquitylation	K303	-0.106	0.280	_NYNK(gl)QASEQNWANYSAEQNR_
GJA1	Ubiquitylation	K345		-0.464	_MGQAGSTISNSHAQPFDFPDDNQNSK(gl)K_
GJA1	Ubiquitylation	K346	-1.004	-0.300	_MGQAGSTISNSHAQPFDFPDDNQNSKK(gl)_
GJA1	Phosphorylation	S364		-0.300	_LAAGHELQPLAIVDQRPS(ph)SR_
GJA1	Phosphorylation	S365		-0.300	_LAAGHELQPLAIVDQRPS(ph)SR_
GJA1	Phosphorylation	S372	0.940	1.430	_AS(ph)SRPRPDDLEI_
GJA1	Phosphorylation	S373	0.664	0.467	_ASS(ph)RPRPDDLEI_
GLB1	Ubiquitylation	K91		0.224	_DSFLK(gl)DGQPFR_
GM2A	Ubiquitylation	K179		0.422	_IESVLSSSGK(gl)R_
GOT1	Ubiquitylation	K97		-0.580	_LALGDDSPALK(gl)EK_
HPS4	Phosphorylation	S272		0.478	_SLAS(ph)PAGLQDGSAQHHPK_
ITM2C	Ubiquitylation	K3	-0.833	-0.100	_VK(gl)ISFQPAVAGIK_
ITM2C	Ubiquitylation	K14	-1.180	-0.498	_ISFQPAVAGIK(gl)GDK(gl)ADK_
ITM2C	Ubiquitylation	K17		-0.656	_ISFQPAVAGIKGDK(gl)_
ITM2C	Ubiquitylation	K20	-2.698		_GDKADK(gl)ASASAPAPASATEILLTPAR_
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_
LAMTOR4	Ubiquitylation	K64	0.203	0.287	_GMNVPFK(gl)R_
LGMN	Ubiquitylation	K125	0.264	-0.241	_GDAEAVK(gl)GIGSGK_
LGMN	Ubiquitylation	K224	0.675	0.933	_ESSYACYYDEK(gl)R_
LGMN	Ubiquitylation	K287		1.040	_VMQFQGMK(gl)R_
LRBA	Phosphorylation	S10	-1.001	-0.916	_(ac)ASEDNRVPS(ph)PPPTGDDGGGGGR_
LRBA	Phosphorylation	S1261	0.534	0.505	_LELKAS(ph)PNVEAPQPHR_
LRBA	Phosphorylation	S1488	2.977	1.630	_SAAKS(ph)PVDIVTGGISPVR_
LRBA	Ubiquitylation	K2024	0.249		_TAVEHATDEDILAK(gl)GK_
LRBA	Ubiquitylation	K2260	-0.351		_DLSK(gl)PIGALNPK_
LRBA	Ubiquitylation	K2268	-1.318	-0.187	_DLSKPIGALNPK(gl)R_
MAN2B1	Ubiquitylation	K740		0.855	_FDTPLETK(gl)GR_
MTOR	Ubiquitylation	K309	-0.762	0.065	_DLMGFGTK(gl)PR_
MTOR	Ubiquitylation	K1257	-1.167	-0.901	_SGQGDALASGPVETGPMKK(gl)_
MTOR	Ubiquitylation	K1395		-1.255	_AYAK(gl)ALHYK_
MTOR	Ubiquitylation	K2066		-1.004	_GPQTLK(gl)ETSFNQAYGR_
MTOR	Ubiquitylation	K2166		-1.304	_IQSIAPSLQVITSK(gl)QRPR_
MTOR	Phosphorylation	T2471		0.329	_KT(ph)GTTVPESIHSFIGDGLVKPEALNK_
NAGA	Ubiquitylation	K154		-0.505	_VDMLK(gl)LDGCFSTPEER_
NAGLU	Ubiquitylation	K59		-0.842	_ALAAK(gl)PGLDTYSLGGGGAAR_
NBR1	Ubiquitylation	K464	-0.807	-2.087	_LSHK(gl)GQQFGPR_
NBR1	Ubiquitylation	K515	-0.852		_TDDLTCQQEETFLLAK(gl)EER_
NBR1	Ubiquitylation	K539	-0.515	-0.635	_QLGEVTEQTEGTAACIPQKAK(gl)_
NBR1	Ubiquitylation	K627	-0.779	-1.425	_ALPDSMVSVK(gl)R_
NBR1	Ubiquitylation	K767	-1.436		_GAEGK(gl)PGVEAGQEPAEAGER_
NPC1	Ubiquitylation	K1191		0.981	_AFTVSMK(gl)GSR_
PLEKHF1	Phosphorylation	S312	-0.501	-0.472	_QEEAEEQGAGS(ph)PGQPAHLAR_
PPT1	Ubiquitylation	K174		-0.445	_TLNAGAYSK(gl)VVQER_
PPT1	Ubiquitylation	K224		1.077	_NLMALKK(gl)_
PPT1	Ubiquitylation	K253		0.222	_SGQAK(gl)ETIPLQETSLYTQDR_
PRDX6	Phosphorylation	T44	0.123	0.216	_DFT(ph)PVCTTELGR_
PRDX6	Ubiquitylation	K63		0.157	_LAPEFAK(gl)R_
PRDX6	Ubiquitylation	K209	-0.199	0.307	_GVFTK(gl)ELPSGK_
RAB12	Phosphorylation	S21	-0.451	0.146	_RAGGGGGLGAGS(ph)PALSGGQGR_
RAB12	Ubiquitylation	K172	0.251	0.981	_QQGEK(gl)FAQQITGMR_
RAB14	Ubiquitylation	K170	-1.161		_TGENVEDAFLEAAK(gl)K_
RAB14	Ubiquitylation	K171	-1.161	-0.915	_TGENVEDAFLEAAKK(gl)_
RAB14	Ubiquitylation	K193		-0.640	_IYQNIQDGSLDLNAAESGVQHK(gl)PSAPQGGR_
RAB7A	Ubiquitylation	K32	0.922	1.260	_K(gl)FSNQYK_
RAB7A	Ubiquitylation	K38	0.713	1.294	_FSNQYK(gl)ATIGADFLTK_
RAB7A	Ubiquitylation	K146		-0.718	_AQAWCYSK(gl)NNIPYFETSAK_
RAB9A	Ubiquitylation	K4	-0.153	-0.091	_(ac)AGK(gl)SSLFK_
RAB9A	Phosphorylation	T175		0.548	_VLAT(ph)EDRSDHLIQTDTVNLHR_
RAB9A	Phosphorylation	S179		0.548	_VLAT(ph)EDRSDHLIQTDTVNLHR_
RPTOR	Phosphorylation	S722	0.393	1.196	_SVSS(ph)YGNIR_
RPTOR	Phosphorylation	T857	-0.348		_VLDTSSLT(ph)QSAPAS(ph)PTNK_
RPTOR	Phosphorylation	S859	-0.462	-0.346	_VLDTSSLTQS(ph)APASPT(ph)NK_
RPTOR	Phosphorylation	S863	-0.208	-0.001	_VLDTSSLTQS(ph)APAS(ph)PTNK_
RPTOR	Phosphorylation	T865		-0.317	_VLDTSSLTQS(ph)APASPT(ph)NK_
RPTOR	Phosphorylation	S877	-0.114	-0.074	_GVHIHQAGGS(ph)PPASSTSSSSLTNDVAK_
RPTOR	Ubiquitylation	K1008		-0.329	_QAQQVIQK(gl)GITR_
RRAGA	Ubiquitylation	K307	0.056	0.970	_VDGPK(gl)HSLLMR_
RRAGB	Ubiquitylation	K307	0.056	0.970	_VDGPK(gl)HSLLMR_
RRAGC	Phosphorylation	S2		0.163	_(ac)S(ph)LQYGAEETPLAGSYGAADSFPK_
RRAGC	Phosphorylation	S15	0.224	-0.282	_(ac)SLQYGAEETPLAGS(ph)YGAADSFPK_
RRAGC	Ubiquitylation	K80	0.785	0.962	_SSIQK(gl)VVFHK_
RRAGC	Phosphorylation	S95		0.296	_MSPNETLFLES(ph)TNK_
RRAGD	Ubiquitylation	K80	0.785	0.962	_SSIQK(gl)VVFHK_
RRAGD	Phosphorylation	S95		0.296	_MSPNETLFLES(ph)TNK_
SLC17A5	Ubiquitylation	K340		-0.681	_NQLSSQK(gl)SVPWVPILK_
SLC35F6	Phosphorylation	T363	0.255		_LLGGT(ph)RTPINDAS_
SLC35F6	Phosphorylation	T365	0.573	0.294	_LLGGTRT(ph)PINDAS_
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_
SRC	Phosphorylation	S17	-0.604	-0.689	_S(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR_
SRC	Phosphorylation	S75	0.060	0.331	_LFGGFNSSDTVTS(ph)PQR_
TIAL1	Ubiquitylation	K91	0.902		_VNWATTPSSQKK(gl)_
TIAL1	Ubiquitylation	K122	0.503	0.809	_SAFAPFGK(gl)ISDAR_
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_
TNFAIP3	Ubiquitylation	K722	0.496	0.176	_ASCK(gl)NILACR_
TOM1L1	Ubiquitylation	K149	-0.037		_EVYLDLVKK(gl)_
TOM1L1	Ubiquitylation	K298		-1.457	_ILEQNK(gl)NQK_
TOM1L1	Ubiquitylation	K301	-1.762	-1.457	_NQK(gl)EATNTTSEPSAPSQDLLDLSPSPR_
TOM1L1	Phosphorylation	S321	0.265	-0.164	_EATNTTSEPSAPSQDLLDLS(ph)PSPR_
TOM1L1	Phosphorylation	S323	-1.219	-1.229	_EATNTTSEPSAPSQDLLDLSPS(ph)PR_
TPCN2	Ubiquitylation	K382		0.584	_QAMMEK(gl)VR_
TRIP10	Phosphorylation	S296	0.064	0.030	_APS(ph)DSSLGTPSDGRPELR_
VAMP4	Ubiquitylation	K19	0.300	0.708	_HLNDDDVTGSVK(gl)SER_
VAMP4	Phosphorylation	S30	0.418	0.593	_NLLEDDS(ph)DEEEDFFLR_
VAMP4	Ubiquitylation	K87	-0.399		_LDELQDK(gl)SESLSDNATAFSNR_
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_
VPS36	Ubiquitylation	K189	1.478	1.592	_AK(gl)EMVELSK_
VPS4B	Phosphorylation	S102	-0.658	-0.952	_EGQPSPADEKGNDS(ph)DGEGESDDPEK_
WDR48	Ubiquitylation	K294	0.228		_VLICEEK(gl)APVLK_