Table S1. Putative miR-322 target transcripts which is highly expressed in MGCs ______0610037L13Rik, 1700037H04Rik, 2310061I04Rik, 2810006K23Rik, Abcc5, Abhd16a, Acbd3, Acox1, Acsbg1, Acsl4, Actr1a, Actr2, Adck5, Adh5, Adrbk1, Aff4, Agk, Ahcyl1, Akap11, Akap7, Akirin1, Alg3, Amfr, Ammecr1, Amotl2, Ankfy1, Ankhd1, Ankrd52, Ap2a1, Ap2b1, Ap3b1, Ap3d1, App, Arcn1, Arf3, Arfgap2, Arhgap12, Arhgap5, Arhgdia, Arhgef11, Arih1, Arl2, Arl3, Arl8b, Armcx6, Asap1, Asnsd1, Atf6, Atg13, Atg4b, Atp13a3, Atp5g1, Atp6v1a, Atxn2, Atxn7l3, Atxn7l3b, AW549877, B4galt1, B4galt7, Bace1, Bag5, Baiap2, Baz2a, BC037034, Bcl2l1, Bcl2l2, Bfar, Bmpr1a, Bptf, Brd2, Brd4, Brpf3, Btbd3, Btg2, Cab39, Cacna2d1, Calm1, Capns1, Caprin1, Capza2, Carm1, Caskin1, Cbfa2t3, Cbx5, Cbx6, Cc2d1b, Ccdc127, Ccdc6, Ccnd2, Ccnt2, Ccnyl1, Cd164, Cd2ap, Cdc25a, Cdc27, Cdc37l1, Cdc42se2, Cdca4, Cdipt, Cdk5rap3, Cdk8, Cdk9, Cdv3, Celf1, Cfl2, Chchd3, Chd6, Chmp1a, Chmp7, Chordc1, Chpf, Chpt1, Chst8, Chtf8, Cisd2, Clasrp, Clcn3, Clstn1, Cmpk1, Cnih2, Cnot1, Cnot2, Col4a3bp, Cope, Cops2, Cops7a, Cops7b, Copz1, Coq6, Cpd, Crebzf, Crim1, Crk, Crkl, Csde1, Cse1l, Ctnnb1, Cul4a, Cul4b, Cxx1a, Cxx1b, Cxx1c, D15Ertd621e, D2hgdh, Dcaf7, Dcbld2, Dcp1a, Dctn5, Ddost, Ddr1, Ddx39, Ddx3x, Ddx6, Dedd, Dhdds, Dhx16, Diap1, Dido1, Dlst, Dmtf1, Dnaja2, Dnajb14, Dnajb2, Dnajc1, Dnajc16, Dnajc25, Dph3, Dpm1, Dpp9, Dpy19l4, Dsel, Dtl, Dvl1, Dync1li2, Dynll2, Dynlt3, Dyrk1a, Dyrk1b, Ebna1bp2, Edc4, Eftud2, Egln2, Eif1a, Eif2b2, Eif2s1, Eif3a, Eif4b, Eif4e, Eif4g1, Eif4g2, Eif5b, Elmo2, Elovl5, Enah, Enc1, Entpd4, Erlin2, Erp29, Etnk1, Etv6, Evi5, Extl3, Faf2, Fam120a, Fam122a, Fam126a, Fam133b, Fam134a, Fam160b2, Fam171a1, Fam178a, Fam53c, Fam60a, Fasn, Fastk, Fbxo21, Fermt2, Fkbp1a, Fkbp5, Fkrp, Flna, Fndc3b, Fnta, Fosl2, Furin, Gabbr1, Gak, Galnt1, Galnt7, Gatad2a, Gbf1, Gclm, Gga2, Gga3, Gigyf1, Git1, Glud1, Gna12, Gna13, Gnai3, Gns, Gpaa1, Gpatch8, Gpn1, Gsk3b, Gtpbp2, H6pd, Haus5, Hdgf, Hdhd2, Hectd1, Herc3, Hiatl1, Higd1a, Hipk3, Hira, Hmmr, Hnrnpa1, Hnrnpa2b1, Hsd17b7, Hspg2, Hsph1, Iars, Idh3a, Igf1, Igf1r, Igf2r, Ihh, Ing4, Ino80b, Insr, Ints3, Ip6k1, Ipo4, Isoc1, Itgav, Itgb1, Itpr1, Jmy, Kank1, Kbtbd2, Kbtbd4, Kcmf1, Kif1b, Kif1c, Kif23, Kif5b, Klc1, Klc4, Kpna1, Kpna3, Kpna4, Lamc1, Larp1, Lats1, Lats2, Leng8, Limk2, Lims1, Lnpep, Lrch4, Lrig1, Lrp5, Lrp6, Lrrc58, Lrrfip2, Lsg1, Lsm14b, Ly6e, Lypla2, Lyrm5, Macf1, Man2a1, Man2a2, Map1lc3b, Map2k1, Map2k3, Map3k3, Map3k4, Mapk1ip1l, Mapk3, Mapk9, Mapkap1, Mapkapk3, Mapre1, March6, Mark2, Med1, Med24, Med28, Mesdc2, Metap1, Mfn2, Mfsd1, Mfsd10, Mfsd4, Mink1, Mknk1, Mllt10, Mllt6, Mlxip, Mms19, Mob4, Morc2a, Mov10, Mpp1, Mrap, Mras, Mrps25, Msl1, Mtap, Mtch2, Mtmr2, Mtmr3, Mtmr4, Mtpn, Mxd4, Myadm, Myo1c, N4bp1, N6amt1, Naa15, Nbr1, Ncaph, Ndor1, Nf2, Nfat5, Nfatc3, Nfe2l1, Nfrkb, Nipsnap1, Nop56, Nras, Nrbp1, Nrn1, Nucks1, Nudt4, Numb, Nup50, Nusap1, Ocrl, Ogt, Otud4, Otud6b, Pacsin2, Pafah1b1, Pafah1b2, Paip2b, Pam, Pan3, Pappa, Patl1, Patz1, Pbxip1, Pcid2, Pcm1, Pcmt1, Pdap1, Pdcd4, Pdcd6ip, Pdia6, Peli2, Pex13, Pex5, Pfas, Pfkl, Pgm2, Phf13, Phf21a, Pi4kb, Pias2, Pik3r1, Pisd, Pitpna, Pkd1, Pkdcc, Plagl1, Plekha1, Plrg1, Plxna1, Plxnc1, Pmpcb, Pnpla6, Pom121, Ppap2b, Ppif, Ppig, Ppih, Ppm1a, Ppme1, Ppp1r11, Ppp2r1a, Ppp2r5c, Ppp6c, Ppt1, Prkrir, Prr11, Prrc2c, Pskh1, Psme3, Ptpn11, Ptprd, Pum2, Purb, Pvrl1, Qars, Qk, R3hdm2, Rab10, Rab14, Rab22a, Rab4b, Rab5b, Rabac1, Rabep1, Rad23b, Rad51, Raf1, Ralgapb, Ranbp3, Rap2c, Rapgef1, Rasgef1b, Rassf2, Rbbp6, Rbfox2, Rbm12, Rbm39, Rbm6, Rbms1, Rcor3, Repin1, Rere, Rfc1, Rfwd2, Rgp1, Rhobtb3, Ric8, Rimklb, Rnf10, Rnf123, Rnf41, Rnf8, Rock2, Rpl22, Rpl6, Rprd1b, Rps6ka3, Rptor, Rrnad1, Rtf1, Rtn3, Rtn4, Rybp, Samd10, Samd8, Sbf1, Scoc, Sdf2, Sec16a, Sec61a1, Sec62, Secisbp2l, Seh1l, Sel1l3, Sept2, Sept6, Serbp1, Serinc3, Sesn1, Setd3, Setd5, Sgcb, Sgk1, Shoc2, Sidt2, Sil1, Ski, Slc12a6, Slc20a2, Slc25a22, Slc25a37, Slc2a1, Slc35c2, Slc39a10, Slc45a4, Smad3, Smad5, Smarca1, Smarcd2, Smc5, Smek2, Smg7, Sms, Smyd5, Snx27, Son, Spag7, Spns1, Spred1, Spsb4, Sptlc1, Spty2d1, Srp14, Srpk1, Srpr, Srprb, Srsf11, Ssr1, Stim1, Stradb, Stxbp6, Sumo3, Suz12, Syde1, Syne2, Sypl, Tacc1, Tarbp2, Tars2, Tbc1d10b, Tbk1, Tbp, Tcta, Tesk1, Tet3, Tgoln1, Tk2, Tlk1, Tm7sf2, Tmem109, Tmem135, Tmem183a, Tmem184b, Tmem201, Tmem206, Tmem33, Tmem39b, Tmem55a, Tmem55b, Tmem87a, Tmem87b, Tmtc4, Tnfaip1, Tnpo1, Tnpo3, Tollip, Top2b, Tpt1, Tram1, Trim35, Trim39, Trip10, Trp53inp2, Tspyl2, Ttc14, Tuba1a, Tubgcp3, Txnl4a, Ubap1, Ube2g2, Ube2j1, Ube2q1, Ube2v1, Ube4b, Ubfd1, Ubl5, Ubn2, Ubr3, Ubr4, Uggt1, Unc119b, Usp12, Usp14, Usp19, Usp25, Usp7, Usp9x, Vamp8, Vapb, Vat1, Vbp1, Vegfa, Vps37c, Vti1b, Wasl, Wbp11, Wdr82, Whsc1, Wibg, Wipi2, Wnt4, Wsb1, Wsb2, Xpr1, Ythdc1, Ywhah, Ywhaq, Zc3h11a, Zdhhc18, Zdhhc21, Zer1, Zfand3, Zfp326, Zfp362, Zfp523, Zfp687, Zmym2, Zmynd11, Znrf2, Zyx ______1

Table S2. Biological processes (GO terms) significantly associated with the putative miR-322 targets expressed in MGCs TermID Term Q Symbols GO:0044267 cellular protein metabolic process 1.24E-19 Adh5,Adrbk1,Amfr,App,Arih1,Atg4b,Atxn7l3,B4galt1,B4galt7,Baz2a,Bfar,Bmpr1a,Brd4,Brpf3,Bt g2,Cab39,Carm1,Cd2ap,Cdc25a,Cdc27,Cdc37l1,Cdk5rap3,Cdk8,Cdk9,Chordc1,Cops7a,Cops 7b,Cul4a,Cul4b,D2hgdh,Ddost,Ddr1,Ddx3x,Dnaja2,Dnajb2,Dnajc1,Dpm1,Dpy19l4,Dtl,Dyrk1a,D yrk1b,Egln2,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Enc1,Erlin2,Erp29,Faf2,Fastk,Fkbp1a,Fkbp5 ,Fkrp,Fnta,Furin,Galnt1,Galnt7,Gpaa1,Gsk3b,Gtpbp2,Hectd1,Herc3,Hipk3,Hsph1,Iars,Igf1,Igf1r ,Ing4,Insr,Itgav,Kcmf1,Larp1,Lats1,Lats2,Limk2,Man2a1,Map2k1,Map2k3,Map3k3,Map3k4,Ma pk3,Mapk9,Mapkapk3,March6,Mark2,Med1,Med24,Mesdc2,Mink1,Mknk1,Mrps25,Msl1,Mtmr2, Mtmr3,N6amt1,Naa15,Ocrl,Ogt,Otud4,Pam,Pcmt1,Pdcd6ip,Pdia6,Pias2,Pik3r1,Pkd1,Pkdcc,Pp ap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1,Ppp2r1a,Ppp2r5c,Ppp6c,Ppt1,Pskh1,Ptpn11,Raf1,Rassf2, Rbbp6,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rtf1,Rybp,Sec16a,Setd3,Sgk1,Slc35c 2,Smad5,Smek2,Srpk1,Stradb,Sumo3,Suz12,Tbk1,Tesk1,Tet3,Tlk1,Tmem55a,Tmem55b,Tnfai p1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4b,Ubl5,Ubr3,Ubr4,Usp12,Usp14,Us p19,Usp25,Usp7,Usp9x,Wdr82,Whsc1,Wipi2,Zdhhc18,Zdhhc21,Zer1,Znrf2 GO:0044260 cellular macromolecule metabolic process 6.15E-18 Adh5,Adrbk1,Ahcyl1,Amfr,App,Arih1,Atg4b,Atxn7l3,B4galt1,B4galt7,Baz2a,Bfar,Bmpr1a,Bptf,Br d4,Brpf3,Btg2,Cab39,Carm1,Cd2ap,Cdc25a,Cdc27,Cdc37l1,Cdk5rap3,Cdk8,Cdk9,Celf1,Chord c1,Chpf,Chst8,Cnot1,Cnot2,Cops7a,Cops7b,Crebzf,Csde1,Cul4a,Cul4b,D2hgdh,Dcp1a,Ddost, Ddr1,Ddx39,Ddx3x,Ddx6,Dhx16,Dnaja2,Dnajb2,Dnajc1,Dpm1,Dpy19l4,Dsel,Dtl,Dvl1,Dyrk1a,Dy rk1b,Ebna1bp2,Egln2,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Enc1,Erlin2,Erp29,Etv6,Faf2,Fastk ,Fkbp1a,Fkbp5,Fkrp,Flna,Fnta,Fosl2,Furin,Galnt1,Galnt7,Gatad2a,Gpaa1,Gsk3b,Gtpbp2,Hectd 1,Herc3,Hipk3,Hnrnpa1,Hnrnpa2b1,Hsph1,Iars,Igf1,Igf1r,Ihh,Ing4,Insr,Ints3,Itgav,Kcmf1,Larp1, Lats1,Lats2,Limk2,Man2a1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,March 6,Mark2,Med1,Med24,Mesdc2,Mink1,Mknk1,Mms19,Mov10,Mrps25,Msl1,Mtmr2,Mtmr3,N6amt 1,Naa15,Nfat5,Nfatc3,Nfe2l1,Nop56,Nucks1,Ocrl,Ogt,Otud4,Pam,Pan3,Patl1,Patz1,Pcmt1,Pdc d6ip,Pdia6,Pgm2,Pias2,Pik3r1,Pkd1,Pkdcc,Plagl1,Plrg1,Ppap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1, Ppp2r1a,Ppp2r5c,Ppp6c,Ppt1,Pskh1,Ptpn11,Qk,Rad23b,Rad51,Raf1,Rassf2,Rbbp6,Rbm39,Re re,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rtf1,Rybp,Sec16a,Setd3,Sgk1,Slc35c2,S mad3,Smad5,Smarca1,Smc5,Smek2,Son,Srpk1,Stradb,Sumo3,Suz12,Tarbp2,Tbk1,Tbp,Tesk1 ,Tet3,Tk2,Tlk1,Tmem55a,Tmem55b,Tnfaip1,Top2b,Trp53inp2,Txnl4a,Ubap1,Ube2g2,Ube2j1,U be2q1,Ube2v1,Ube4b,Ubl5,Ubr3,Ubr4,Usp12,Usp14,Usp19,Usp25,Usp7,Usp9x,Wbp11,Wdr82, Whsc1,Wibg,Wipi2,Ythdc1,Zdhhc18,Zdhhc21,Zer1,Zfp326,Znrf2

Table S2_2 2

GO:0006464 cellular protein modification process 3.26E-17 Adh5,Adrbk1,Amfr,App,Arih1,Atg4b,Atxn7l3,B4galt1,B4galt7,Baz2a,Bfar,Bmpr1a,Brd4,Brpf3,Bt g2,Cab39,Carm1,Cdc25a,Cdc27,Cdk5rap3,Cdk8,Cdk9,Cops7a,Cops7b,Cul4a,Cul4b,Ddost,Ddr 1,Dpm1,Dpy19l4,Dtl,Dyrk1a,Dyrk1b,Egln2,Eif2s1,Enc1,Fastk,Fkbp1a,Fkbp5,Fkrp,Fnta,Galnt1, Galnt7,Gpaa1,Gsk3b,Hectd1,Herc3,Hipk3,Igf1,Igf1r,Ing4,Insr,Itgav,Kcmf1,Lats1,Lats2,Limk2,M an2a1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,March6,Mark2,Med1,Med2 4,Mink1,Mknk1,Msl1,Mtmr2,Mtmr3,N6amt1,Naa15,Ocrl,Ogt,Otud4,Pam,Pcmt1,Pias2,Pik3r1,Pk d1,Pkdcc,Ppap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1,Ppp2r1a,Ppp6c,Ppt1,Pskh1,Ptpn11,Raf1,Rass f2,Rbbp6,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rtf1,Rybp,Sec16a,Setd3,Sgk1,Slc 35c2,Smad5,Smek2,Srpk1,Stradb,Sumo3,Suz12,Tbk1,Tesk1,Tet3,Tlk1,Tmem55a,Tmem55b,T nfaip1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4b,Ubl5,Ubr3,Ubr4,Usp12,Usp14,Usp19,Usp25,Us p7,Usp9x,Wdr82,Whsc1,Wipi2,Zdhhc18,Zdhhc21,Zer1,Znrf2 GO:0036211 protein modification process 3.26E-17 Adh5,Adrbk1,Amfr,App,Arih1,Atg4b,Atxn7l3,B4galt1,B4galt7,Baz2a,Bfar,Bmpr1a,Brd4,Brpf3,Bt g2,Cab39,Carm1,Cdc25a,Cdc27,Cdk5rap3,Cdk8,Cdk9,Cops7a,Cops7b,Cul4a,Cul4b,Ddost,Ddr 1,Dpm1,Dpy19l4,Dtl,Dyrk1a,Dyrk1b,Egln2,Eif2s1,Enc1,Fastk,Fkbp1a,Fkbp5,Fkrp,Fnta,Galnt1, Galnt7,Gpaa1,Gsk3b,Hectd1,Herc3,Hipk3,Igf1,Igf1r,Ing4,Insr,Itgav,Kcmf1,Lats1,Lats2,Limk2,M an2a1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,March6,Mark2,Med1,Med2 4,Mink1,Mknk1,Msl1,Mtmr2,Mtmr3,N6amt1,Naa15,Ocrl,Ogt,Otud4,Pam,Pcmt1,Pias2,Pik3r1,Pk d1,Pkdcc,Ppap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1,Ppp2r1a,Ppp6c,Ppt1,Pskh1,Ptpn11,Raf1,Rass f2,Rbbp6,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rtf1,Rybp,Sec16a,Setd3,Sgk1,Slc 35c2,Smad5,Smek2,Srpk1,Stradb,Sumo3,Suz12,Tbk1,Tesk1,Tet3,Tlk1,Tmem55a,Tmem55b,T nfaip1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4b,Ubl5,Ubr3,Ubr4,Usp12,Usp14,Usp19,Usp25,Us p7,Usp9x,Wdr82,Whsc1,Wipi2,Zdhhc18,Zdhhc21,Zer1,Znrf2 GO:0043412 macromolecule modification 4.35E-16 Adh5,Adrbk1,Amfr,App,Arih1,Atg4b,Atxn7l3,B4galt1,B4galt7,Baz2a,Bfar,Bmpr1a,Brd4,Brpf3,Bt g2,Cab39,Carm1,Cdc25a,Cdc27,Cdk5rap3,Cdk8,Cdk9,Cops7a,Cops7b,Cul4a,Cul4b,Ddost,Ddr 1,Dpm1,Dpy19l4,Dtl,Dyrk1a,Dyrk1b,Egln2,Eif2s1,Enc1,Fastk,Fkbp1a,Fkbp5,Fkrp,Fnta,Galnt1, Galnt7,Gatad2a,Gpaa1,Gsk3b,Hectd1,Herc3,Hipk3,Igf1,Igf1r,Ing4,Insr,Itgav,Kcmf1,Lats1,Lats2 ,Limk2,Man2a1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,March6,Mark2,Me d1,Med24,Mink1,Mknk1,Msl1,Mtmr2,Mtmr3,N6amt1,Naa15,Nop56,Ocrl,Ogt,Otud4,Pam,Pcmt1, Pias2,Pik3r1,Pkd1,Pkdcc,Ppap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1,Ppp2r1a,Ppp6c,Ppt1,Pskh1,Pt pn11,Raf1,Rassf2,Rbbp6,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rtf1,Rybp,Sec16a, Setd3,Sgk1,Slc35c2,Smad5,Smek2,Srpk1,Stradb,Sumo3,Suz12,Tbk1,Tesk1,Tet3,Tlk1,Tmem5 5a,Tmem55b,Tnfaip1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4b,Ubl5,Ubr3,Ubr4,Usp12,Usp14,U sp19,Usp25,Usp7,Usp9x,Wdr82,Whsc1,Wipi2,Zdhhc18,Zdhhc21,Zer1,Znrf2

Table S2_2 3

GO:0019538 protein metabolic process 3.46E-15 Adh5,Adrbk1,Amfr,App,Arih1,Atg4b,Atxn7l3,B4galt1,B4galt7,Bace1,Baz2a,Bfar,Bmpr1a,Brd4,B rpf3,Btg2,Cab39,Capns1,Carm1,Cd2ap,Cdc25a,Cdc27,Cdc37l1,Cdk5rap3,Cdk8,Cdk9,Chordc1 ,Chpf,Chst8,Cops7a,Cops7b,Cul4a,Cul4b,D2hgdh,Ddost,Ddr1,Ddx3x,Dnaja2,Dnajb2,Dnajc1,D pm1,Dpy19l4,Dsel,Dtl,Dyrk1a,Dyrk1b,Egln2,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Enc1,Erlin2, Erp29,Faf2,Fastk,Fkbp1a,Fkbp5,Fkrp,Fnta,Furin,Galnt1,Galnt7,Gpaa1,Gsk3b,Gtpbp2,Hectd1, Herc3,Hipk3,Hsph1,Iars,Igf1,Igf1r,Ihh,Ing4,Insr,Itgav,Kcmf1,Larp1,Lats1,Lats2,Limk2,Lnpep,Ma n2a1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,March6,Mark2,Med1,Med24, Mesdc2,Mink1,Mknk1,Mrps25,Msl1,Mtmr2,Mtmr3,N6amt1,Naa15,Ocrl,Ogt,Otud4,Pam,Pappa, Pcmt1,Pdcd6ip,Pdia6,Pias2,Pik3r1,Pkd1,Pkdcc,Pmpcb,Ppap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1, Ppp2r1a,Ppp2r5c,Ppp6c,Ppt1,Pskh1,Ptpn11,Raf1,Rassf2,Rbbp6,Rfwd2,Rnf10,Rnf41,Rnf8,Roc k2,Rprd1b,Rps6ka3,Rtf1,Rybp,Sec16a,Setd3,Sgk1,Slc35c2,Smad3,Smad5,Smek2,Srpk1,Stra db,Sumo3,Suz12,Tbk1,Tesk1,Tet3,Tlk1,Tmem55a,Tmem55b,Tnfaip1,Trp53inp2,Ubap1,Ube2g 2,Ube2j1,Ube2q1,Ube2v1,Ube4b,Ubl5,Ubr3,Ubr4,Usp12,Usp14,Usp19,Usp25,Usp7,Usp9x,Wd r82,Whsc1,Wipi2,Zdhhc18,Zdhhc21,Zer1,Znrf2 GO:0044237 cellular metabolic process 5.94E-15 Acox1,Acsbg1,Acsl4,Adh5,Adrbk1,Agk,Ahcyl1,Amfr,App,Arih1,Asnsd1,Atg13,Atg4b,Atp5g1,Atx n7l3,B4galt1,B4galt7,Bace1,Baz2a,Bfar,Bmpr1a,Bptf,Brd4,Brpf3,Btg2,Cab39,Carm1,Cd2ap,Cd c25a,Cdc27,Cdc37l1,Cdipt,Cdk5rap3,Cdk8,Cdk9,Celf1,Chordc1,Chpf,Chpt1,Chst8,Cisd2,Cmp k1,Cnot1,Cnot2,Col4a3bp,Cops7a,Cops7b,Coq6,Crebzf,Csde1,Cul4a,Cul4b,D2hgdh,Dcp1a,Dd ost,Ddr1,Ddx39,Ddx3x,Ddx6,Dhx16,Dlst,Dnaja2,Dnajb2,Dnajc1,Dpm1,Dpy19l4,Dsel,Dtl,Dvl1,D yrk1a,Dyrk1b,Ebna1bp2,Egln2,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Elovl5,Enc1,Entpd4,Erlin2 ,Erp29,Etnk1,Etv6,Faf2,Fasn,Fastk,Fkbp1a,Fkbp5,Fkrp,Flna,Fnta,Fosl2,Furin,Galnt1,Galnt7,G atad2a,Gbf1,Gclm,Glud1,Gpaa1,Gsk3b,Gtpbp2,H6pd,Hectd1,Herc3,Hipk3,Hnrnpa1,Hnrnpa2b1 ,Hsph1,Iars,Idh3a,Igf1,Igf1r,Ihh,Ing4,Insr,Ints3,Ip6k1,Itgav,Kcmf1,Larp1,Lats1,Lats2,Limk2,Ly6e ,Man2a1,Map1lc3b,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,March6,Mark2, Med1,Med24,Mesdc2,Mink1,Mknk1,Mms19,Mov10,Mrps25,Msl1,Mtap,Mtmr2,Mtmr3,N6amt1,N aa15,Nbr1,Nfat5,Nfatc3,Nfe2l1,Nop56,Nucks1,Ocrl,Ogt,Otud4,Pam,Pan3,Patl1,Patz1,Pcmt1,P dcd6ip,Pdia6,Pex13,Pex5,Pfas,Pfkl,Pgm2,Pi4kb,Pias2,Pik3r1,Pkd1,Pkdcc,Plagl1,Plekha1,Plrg1 ,Pmpcb,Ppap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1,Ppp2r1a,Ppp2r5c,Ppp6c,Ppt1,Pskh1,Ptpn11,Qk ,Rad23b,Rad51,Raf1,Rassf2,Rbbp6,Rbm39,Rere,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps 6ka3,Rtf1,Rybp,Samd8,Sec16a,Setd3,Sgk1,Slc35c2,Smad3,Smad5,Smarca1,Smc5,Smek2,S ms,Son,Sptlc1,Srpk1,Stradb,Sumo3,Suz12,Tarbp2,Tbk1,Tbp,Tesk1,Tet3,Tk2,Tlk1,Tmem55a,T mem55b,Tnfaip1,Tollip,Top2b,Trp53inp2,Txnl4a,Ubap1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4 b,Ubl5,Ubr3,Ubr4,Uggt1,Usp12,Usp14,Usp19,Usp25,Usp7,Usp9x,Vamp8,Wbp11,Wdr82,Whsc 1,Wibg,Wipi2,Wnt4,Ythdc1,Zdhhc18,Zdhhc21,Zer1,Zfp326,Znrf2

Table S2_2 4

GO:0043170 macromolecule metabolic process 1.43E-13 Adh5,Adrbk1,Ahcyl1,Amfr,App,Arih1,Atg4b,Atxn7l3,B4galt1,B4galt7,Bace1,Baz2a,Bfar,Bmpr1a, Bptf,Brd4,Brpf3,Btg2,Cab39,Capns1,Carm1,Cd2ap,Cdc25a,Cdc27,Cdc37l1,Cdk5rap3,Cdk8,Cd k9,Celf1,Chordc1,Chpf,Chst8,Cnot1,Cnot2,Cops7a,Cops7b,Crebzf,Csde1,Cul4a,Cul4b,D2hgdh ,Dcp1a,Ddost,Ddr1,Ddx39,Ddx3x,Ddx6,Dhx16,Dnaja2,Dnajb2,Dnajc1,Dpm1,Dpy19l4,Dsel,Dtl, Dvl1,Dyrk1a,Dyrk1b,Ebna1bp2,Egln2,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Enc1,Erlin2,Erp29, Etv6,Faf2,Fastk,Fkbp1a,Fkbp5,Fkrp,Flna,Fnta,Fosl2,Furin,Galnt1,Galnt7,Gatad2a,Gpaa1,Gsk3 b,Gtpbp2,Hectd1,Herc3,Hipk3,Hnrnpa1,Hnrnpa2b1,Hsph1,Iars,Igf1,Igf1r,Ihh,Ing4,Insr,Ints3,Itga v,Kcmf1,Larp1,Lats1,Lats2,Limk2,Lnpep,Man2a1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Ma pk9,Mapkapk3,March6,Mark2,Med1,Med24,Mesdc2,Mink1,Mknk1,Mms19,Mov10,Mrps25,Msl1 ,Mtmr2,Mtmr3,N6amt1,Naa15,Nfat5,Nfatc3,Nfe2l1,Nop56,Nucks1,Ocrl,Ogt,Otud4,Pam,Pan3,P appa,Patl1,Patz1,Pcmt1,Pdcd6ip,Pdia6,Pgm2,Pias2,Pik3r1,Pkd1,Pkdcc,Plagl1,Plrg1,Pmpcb,Pp ap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1,Ppp2r1a,Ppp2r5c,Ppp6c,Ppt1,Pskh1,Ptpn11,Qk,Rad23b,R ad51,Raf1,Rassf2,Rbbp6,Rbm39,Rere,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rtf1, Rybp,Sec16a,Setd3,Sgk1,Slc35c2,Smad3,Smad5,Smarca1,Smc5,Smek2,Son,Srpk1,Stradb,Su mo3,Suz12,Tarbp2,Tbk1,Tbp,Tesk1,Tet3,Tk2,Tlk1,Tmem55a,Tmem55b,Tnfaip1,Top2b,Trp53i np2,Txnl4a,Ubap1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4b,Ubl5,Ubr3,Ubr4,Usp12,Usp14,Usp1 9,Usp25,Usp7,Usp9x,Wbp11,Wdr82,Whsc1,Wibg,Wipi2,Ythdc1,Zc3h11a,Zdhhc18,Zdhhc21,Ze r1,Zfp326,Znrf2 GO:0044238 primary metabolic process 3.84E-13 Acox1,Acsbg1,Acsl4,Adh5,Adrbk1,Agk,Ahcyl1,Alg3,Amfr,App,Arih1,Asnsd1,Atg4b,Atp5g1,Atxn 7l3,B4galt1,B4galt7,Bace1,Baz2a,Bfar,Bmpr1a,Bptf,Brd4,Brpf3,Btg2,Cab39,Capns1,Carm1,Cd 2ap,Cdc25a,Cdc27,Cdc37l1,Cdipt,Cdk5rap3,Cdk8,Cdk9,Celf1,Chordc1,Chpf,Chpt1,Chst8,Cmp k1,Cnot1,Cnot2,Col4a3bp,Cops7a,Cops7b,Crebzf,Csde1,Cul4a,Cul4b,D2hgdh,Dcp1a,Ddost,D dr1,Ddx39,Ddx3x,Ddx6,Dhx16,Dlst,Dnaja2,Dnajb2,Dnajc1,Dpm1,Dpy19l4,Dsel,Dtl,Dvl1,Dyrk1a ,Dyrk1b,Ebna1bp2,Egln2,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Elovl5,Enc1,Entpd4,Erlin2,Erp2 9,Etnk1,Etv6,Faf2,Fasn,Fastk,Fkbp1a,Fkbp5,Fkrp,Flna,Fnta,Fosl2,Furin,Galnt1,Galnt7,Gatad2 a,Gclm,Glud1,Gpaa1,Gsk3b,Gtpbp2,H6pd,Hectd1,Herc3,Hipk3,Hnrnpa1,Hnrnpa2b1,Hsd17b7, Hsph1,Iars,Idh3a,Igf1,Igf1r,Ihh,Ing4,Insr,Ints3,Ip6k1,Itgav,Kcmf1,Larp1,Lats1,Lats2,Limk2,Lnpe p,Lrp5,Man2a1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,March6,Mark2,Me d1,Med24,Mesdc2,Mink1,Mknk1,Mms19,Mov10,Mrps25,Msl1,Mtap,Mtmr2,Mtmr3,N6amt1,Naa 15,Nfat5,Nfatc3,Nfe2l1,Nop56,Nucks1,Ocrl,Ogt,Otud4,Pam,Pan3,Pappa,Patl1,Patz1,Pcmt1,Pd cd6ip,Pdia6,Pex13,Pex5,Pfas,Pfkl,Pgm2,Pi4kb,Pias2,Pik3r1,Pkd1,Pkdcc,Plagl1,Plekha1,Plrg1, Pmpcb,Ppap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1,Ppp2r1a,Ppp2r5c,Ppp6c,Ppt1,Pskh1,Ptpn11,Qk, Rad23b,Rad51,Raf1,Rassf2,Rbbp6,Rbm39,Rere,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps 6ka3,Rtf1,Rybp,Samd8,Sec16a,Setd3,Sgk1,Slc35c2,Smad3,Smad5,Smarca1,Smc5,Smek2,So n,Sptlc1,Srpk1,Stradb,Sumo3,Suz12,Tarbp2,Tbk1,Tbp,Tesk1,Tet3,Tk2,Tlk1,Tmem55a,Tmem5 5b,Tnfaip1,Top2b,Trp53inp2,Txnl4a,Ubap1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4b,Ubl5,Ubr3, Ubr4,Uggt1,Usp12,Usp14,Usp19,Usp25,Usp7,Usp9x,Wbp11,Wdr82,Whsc1,Wibg,Wipi2,Wnt4, Ythdc1,Ywhah,Zdhhc18,Zdhhc21,Zer1,Zfp326,Znrf2

Table S2_2 5

GO:0071704 organic substance metabolic process 4.30E-11 Acox1,Acsbg1,Acsl4,Adh5,Adrbk1,Agk,Ahcyl1,Alg3,Amfr,App,Arih1,Asnsd1,Atg4b,Atp5g1,Atxn 7l3,B4galt1,B4galt7,Bace1,Baz2a,Bfar,Bmpr1a,Bptf,Brd4,Brpf3,Btg2,Cab39,Capns1,Carm1,Cd 2ap,Cdc25a,Cdc27,Cdc37l1,Cdipt,Cdk5rap3,Cdk8,Cdk9,Celf1,Chordc1,Chpf,Chpt1,Chst8,Cmp k1,Cnot1,Cnot2,Col4a3bp,Cops7a,Cops7b,Coq6,Crebzf,Csde1,Cul4a,Cul4b,D2hgdh,Dcp1a,Dd ost,Ddr1,Ddx39,Ddx3x,Ddx6,Dhx16,Dlst,Dnaja2,Dnajb2,Dnajc1,Dpm1,Dpy19l4,Dsel,Dtl,Dvl1,D yrk1a,Dyrk1b,Ebna1bp2,Egln2,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Elovl5,Enc1,Entpd4,Erlin2 ,Erp29,Etnk1,Etv6,Faf2,Fasn,Fastk,Fkbp1a,Fkbp5,Fkrp,Flna,Fnta,Fosl2,Furin,Galnt1,Galnt7,G atad2a,Gclm,Glud1,Gpaa1,Gsk3b,Gtpbp2,H6pd,Hectd1,Herc3,Hipk3,Hnrnpa1,Hnrnpa2b1,Hsd 17b7,Hsph1,Iars,Idh3a,Igf1,Igf1r,Ihh,Ing4,Insr,Ints3,Ip6k1,Itgav,Kcmf1,Larp1,Lats1,Lats2,Limk2 ,Lnpep,Lrp5,Ly6e,Man2a1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,March6, Mark2,Med1,Med24,Mesdc2,Mink1,Mknk1,Mms19,Mov10,Mrps25,Msl1,Mtap,Mtmr2,Mtmr3,N6 amt1,Naa15,Nfat5,Nfatc3,Nfe2l1,Nop56,Nucks1,Ocrl,Ogt,Otud4,Pam,Pan3,Pappa,Patl1,Patz1, Pcmt1,Pdcd6ip,Pdia6,Pex13,Pex5,Pfas,Pfkl,Pgm2,Pi4kb,Pias2,Pik3r1,Pkd1,Pkdcc,Plagl1,Plek ha1,Plrg1,Pmpcb,Ppap2b,Ppif,Ppig,Ppih,Ppm1a,Ppme1,Ppp2r1a,Ppp2r5c,Ppp6c,Ppt1,Pskh1,P tpn11,Qk,Rad23b,Rad51,Raf1,Rassf2,Rbbp6,Rbm39,Rere,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rp rd1b,Rps6ka3,Rtf1,Rybp,Samd8,Sec16a,Setd3,Sgk1,Slc35c2,Smad3,Smad5,Smarca1,Smc5,S mek2,Sms,Son,Sptlc1,Srpk1,Stradb,Sumo3,Suz12,Tarbp2,Tbk1,Tbp,Tesk1,Tet3,Tk2,Tlk1,Tme m55a,Tmem55b,Tnfaip1,Top2b,Trp53inp2,Txnl4a,Ubap1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube 4b,Ubl5,Ubr3,Ubr4,Uggt1,Usp12,Usp14,Usp19,Usp25,Usp7,Usp9x,Wbp11,Wdr82,Whsc1,Wib g,Wipi2,Wnt4,Ythdc1,Ywhah,Zc3h11a,Zdhhc18,Zdhhc21,Zer1,Zfp326,Znrf2 GO:0008152 metabolic process 3.09E-10 Acox1,Acsbg1,Acsl4,Adh5,Adrbk1,Agk,Ahcyl1,Alg3,Amfr,App,Arih1,Asnsd1,Atg13,Atg4b,Atp5g 1,Atxn7l3,B4galt1,B4galt7,Bace1,Baz2a,Bfar,Bmpr1a,Bptf,Brd4,Brpf3,Btg2,Cab39,Capns1,Car m1,Cd2ap,Cdc25a,Cdc27,Cdc37l1,Cdipt,Cdk5rap3,Cdk8,Cdk9,Celf1,Chordc1,Chpf,Chpt1,Chst 8,Cisd2,Cmpk1,Cnot1,Cnot2,Col4a3bp,Cops7a,Cops7b,Coq6,Crebzf,Csde1,Cul4a,Cul4b,D2hg dh,Dcp1a,Ddost,Ddr1,Ddx39,Ddx3x,Ddx6,Dhx16,Dlst,Dnaja2,Dnajb2,Dnajc1,Dpm1,Dpy19l4,Ds el,Dtl,Dvl1,Dyrk1a,Dyrk1b,Ebna1bp2,Egln2,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Elovl5,Enc1, Entpd4,Erlin2,Erp29,Etnk1,Etv6,Faf2,Fasn,Fastk,Fkbp1a,Fkbp5,Fkrp,Flna,Fnta,Fosl2,Furin,Gal nt1,Galnt7,Gatad2a,Gbf1,Gclm,Glud1,Gpaa1,Gsk3b,Gtpbp2,H6pd,Hectd1,Herc3,Hipk3,Hnrnpa 1,Hnrnpa2b1,Hsd17b7,Hsph1,Iars,Idh3a,Igf1,Igf1r,Ihh,Ing4,Insr,Ints3,Ip6k1,Itgav,Kcmf1,Larp1, Lats1,Lats2,Limk2,Lnpep,Lrp5,Ly6e,Man2a1,Map1lc3b,Map2k1,Map2k3,Map3k3,Map3k4,Map k3,Mapk9,Mapkapk3,March6,Mark2,Med1,Med24,Mesdc2,Mink1,Mknk1,Mms19,Mov10,Mrps2 5,Msl1,Mtap,Mtmr2,Mtmr3,N6amt1,Naa15,Nbr1,Ndor1,Nfat5,Nfatc3,Nfe2l1,Nop56,Nucks1,Ocrl ,Ogt,Otud4,Pam,Pan3,Pappa,Patl1,Patz1,Pcmt1,Pdcd6ip,Pdia6,Pex13,Pex5,Pfas,Pfkl,Pgm2,Pi 4kb,Pias2,Pik3r1,Pkd1,Pkdcc,Plagl1,Plekha1,Plrg1,Pmpcb,Ppap2b,Ppif,Ppig,Ppih,Ppm1a,Ppm e1,Ppp2r1a,Ppp2r5c,Ppp6c,Ppt1,Pskh1,Ptpn11,Qk,Rad23b,Rad51,Raf1,Rassf2,Rbbp6,Rbm39 ,Rere,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rtf1,Rybp,Samd8,Sec16a,Setd3,Sgk1, Slc35c2,Smad3,Smad5,Smarca1,Smc5,Smek2,Sms,Son,Sptlc1,Srpk1,Stradb,Sumo3,Suz12,T arbp2,Tbk1,Tbp,Tesk1,Tet3,Tk2,Tlk1,Tmem55a,Tmem55b,Tnfaip1,Tollip,Top2b,Trp53inp2,Tx nl4a,Ubap1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4b,Ubl5,Ubr3,Ubr4,Uggt1,Usp12,Usp14,Usp1 9,Usp25,Usp7,Usp9x,Vamp8,Wbp11,Wdr82,Whsc1,Wibg,Wipi2,Wnt4,Ythdc1,Ywhah,Zc3h11a, Zdhhc18,Zdhhc21,Zer1,Zfp326,Znrf2 Table S2_2 6

GO:0051641 cellular localization 6.44E-10 Actr2,Ahcyl1,Ankfy1,Ap2a1,Ap3b1,Ap3d1,App,Arcn1,Arl2,Arl3,Atg4b,Bcl2l1,Chmp1a,Chmp7,C nih2,Col4a3bp,Cope,Copz1,Ctnnb1,Ddx39,Diap1,Dvl1,Dync1li2,Dynll2,Erp29,Evi5,Faf2,Fermt2, Fkbp1a,Flna,Furin,Gbf1,Gsk3b,Hdgf,Ipo4,Itgav,Itgb1,Itpr1,Kif1b,Kif1c,Kif5b,Klc1,Kpna4,Lats1,L ats2,Lrp6,Lsg1,Ly6e,Macf1,Map2k1,Mapk3,Mapre1,Mesdc2,Mfn2,Mlxip,Mrap,Mtch2,Myadm,My o1c,Nras,Nrbp1,Nup50,Nusap1,Ogt,Pacsin2,Pafah1b1,Pan3,Pcm1,Pex13,Pex5,Pik3r1,Pkd1,Pl rg1,Ppif,Ppt1,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Raf1,Rgp1,Rhobtb3,Sec61a1,Sec62,Seh1l, Snx27,Srp14,Stradb,Stxbp6,Sumo3,Syde1,Syne2,Tacc1,Tbc1d10b,Tgoln1,Tlk1,Tmem201,Tm em33,Tnpo3,Tollip,Ube2q1,Vamp8,Vapb,Vti1b,Wasl,Wipi2,Wnt4,Ywhah,Ywhaq,Zc3h11a,Zdhh c18 GO:0046907 intracellular transport 2.64E-09 Actr2,Ahcyl1,Ankfy1,Ap2a1,Ap3b1,Ap3d1,App,Arcn1,Arl3,Atg4b,Bcl2l1,Chmp7,Col4a3bp,Cope, Copz1,Ddx39,Dynll2,Erp29,Evi5,Faf2,Fkbp1a,Flna,Gbf1,Gsk3b,Ipo4,Itgav,Itgb1,Itpr1,Kif1b,Kif1 c,Kif5b,Klc1,Kpna4,Lrp6,Lsg1,Macf1,Map2k1,Mapk3,Mfn2,Mlxip,Mtch2,Myadm,Myo1c,Nrbp1,N up50,Pafah1b1,Pan3,Pcm1,Pex13,Pex5,Pik3r1,Pkd1,Ppif,Rab10,Rab14,Rab22a,Rab4b,Rab5b ,Rgp1,Rhobtb3,Sec61a1,Sec62,Snx27,Srp14,Stradb,Stxbp6,Tbc1d10b,Tgoln1,Tlk1,Tnpo3,Vap b,Vti1b,Ywhah,Ywhaq,Zc3h11a GO:0051649 establishment of localization in cell 2.69E-08 Actr2,Ahcyl1,Ankfy1,Ap2a1,Ap3b1,Ap3d1,App,Arcn1,Arl3,Atg4b,Bcl2l1,Chmp1a,Chmp7,Col4a3 bp,Cope,Copz1,Ctnnb1,Ddx39,Dvl1,Dynll2,Erp29,Evi5,Faf2,Fkbp1a,Flna,Furin,Gbf1,Gsk3b,Ipo 4,Itgav,Itgb1,Itpr1,Kif1b,Kif1c,Kif5b,Klc1,Kpna4,Lrp6,Lsg1,Ly6e,Macf1,Map2k1,Mapk3,Mfn2,Mlx ip,Mtch2,Myadm,Myo1c,Nrbp1,Nup50,Nusap1,Pafah1b1,Pan3,Pcm1,Pex13,Pex5,Pik3r1,Pkd1, Ppif,Ppt1,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Raf1,Rgp1,Rhobtb3,Sec61a1,Sec62,Seh1l,Snx 27,Srp14,Stradb,Stxbp6,Syde1,Syne2,Tbc1d10b,Tgoln1,Tlk1,Tmem201,Tnpo3,Ube2q1,Vamp8 ,Vapb,Vti1b,Wasl,Ywhah,Ywhaq,Zc3h11a GO:1902582 single-organism intracellular transport 6.60E-08 Ahcyl1,Ankfy1,Ap3b1,Ap3d1,App,Arcn1,Arl3,Atg4b,Bcl2l1,Chmp7,Col4a3bp,Cope,Copz1,Ddx3 9,Erp29,Evi5,Faf2,Fkbp1a,Flna,Gbf1,Gsk3b,Ipo4,Itgav,Itgb1,Itpr1,Kif1b,Kif1c,Kif5b,Klc1,Kpna4, Lrp6,Macf1,Map2k1,Mapk3,Mfn2,Mtch2,Myadm,Myo1c,Nrbp1,Pafah1b1,Pan3,Pcm1,Pex13,Pe x5,Pik3r1,Pkd1,Ppif,Rab10,Rab14,Rab5b,Rgp1,Rhobtb3,Sec61a1,Sec62,Snx27,Srp14,Stradb, Stxbp6,Tbc1d10b,Tgoln1,Tnpo3,Vapb,Vti1b,Ywhaq,Zc3h11a GO:0034613 cellular protein localization 8.48E-07 Ahcyl1,Ap2a1,Ap3b1,Ap3d1,Arl2,Atg4b,Ctnnb1,Diap1,Dvl1,Erp29,Faf2,Fermt2,Flna,Gbf1,Gsk3 b,Hdgf,Ipo4,Itgb1,Klc1,Kpna4,Lats1,Lats2,Macf1,Mapk3,Mapre1,Mesdc2,Mfn2,Mrap,Mtch2,My adm,Myo1c,Nras,Pacsin2,Pan3,Pcm1,Pex13,Pex5,Pik3r1,Pkd1,Plrg1,Rab10,Rab14,Rab22a,R ab4b,Rab5b,Sec61a1,Sec62,Seh1l,Snx27,Srp14,Stradb,Stxbp6,Sumo3,Syne2,Tlk1,Tmem33,T npo3,Tollip,Vti1b,Wasl,Wipi2,Wnt4,Ywhah,Ywhaq,Zdhhc18 GO:0070727 cellular macromolecule localization 1.10E-06 Ahcyl1,Ap2a1,Ap3b1,Ap3d1,Arl2,Atg4b,Ctnnb1,Diap1,Dvl1,Erp29,Faf2,Fermt2,Flna,Gbf1,Gsk3 b,Hdgf,Ipo4,Itgb1,Klc1,Kpna4,Lats1,Lats2,Macf1,Mapk3,Mapre1,Mesdc2,Mfn2,Mrap,Mtch2,My adm,Myo1c,Nras,Pacsin2,Pan3,Pcm1,Pex13,Pex5,Pik3r1,Pkd1,Plrg1,Rab10,Rab14,Rab22a,R ab4b,Rab5b,Sec61a1,Sec62,Seh1l,Snx27,Srp14,Stradb,Stxbp6,Sumo3,Syne2,Tlk1,Tmem33,T npo3,Tollip,Vti1b,Wasl,Wipi2,Wnt4,Ywhah,Ywhaq,Zdhhc18

Table S2_2 7

GO:0008104 protein localization 1.33E-06 Ahcyl1,Akap7,Ap2a1,Ap3b1,Ap3d1,Arf3,Arl2,Atg4b,Chmp7,Ctnnb1,Diap1,Dvl1,Erp29,Faf2,Fer mt2,Flna,Gbf1,Gsk3b,Hdgf,Hspg2,Ipo4,Itgb1,Kif5b,Klc1,Kpna4,Lats1,Lats2,Lims1,Macf1,Mapk 3,Mapre1,Mesdc2,Mfn2,Mrap,Mtch2,Myadm,Myo1c,Nras,Pacsin2,Pafah1b1,Pan3,Pcm1,Pex13 ,Pex5,Pik3r1,Pkd1,Plekha1,Plrg1,Ppt1,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Raf1,Sec61a1,Sec 62,Seh1l,Snx27,Srp14,Stradb,Stxbp6,Sumo3,Syne2,Tlk1,Tmem33,Tnpo3,Tollip,Ube2q1,Unc11 9b,Vti1b,Wasl,Wipi2,Wnt4,Ywhah,Ywhaq,Zdhhc18 GO:0070647 protein modification by small protein 3.13E-06 Amfr,Arih1,Atxn7l3,Bfar,Cdc27,Cdk5rap3,Cdk8,Cops7a,Cops7b,Cul4a,Cul4b,Dtl,Enc1,Hectd1, conjugation or removal Herc3,Kcmf1,March6,Med1,Med24,Otud4,Pias2,Rbbp6,Rfwd2,Rnf10,Rnf41,Rnf8,Rybp,Sumo3, Suz12,Tnfaip1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4b,Ubr3,Ubr4,Usp12,Usp14,Usp19,Usp25, Usp7,Usp9x,Zer1,Znrf2 GO:0051726 regulation of cell cycle 3.13E-06 App,Bcl2l1,Brd4,Ccnd2,Cdc27,Cdk5rap3,Cdk9,Chmp1a,Chordc1,Ctnnb1,Cul4a,Cul4b,Ddx3x,D tl,Dynlt3,Eif4e,Fnta,Gbf1,Git1,Igf1,Igf1r,Ing4,Insr,Ints3,Itgb1,Jmy,Kif23,Lats1,Lats2,Lrp5,Lrp6,M ap2k1,Map2k3,Med1,Mink1,Nras,Nusap1,Pafah1b1,Pcid2,Pdcd6ip,Pkd1,Plrg1,Ppp2r1a,Prr11, Ptpn11,Rock2,Rprd1b,Sgk1,Smad3,Smc5,Son,Stradb,Top2b,Trim35,Usp19,Wnt4,Ywhah GO:0006417 regulation of translation 3.13E-06 App,Btg2,Caprin1,Cnot1,Cnot2,Ddx3x,Ddx6,Dnajc1,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc 1,Gtpbp2,Igf1,Larp1,Mapk3,Mknk1,Paip2b,Patl1,Purb,Qk,Rps6ka3,Tarbp2,Wibg GO:0048518 positive regulation of biological process 3.13E-06 Acox1,Acsl4,Actr2,Adrbk1,Ahcyl1,Akap7,Ankfy1,Ap3b1,Ap3d1,App,Arhgap5,Arhgef11,Arl2,Asa p1,Atf6,Atg13,Atg4b,Atxn7l3,B4galt1,Baiap2,Bcl2l1,Bmpr1a,Bptf,Brd4,Btg2,Cab39,Caprin1,Car m1,Ccnd2,Cd2ap,Cdk5rap3,Cdk9,Celf1,Cfl2,Chd6,Clcn3,Clstn1,Cnot1,Cnot2,Crk,Crkl,Ctnnb1, Cul4a,Cul4b,Dcp1a,Ddx3x,Diap1,Dnajb2,Dvl1,Dyrk1a,Dyrk1b,Egln2,Eif2b2,Eif2s1,Eif4e,Eif4g1, Enc1,Erlin2,Erp29,Etv6,Evi5,Extl3,Fkbp1a,Flna,Fndc3b,Fnta,Fosl2,Furin,Gabbr1,Gak,Gbf1,Gcl m,Gga3,Git1,Glud1,Gna13,Gsk3b,Hdgf,Higd1a,Hsph1,Igf1,Igf1r,Igf2r,Ihh,Ing4,Insr,Itgav,Itgb1,It pr1,Jmy,Kank1,Kif23,Kif5b,Kpna1,Larp1,Lats1,Lims1,Lrp5,Lrp6,Macf1,Man2a1,Map1lc3b,Map2 k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,Mark2,Med1,Med24,Mink1,Mllt10,Mms1 9,Mrap,Mtmr2,Mtpn,Myadm,Myo1c,N6amt1,Naa15,Nf2,Nfat5,Nfatc3,Nfe2l1,Nras,Nucks1,Numb ,Nusap1,Ocrl,Ogt,Pafah1b1,Pafah1b2,Pan3,Patz1,Pcid2,Pcm1,Pdcd4,Pdcd6ip,Peli2,Pex13,Pe x5,Pias2,Pik3r1,Pkd1,Pkdcc,Plagl1,Plekha1,Plrg1,Ppap2b,Ppif,Ppih,Ppm1a,Ppp2r1a,Ppt1,Psm e3,Ptpn11,Ptprd,Pum2,Qk,Rad51,Raf1,Ralgapb,Rap2c,Rapgef1,Rasgef1b,Rassf2,Rere,Rfc1,R fwd2,Rgp1,Ric8,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rptor,Rtf1,Rtn4,Sbf1,Scoc,Seh1l,S erinc3,Setd3,Sgk1,Shoc2,Ski,Slc35c2,Slc39a10,Smad3,Smad5,Smarca1,Smc5,Smek2,Spred1 ,Srpk1,Stim1,Stradb,Sumo3,Suz12,Syde1,Syne2,Tarbp2,Tbc1d10b,Tbk1,Tbp,Tet3,Tmem39b, Tnfaip1,Tollip,Trim35,Trim39,Trp53inp2,Ube2v1,Ubl5,Usp19,Usp7,Vamp8,Vapb,Vegfa,Wasl,W bp11,Whsc1,Wibg,Wnt4,Ywhah,Zfp326

Table S2_2 8

GO:0016043 cellular component organization 4.26E-06 Acox1,Acsl4,Actr2,Amfr,Ankfy1,Ap3b1,Ap3d1,App,Arhgap5,Arl2,Arl3,Asap1,Atg13,Atg4b,Atxn2, Atxn7l3,B4galt1,B4galt7,Baiap2,Baz2a,Bcl2l1,Bptf,Brd2,Brd4,Brpf3,Btbd3,Btg2,Carm1,Cd2ap,C dc27,Celf1,Cfl2,Chchd3,Chmp1a,Chmp7,Cisd2,Clcn3,Col4a3bp,Ctnnb1,Cul4b,Ddx3x,Ddx6,Dia p1,Dvl1,Dync1li2,Eif3a,Enah,Faf2,Fermt2,Fkbp1a,Flna,Fndc3b,Gak,Gbf1,Gclm,Git1,Gnai3,Gsk 3b,Haus5,Hira,Hspg2,Igf1r,Ihh,Ing4,Insr,Ipo4,Itgav,Itgb1,Jmy,Kank1,Kif23,Kif5b,Klc1,Lamc1,Lat s1,Lats2,Lims1,Lrp6,Macf1,Man2a1,Map1lc3b,Map2k1,Mapk3,Mapk9,Med1,Med24,Mfn2,Mink 1,Mms19,Mrps25,Msl1,Mtch2,Mtmr2,Myadm,Myo1c,Nbr1,Ncaph,Nf2,Nrn1,Numb,Nusap1,Ocrl, Ogt,Pacsin2,Pafah1b1,Pam,Patl1,Pcm1,Pdcd6ip,Pex13,Pex5,Pfkl,Phf13,Plekha1,Plxna1,Pom1 21,Ppif,Ppp2r1a,Ppt1,Ptpn11,Ptprd,Pum2,Pvrl1,Rab10,Rab14,Rab22a,Rab5b,Rad23b,Rad51, Raf1,Rbfox2,Rere,Ric8,Rnf8,Rock2,Rptor,Rtf1,Rtn3,Rtn4,Rybp,Sec16a,Sec61a1,Sec62,Seh1l, Sept11,Sept2,Setd3,Sgcb,Sgk1,Sidt2,Ski,Slc2a1,Smad3,Smarca1,Smarcd2,Smc5,Son,Stradb, Suz12,Syde1,Syne2,Tacc1,Tarbp2,Tet3,Tk2,Tmem135,Tmem33,Tnfaip1,Top2b,Trp53inp2,Txn l4a,Ube4b,Unc119b,Usp7,Usp9x,Vamp8,Vapb,Vbp1,Vegfa,Vti1b,Wasl,Wdr82,Whsc1,Wibg,Wi pi2,Wnt4,Ythdc1,Ywhah,Zyx GO:0016482 cytoplasmic transport 4.54E-06 Actr2,Ahcyl1,Ankfy1,Ap3b1,Ap3d1,Chmp7,Cope,Ddx39,Erp29,Faf2,Fkbp1a,Flna,Gbf1,Gsk3b,Ip o4,Itgav,Itpr1,Kpna4,Lsg1,Macf1,Mapk3,Mfn2,Mlxip,Nrbp1,Nup50,Pex13,Pex5,Pik3r1,Pkd1,Ra b10,Rab14,Rab5b,Sec61a1,Sec62,Snx27,Srp14,Stradb,Stxbp6,Tgoln1,Tnpo3,Vapb,Vti1b,Zc3h 11a GO:0034248 regulation of cellular amide metabolic process 5.10E-06 App,Btg2,Caprin1,Cnot1,Cnot2,Ddx3x,Ddx6,Dnajc1,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc 1,Gtpbp2,Igf1,Larp1,Mapk3,Mknk1,Paip2b,Patl1,Purb,Qk,Rps6ka3,Samd8,Tarbp2,Wibg GO:0071840 cellular component organization or biogenesis 5.51E-06 Acox1,Acsl4,Actr2,Amfr,Ankfy1,Ap3b1,Ap3d1,App,Arhgap5,Arl2,Arl3,Asap1,Atg13,Atg4b,Atxn2, Atxn7l3,B4galt1,B4galt7,Baiap2,Baz2a,Bcl2l1,Bptf,Brd2,Brd4,Brpf3,Btbd3,Btg2,Carm1,Cd2ap,C dc27,Celf1,Cfl2,Chchd3,Chmp1a,Chmp7,Cisd2,Clcn3,Col4a3bp,Ctnnb1,Cul4b,Ddx3x,Ddx6,Dia p1,Dvl1,Dync1li2,Ebna1bp2,Eif3a,Enah,Faf2,Fermt2,Fkbp1a,Flna,Fndc3b,Gak,Gbf1,Gclm,Git1, Gnai3,Gsk3b,Haus5,Hira,Hspg2,Igf1r,Ihh,Ing4,Insr,Ipo4,Itgav,Itgb1,Jmy,Kank1,Kif23,Kif5b,Klc1, Lamc1,Lats1,Lats2,Lims1,Lrp6,Lsg1,Macf1,Man2a1,Map1lc3b,Map2k1,Mapk3,Mapk9,Med1,M ed24,Mfn2,Mink1,Mms19,Mrps25,Msl1,Mtch2,Mtmr2,Myadm,Myo1c,Nbr1,Ncaph,Nf2,Nop56,Nr n1,Numb,Nusap1,Ocrl,Ogt,Pacsin2,Pafah1b1,Pam,Patl1,Pcm1,Pdcd6ip,Pex13,Pex5,Pfkl,Phf13 ,Plekha1,Plxna1,Pom121,Ppif,Ppp2r1a,Ppt1,Ptpn11,Ptprd,Pum2,Pvrl1,Rab10,Rab14,Rab22a,R ab5b,Rad23b,Rad51,Raf1,Rbfox2,Rere,Ric8,Rnf8,Rock2,Rptor,Rtf1,Rtn3,Rtn4,Rybp,Sec16a,S ec61a1,Sec62,Seh1l,Sept11,Sept2,Setd3,Sgcb,Sgk1,Sidt2,Ski,Slc2a1,Smad3,Smarca1,Smarc d2,Smc5,Son,Stradb,Suz12,Syde1,Syne2,Tacc1,Tarbp2,Tet3,Tk2,Tmem135,Tmem33,Tnfaip1, Top2b,Trp53inp2,Txnl4a,Ube4b,Unc119b,Usp7,Usp9x,Vamp8,Vapb,Vbp1,Vegfa,Vti1b,Wasl,W dr82,Whsc1,Wibg,Wipi2,Wnt4,Ythdc1,Ywhah,Zyx GO:0033036 macromolecule localization 5.74E-06 Acsl4,Ahcyl1,Akap7,Ap2a1,Ap3b1,Ap3d1,Arf3,Arl2,Atg4b,Chmp7,Col4a3bp,Ctnnb1,Ddx39,Diap 1,Dvl1,Erp29,Faf2,Fermt2,Flna,Gbf1,Gsk3b,Hdgf,Hnrnpa2b1,Hspg2,Ipo4,Itgb1,Kif5b,Klc1,Kpna 4,Lats1,Lats2,Lims1,Lrp6,Macf1,Mapk3,Mapre1,Mesdc2,Mfn2,Mrap,Mtch2,Myadm,Myo1c,Nras ,Pacsin2,Pafah1b1,Pan3,Pcm1,Pex13,Pex5,Pik3r1,Pitpna,Pkd1,Plekha1,Plrg1,Ppt1,Rab10,Ra b14,Rab22a,Rab4b,Rab5b,Raf1,Sec61a1,Sec62,Seh1l,Snx27,Spns1,Srp14,Stradb,Stxbp6,Su mo3,Syne2,Tlk1,Tmem33,Tnpo3,Tollip,Ube2q1,Unc119b,Vti1b,Wasl,Wipi2,Wnt4,Ywhah,Ywha q,Zc3h11a,Zdhhc18

Table S2_2 9

GO:0006996 organelle organization 7.60E-06 Acox1,Actr2,Ankfy1,Ap3b1,Arl2,Arl3,Atg13,Atg4b,Atxn2,Atxn7l3,Baiap2,Baz2a,Bcl2l1,Bptf,Brd2, Brd4,Brpf3,Carm1,Cd2ap,Cdc27,Cfl2,Chchd3,Chmp1a,Chmp7,Cisd2,Clcn3,Col4a3bp,Ctnnb1, Cul4b,Ddx3x,Ddx6,Diap1,Dvl1,Dync1li2,Enah,Faf2,Flna,Gak,Gbf1,Gclm,Gnai3,Gsk3b,Haus5,H ira,Ing4,Ipo4,Itgb1,Jmy,Kif23,Kif5b,Klc1,Lats1,Man2a1,Map1lc3b,Map2k1,Mapk9,Med24,Mfn2, Mink1,Mrps25,Msl1,Mtch2,Ncaph,Nf2,Nusap1,Ocrl,Ogt,Pacsin2,Pafah1b1,Patl1,Pcm1,Pdcd6ip, Pex13,Pex5,Phf13,Pom121,Ppif,Ppp2r1a,Ppt1,Pum2,Rab10,Rab14,Rab5b,Rad23b,Rad51,Raf 1,Rere,Rnf8,Rock2,Rtf1,Rtn3,Rtn4,Rybp,Sec16a,Sec61a1,Seh1l,Sept2,Setd3,Sgk1,Smarca1,S marcd2,Smc5,Son,Stradb,Suz12,Syde1,Syne2,Tacc1,Tet3,Tk2,Tmem135,Tmem33,Tnfaip1,To p2b,Trp53inp2,Usp7,Vamp8,Vapb,Vti1b,Wasl,Wdr82,Whsc1,Wipi2,Ywhah,Zyx GO:0051246 regulation of protein metabolic process 1.88E-05 App,Atg4b,Bag5,Bcl2l1,Bmpr1a,Btg2,Cab39,Caprin1,Ccnd2,Cdk5rap3,Cdk9,Chordc1,Cnot1,Cn ot2,Ctnnb1,Cul4a,Cul4b,Ddx3x,Ddx6,Dedd,Dnajb2,Dnajc1,Dvl1,Dyrk1a,Egln2,Eif2b2,Eif2s1,Eif 4e,Eif4g1,Eif4g2,Eif5b,Enc1,Erp29,Fkbp1a,Flna,Fnta,Furin,Gga3,Gna12,Gsk3b,Gtpbp2,Higd1a ,Hipk3,Hsph1,Igf1,Igf1r,Insr,Itgav,Itgb1,Larp1,Lats1,Lats2,Lrp5,Lrp6,Map2k1,Map2k3,Map3k3, Map3k4,Mapk3,Mapk9,Mink1,Mknk1,Mtpn,Myadm,N4bp1,Nbr1,Nf2,Nras,Ogt,Pafah1b1,Paip2b, Patl1,Pcid2,Pdcd4,Peli2,Pik3r1,Pkd1,Ppap2b,Ppp1r11,Psme3,Ptpn11,Purb,Qk,Rad23b,Rad51, Raf1,Rap2c,Rapgef1,Rassf2,Rfwd2,Rgp1,Rnf41,Rock2,Rps6ka3,Rptor,Rtf1,Ski,Slc39a10,Sma d3,Smc5,Spred1,Stradb,Sumo3,Suz12,Tarbp2,Tbk1,Tollip,Trim39,Tspyl2,Ube2g2,Ube2j1,Usp1 4,Usp19,Usp25,Usp7,Usp9x,Vapb,Vegfa,Wibg,Zer1,Zmynd11 GO:0009894 regulation of catabolic process 1.88E-05 Atg13,Atg4b,Bag5,Btg2,Cdk5rap3,Cisd2,Cnot1,Cul4a,Cul4b,Dedd,Dnajb2,Dvl1,Egln2,Eif2s1,Fl na,Furin,Gga3,Gna12,Gsk3b,Igf1,Insr,Itgb1,Larp1,Map1lc3b,Map2k1,Mtmr2,Mtmr3,N4bp1,Ogt, Pafah1b2,Pex13,Pkd1,Psme3,Rad23b,Rfwd2,Rgp1,Scoc,Smad3,Smc5,Sumo3,Tbk1,Tmem39 b,Trim39,Trp53inp2,Ube2g2,Ube2j1,Usp14,Usp19,Usp25,Usp7,Usp9x,Wbp11 GO:0048522 positive regulation of cellular process 2.77E-05 Acsl4,Actr2,Adrbk1,Akap7,Ankfy1,Ap3b1,Ap3d1,App,Arhgap5,Arhgef11,Arl2,Atf6,Atg13,Atg4b, Atxn7l3,B4galt1,Baiap2,Bcl2l1,Bmpr1a,Bptf,Brd4,Btg2,Cab39,Caprin1,Carm1,Ccnd2,Cd2ap,Cd k5rap3,Cdk9,Cfl2,Chd6,Clcn3,Clstn1,Cnot1,Cnot2,Crk,Crkl,Ctnnb1,Cul4a,Cul4b,Dcp1a,Ddx3x, Diap1,Dnajb2,Dvl1,Dyrk1a,Dyrk1b,Eif2s1,Eif4e,Eif4g1,Enc1,Erlin2,Erp29,Etv6,Extl3,Fkbp1a,Fln a,Fndc3b,Fnta,Fosl2,Furin,Gabbr1,Gak,Glud1,Gsk3b,Hdgf,Higd1a,Hsph1,Igf1,Igf1r,Igf2r,Ihh,In g4,Insr,Itgav,Itgb1,Jmy,Kank1,Kif23,Kif5b,Kpna1,Larp1,Lats1,Lims1,Lrp5,Lrp6,Macf1,Man2a1, Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mark2,Med1,Med24,Mink1,Mllt10,Mms19,Mra p,Mtmr2,Mtpn,Myadm,Myo1c,N6amt1,Naa15,Nf2,Nfat5,Nfatc3,Nfe2l1,Nras,Nucks1,Numb,Nus ap1,Ogt,Pafah1b1,Pafah1b2,Pan3,Patz1,Pcid2,Pdcd4,Pdcd6ip,Peli2,Pex13,Pias2,Pik3r1,Pkd1, Pkdcc,Plagl1,Plrg1,Ppap2b,Ppif,Ppih,Ppm1a,Ppp2r1a,Ppt1,Psme3,Ptpn11,Ptprd,Pum2,Qk,Rad 51,Raf1,Rap2c,Rapgef1,Rassf2,Rere,Rfc1,Rfwd2,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,R ptor,Rtf1,Rtn4,Scoc,Seh1l,Serinc3,Setd3,Sgk1,Shoc2,Ski,Slc35c2,Slc39a10,Smad3,Smad5,S marca1,Smc5,Smek2,Spred1,Srpk1,Stim1,Stradb,Sumo3,Suz12,Syde1,Syne2,Tarbp2,Tbk1,Tb p,Tet3,Tmem39b,Tnfaip1,Tollip,Trim35,Trim39,Trp53inp2,Ube2v1,Ubl5,Usp19,Usp7,Vamp8,Va pb,Vegfa,Wasl,Wbp11,Whsc1,Wibg,Wnt4,Ywhah,Zfp326 GO:0007029 endoplasmic reticulum organization 2.77E-05 Col4a3bp,Gak,Pex5,Rab10,Rtn3,Rtn4,Sec16a,Sec61a1,Tmem33,Vapb

Table S2_2 10

GO:0080135 regulation of cellular response to stress 4.63E-05 Atg13,Bag5,Bcl2l1,Bfar,Bmpr1a,Cdk9,Chordc1,Cul4a,Dyrk1a,Eif2s1,Erp29,Hipk3,Hsph1,Igf1r,L arp1,Map1lc3b,Map2k1,Map3k3,Map3k4,Mapk3,Mapk9,Mink1,Mtmr3,Nbr1,Ogt,Pafah1b1,Pafa h1b2,Pex13,Pik3r1,Rad51,Rassf2,Rnf8,Rtn4,Scoc,Serinc3,Spred1,Tbk1,Tmem39b,Tpt1,Ube2g 2,Ube2j1,Usp14,Usp19,Usp25,Vegfa,Wbp11,Whsc1,Zmynd11 GO:0006796 phosphate-containing compound metabolic 1.16E-04 Adrbk1,Agk,App,Atp5g1,Bmpr1a,Brd4,Cab39,Cdc25a,Cdipt,Cdk9,Chpt1,Cmpk1,Col4a3bp,Ddr process 1,Dlst,Dpm1,Dyrk1a,Dyrk1b,Eif2s1,Entpd4,Etnk1,Fastk,Gpaa1,Gsk3b,H6pd,Hipk3,Idh3a,Igf1,Ig f1r,Insr,Ip6k1,Itgav,Lats1,Lats2,Limk2,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapka pk3,Mark2,Med1,Mink1,Mknk1,Mtmr2,Mtmr3,Ocrl,Pfas,Pfkl,Pi4kb,Pik3r1,Pkd1,Pkdcc,Pmpcb,P pap2b,Ppm1a,Ppp2r1a,Ppp6c,Pskh1,Ptpn11,Raf1,Rassf2,Rock2,Rprd1b,Rps6ka3,Samd8,Sec 16a,Sgk1,Smad5,Smek2,Sptlc1,Srpk1,Stradb,Tbk1,Tesk1,Tk2,Tlk1,Tmem55a,Tmem55b,Tollip ,Uggt1 GO:0006886 intracellular protein transport 1.56E-04 Ahcyl1,Ap2a1,Ap3b1,Ap3d1,Atg4b,Erp29,Faf2,Gsk3b,Ipo4,Itgb1,Klc1,Kpna4,Macf1,Mapk3,Mfn 2,Myadm,Myo1c,Pan3,Pex13,Pex5,Pik3r1,Pkd1,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Sec61a1, Sec62,Snx27,Srp14,Stradb,Tlk1,Tnpo3,Vti1b,Ywhah,Ywhaq GO:0042176 regulation of protein catabolic process 1.65E-04 Atg4b,Bag5,Cdk5rap3,Cul4a,Cul4b,Dedd,Dnajb2,Dvl1,Egln2,Flna,Furin,Gga3,Gna12,Gsk3b,N4 bp1,Pkd1,Psme3,Rad23b,Rfwd2,Rgp1,Smad3,Smc5,Sumo3,Trim39,Ube2g2,Ube2j1,Usp14,Us p19,Usp25,Usp7,Usp9x GO:0044265 cellular macromolecule catabolic process 1.65E-04 Amfr,Arih1,Bfar,Cd2ap,Cdc27,Cnot1,Cnot2,Csde1,Cul4a,Cul4b,Dcp1a,Dnajb2,Dtl,Enc1,Erlin2, Faf2,Gtpbp2,Hectd1,Herc3,March6,Pan3,Patl1,Pdcd6ip,Ppp2r5c,Ppt1,Rbbp6,Rnf41,Rnf8,Tnfai p1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ube4b,Ubr3,Ubr4,Usp14,Usp19,Usp25,Usp7,Usp9x,Wibg GO:0051128 regulation of cellular component organization 1.65E-04 Acsl4,Actr2,Ankfy1,Arhgdia,Arl2,Asap1,Atg13,Atxn2,Bag5,Baiap2,Bcl2l1,Caprin1,Carm1,Cd2ap ,Cdc27,Cdk9,Cfl2,Chmp1a,Chordc1,Clstn1,Cnot1,Cnot2,Crk,Ctnnb1,Dcbld2,Ddr1,Ddx3x,Diap1 ,Dnajb2,Dvl1,Eif2s1,Enc1,Extl3,Flna,Gna12,Gna13,Gsk3b,Hectd1,Higd1a,Hsph1,Igf1,Igf1r,Insr, Itgav,Itgb1,Jmy,Kank1,Kif5b,Lats1,Lims1,Lrp5,Macf1,Map1lc3b,Map2k1,Mapk3,Mapk9,Mapre1, Mark2,Mtmr2,Mtmr3,Mtpn,Myadm,Myo1c,N6amt1,Nf2,Numb,Nusap1,Ogt,Pacsin2,Pafah1b1,Pa m,Pan3,Pdcd6ip,Pex13,Pex5,Pias2,Pik3r1,Pkd1,Pkdcc,Ppif,Ppm1a,Ppt1,Ptprd,Pvrl1,Qk,Rab4b ,Rab5b,Raf1,Rapgef1,Rock2,Rtf1,Rtn4,Sbf1,Sgk1,Ski,Smad3,Smc5,Stxbp6,Tlk1,Tmem39b,Ts pyl2,Ubl5,Vamp8,Vat1,Vegfa,Vti1b,Wasl,Wbp11,Wnt4,Ywhah GO:0032446 protein modification by small protein 1.65E-04 Amfr,Arih1,Bfar,Cdc27,Cdk5rap3,Cdk8,Cul4a,Cul4b,Dtl,Enc1,Hectd1,Herc3,Kcmf1,March6,Me conjugation d1,Med24,Pias2,Rbbp6,Rfwd2,Rnf10,Rnf41,Rnf8,Rybp,Sumo3,Suz12,Tnfaip1,Ube2g2,Ube2j1, Ube2q1,Ube2v1,Ube4b,Ubr3,Ubr4,Zer1,Znrf2 GO:0006793 phosphorus metabolic process 1.79E-04 Adrbk1,Agk,App,Atp5g1,Bmpr1a,Brd4,Cab39,Cdc25a,Cdipt,Cdk9,Chpt1,Cmpk1,Col4a3bp,Ddr 1,Dlst,Dpm1,Dyrk1a,Dyrk1b,Eif2s1,Entpd4,Etnk1,Fasn,Fastk,Gpaa1,Gsk3b,H6pd,Hipk3,Idh3a,I gf1,Igf1r,Insr,Ip6k1,Itgav,Lats1,Lats2,Limk2,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,M apkapk3,Mark2,Med1,Mink1,Mknk1,Mtmr2,Mtmr3,Ocrl,Pfas,Pfkl,Pi4kb,Pik3r1,Pkd1,Pkdcc,Pmp cb,Ppap2b,Ppm1a,Ppp2r1a,Ppp6c,Pskh1,Ptpn11,Raf1,Rassf2,Rock2,Rprd1b,Rps6ka3,Samd8, Sec16a,Sgk1,Smad5,Smek2,Sptlc1,Srpk1,Stradb,Tbk1,Tesk1,Tk2,Tlk1,Tmem55a,Tmem55b,T ollip,Uggt1

Table S2_2 11

GO:0016310 phosphorylation 1.92E-04 Adrbk1,Agk,App,Bmpr1a,Brd4,Cab39,Cdk9,Cmpk1,Col4a3bp,Ddr1,Dyrk1a,Dyrk1b,Eif2s1,Etnk 1,Fastk,Gsk3b,Hipk3,Igf1,Igf1r,Insr,Ip6k1,Itgav,Lats1,Lats2,Limk2,Map2k1,Map2k3,Map3k3,Ma p3k4,Mapk3,Mapk9,Mapkapk3,Mark2,Med1,Mink1,Mknk1,Pfkl,Pi4kb,Pik3r1,Pkd1,Pkdcc,Pmpc b,Pskh1,Raf1,Rassf2,Rock2,Rps6ka3,Sgk1,Smad5,Srpk1,Stradb,Tbk1,Tesk1,Tk2,Tlk1,Tollip GO:1903827 regulation of cellular protein localization 1.97E-04 Atg13,Bcl2l1,Bmpr1a,Cd2ap,Cdk5rap3,Ctnnb1,Flna,Gbf1,Gsk3b,Hectd1,Hsph1,Igf1,Itgb1,Kank 1,Kif5b,Kpna1,Med1,Myo1c,Nf2,Numb,Ogt,Pcm1,Pik3r1,Pkd1,Pkdcc,Ppm1a,Ptpn11,Ralgapb,S mad3,Trp53inp2,Ube2g2,Ube2j1,Ubl5,Vamp8,Vegfa,Vti1b,Wbp11 GO:0010608 posttranscriptional regulation of gene 2.14E-04 App,Btg2,Caprin1,Cnot1,Cnot2,Ddx3x,Ddx6,Dnajc1,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc expression 1,Gtpbp2,Igf1,Larp1,Mapk3,Mknk1,Mov10,Paip2b,Patl1,Pcid2,Purb,Qk,Rps6ka3,Tarbp2,Vegfa, Wibg GO:0019222 regulation of metabolic process 2.15E-04 Acsl4,Ahcyl1,Akap11,Ap2a1,App,Arhgdia,Arhgef11,Arl2,Asap1,Atf6,Atg13,Atg4b,Atxn2,Atxn7l3, Bag5,Baz2a,Bcl2l1,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Cab39,Calm1,Caprin1,Carm1,Cbfa2t3,Cbx5,C bx6,Cc2d1b,Ccnd2,Cdk5rap3,Cdk8,Cdk9,Chchd3,Chd6,Chmp1a,Chordc1,Cisd2,Clcn3,Cnot1, Cnot2,Cops2,Crebzf,Crk,Ctnnb1,Cul4a,Cul4b,Dcp1a,Ddx39,Ddx3x,Ddx6,Dedd,Dnajb2,Dnajc1, Dvl1,Dyrk1a,Dyrk1b,Egln2,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc1,Erlin2,Erp29,Etv6,Evi5, Faf2,Fastk,Fkbp1a,Flna,Fnta,Fosl2,Furin,Gabbr1,Gatad2a,Gbf1,Gclm,Gga3,Git1,Gna12,Gna13 ,Gsk3b,Gtpbp2,Hdgf,Higd1a,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Itgav,Itgb1,Jmy,La rp1,Lats1,Lats2,Lims1,Lrch4,Lrp5,Lrp6,Map1lc3b,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Ma pk9,Med1,Med24,Mink1,Mknk1,Mllt10,Mlxip,Mms19,Mov10,Mrap,Mtmr2,Mtmr3,Mtpn,Mxd4,My adm,N4bp1,Naa15,Nbr1,Nf2,Nfat5,Nfatc3,Nfe2l1,Nras,Nucks1,Ocrl,Ogt,Pafah1b1,Pafah1b2,Pa ip2b,Pam,Patl1,Patz1,Pcid2,Pdcd4,Peli2,Pex13,Phf21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppif, Ppm1a,Ppp1r11,Ppt1,Psme3,Ptpn11,Purb,Qk,Rad23b,Rad51,Raf1,Ralgapb,Rap2c,Rapgef1,R asgef1b,Rassf2,Rbfox2,Rbm39,Rere,Rfc1,Rfwd2,Rgp1,Ric8,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b, Rps6ka3,Rptor,Rtf1,Rybp,Samd8,Sbf1,Scoc,Sept2,Setd3,Ski,Slc35c2,Slc39a10,Smad3,Smad5 ,Smarca1,Smc5,Smek2,Son,Spred1,Srpk1,Stradb,Sumo3,Suz12,Syde1,Tarbp2,Tbc1d10b,Tbk 1,Tbp,Tet3,Tmem39b,Tnfaip1,Tollip,Trim39,Trp53inp2,Tspyl2,Ube2g2,Ube2j1,Ube2v1,Ubn2,U sp14,Usp19,Usp25,Usp7,Usp9x,Vapb,Vegfa,Wbp11,Whsc1,Wibg,Wnt4,Ywhah,Ywhaq,Zer1,Zf p326,Zmynd11

Table S2_2 12

GO:0031323 regulation of cellular metabolic process 2.23E-04 Acsl4,Ahcyl1,Akap11,App,Arhgef11,Atf6,Atg13,Atg4b,Atxn2,Atxn7l3,Bag5,Baz2a,Bcl2l1,Bmpr1 a,Bptf,Brd2,Brd4,Btg2,Cab39,Caprin1,Carm1,Cbfa2t3,Cbx5,Cbx6,Cc2d1b,Ccnd2,Cdk5rap3,Cd k8,Cdk9,Chchd3,Chd6,Chmp1a,Chordc1,Cisd2,Clcn3,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Cul4 a,Dcp1a,Ddx3x,Ddx6,Dedd,Dnajb2,Dnajc1,Dvl1,Dyrk1a,Dyrk1b,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4 g2,Eif5b,Enc1,Erlin2,Erp29,Etv6,Fastk,Fkbp1a,Flna,Fnta,Fosl2,Furin,Gabbr1,Gatad2a,Gna12, Gsk3b,Gtpbp2,Hdgf,Higd1a,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Itgav,Itgb1,Jmy,Lar p1,Lats1,Lats2,Lims1,Lrch4,Lrp5,Lrp6,Map1lc3b,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Map k9,Med1,Med24,Mink1,Mknk1,Mllt10,Mlxip,Mms19,Mrap,Mtmr2,Mtmr3,Mtpn,Mxd4,Myadm,N4b p1,Naa15,Nbr1,Nf2,Nfat5,Nfatc3,Nfe2l1,Nras,Nucks1,Ogt,Pafah1b1,Pafah1b2,Paip2b,Pam,Patl 1,Patz1,Pcid2,Pdcd4,Peli2,Pex13,Phf21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppif,Ppm1a,Ppp1r 11,Psme3,Ptpn11,Purb,Qk,Rad23b,Rad51,Raf1,Rap2c,Rapgef1,Rassf2,Rbfox2,Rbm39,Rere,R fc1,Rfwd2,Rgp1,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rptor,Rtf1,Rybp,Samd8,Scoc,Setd 3,Ski,Slc39a10,Smad3,Smad5,Smarca1,Smc5,Smek2,Son,Spred1,Srpk1,Stradb,Sumo3,Suz12 ,Tarbp2,Tbk1,Tbp,Tet3,Tmem39b,Tnfaip1,Tollip,Trim39,Trp53inp2,Tspyl2,Ube2j1,Ube2v1,Ubn 2,Usp14,Usp19,Usp25,Usp7,Usp9x,Vapb,Vegfa,Wbp11,Whsc1,Wibg,Wnt4,Ywhah,Ywhaq,Zer1 ,Zfp326,Zmynd11 GO:0032268 regulation of cellular protein metabolic process 2.45E-04 App,Bag5,Bcl2l1,Bmpr1a,Btg2,Cab39,Caprin1,Ccnd2,Cdk5rap3,Cdk9,Chordc1,Cnot1,Cnot2,Ct nnb1,Ddx3x,Ddx6,Dnajb2,Dnajc1,Dvl1,Dyrk1a,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc1,Erp 29,Fkbp1a,Fnta,Furin,Gna12,Gsk3b,Gtpbp2,Higd1a,Hipk3,Hsph1,Igf1,Igf1r,Insr,Itgav,Itgb1,Lar p1,Lats1,Lats2,Lrp5,Lrp6,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mink1,Mknk1,Myad m,N4bp1,Nbr1,Nf2,Nras,Ogt,Pafah1b1,Paip2b,Patl1,Pcid2,Peli2,Pik3r1,Pkd1,Ppap2b,Ppp1r11, Psme3,Ptpn11,Purb,Qk,Rad23b,Rad51,Raf1,Rap2c,Rapgef1,Rassf2,Rfwd2,Rgp1,Rnf41,Rock 2,Rps6ka3,Rptor,Rtf1,Ski,Slc39a10,Smad3,Smc5,Spred1,Stradb,Sumo3,Suz12,Tarbp2,Tollip,T rim39,Tspyl2,Usp14,Usp19,Usp25,Usp7,Usp9x,Vapb,Vegfa,Wibg,Zer1,Zmynd11 GO:0010556 regulation of macromolecule biosynthetic 2.49E-04 process Ap2a1,App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Caprin1,Carm1,Cbfa2t3, Cbx5,Cbx6,Cc2d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1 ,Dcp1a,Ddx3x,Ddx6,Dedd,Dnajc1,Dvl1,Dyrk1b,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc1,Erl in2,Etv6,Flna,Fnta,Fosl2,Furin,Gatad2a,Gsk3b,Gtpbp2,Hdgf,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r, Ihh,Ing4,Insr,Itgav,Jmy,Larp1,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,Mapk9,Med1,Me d24,Mknk1,Mllt10,Mlxip,Mms19,Mtpn,Mxd4,Naa15,Nf2,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Paip2b ,Pam,Patl1,Patz1,Pcid2,Pdcd4,Phf21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Purb,Qk,Raf1, Rap2c,Rbfox2,Rbm39,Rere,Rfc1,Rnf10,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rptor,Rtf1,Rybp,Samd8, Setd3,Ski,Smad3,Smad5,Smarca1,Suz12,Tarbp2,Tbk1,Tbp,Tet3,Tnfaip1,Trp53inp2,Tspyl2,Ub e2j1,Ube2v1,Ubn2,Usp7,Usp9x,Vegfa,Whsc1,Wibg,Wnt4,Ywhah,Ywhaq,Zfp326,Zmynd11 GO:0045184 establishment of protein localization 2.89E-04 Ahcyl1,Ap2a1,Ap3b1,Ap3d1,Arf3,Atg4b,Chmp7,Erp29,Faf2,Flna,Gsk3b,Ipo4,Itgb1,Klc1,Kpna4, Lims1,Macf1,Mapk3,Mfn2,Myadm,Myo1c,Nras,Pafah1b1,Pan3,Pex13,Pex5,Pik3r1,Pkd1,Plekh a1,Ppt1,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Raf1,Sec61a1,Sec62,Snx27,Srp14,Stradb,Tlk1,T npo3,Ube2q1,Unc119b,Vti1b,Wnt4,Ywhah,Ywhaq

Table S2_2 13

GO:0044257 cellular protein catabolic process 3.19E-04 Amfr,Arih1,Bfar,Cd2ap,Cdc27,Cul4a,Cul4b,Dnajb2,Dtl,Enc1,Erlin2,Faf2,Hectd1,Herc3,March6, Pdcd6ip,Ppp2r5c,Ppt1,Rbbp6,Rnf41,Rnf8,Tnfaip1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ube4b,Ub r3,Ubr4,Usp14,Usp19,Usp25,Usp7,Usp9x GO:0045787 positive regulation of cell cycle 3.62E-04 App,Brd4,Ccnd2,Cul4a,Cul4b,Ddx3x,Eif4e,Fnta,Igf1,Igf1r,Insr,Kif23,Lrp5,Lrp6,Med1,Nusap1,Pa fah1b1,Pcid2,Pkd1,Plrg1,Ptpn11,Rock2,Smc5,Usp19,Wnt4 GO:0051603 proteolysis involved in cellular protein catabolic 4.13E-04 Amfr,Arih1,Bfar,Cd2ap,Cdc27,Cul4a,Cul4b,Dnajb2,Dtl,Enc1,Erlin2,Faf2,Hectd1,Herc3,March6, process Pdcd6ip,Ppp2r5c,Rbbp6,Rnf41,Rnf8,Tnfaip1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ube4b,Ubr3,Ub r4,Usp14,Usp19,Usp25,Usp7,Usp9x GO:0080090 regulation of primary metabolic process 4.27E-04 Acsl4,Ahcyl1,Ap2a1,App,Arhgef11,Atf6,Atg4b,Atxn7l3,Bag5,Baz2a,Bcl2l1,Bmpr1a,Bptf,Brd2,Br d4,Btg2,Cab39,Caprin1,Carm1,Cbfa2t3,Cbx5,Cbx6,Cc2d1b,Ccnd2,Cdk5rap3,Cdk8,Cdk9,Chch d3,Chd6,Chmp1a,Chordc1,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Cul4a,Cul4b,Dcp1a,Ddx3x,Ddx6 ,Dedd,Dnajb2,Dnajc1,Dvl1,Dyrk1a,Dyrk1b,Egln2,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc1, Erlin2,Erp29,Etv6,Fastk,Fkbp1a,Flna,Fnta,Fosl2,Furin,Gabbr1,Gatad2a,Gga3,Gna12,Gsk3b,Gt pbp2,Hdgf,Higd1a,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Itgav,Itgb1,Jmy,Larp1,Lats1, Lats2,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Med1,Med24,Mi nk1,Mknk1,Mllt10,Mlxip,Mms19,Mrap,Mtpn,Mxd4,Myadm,N4bp1,Naa15,Nbr1,Nf2,Nfat5,Nfatc3, Nfe2l1,Nras,Nucks1,Ogt,Pafah1b1,Paip2b,Pam,Patl1,Patz1,Pcid2,Pdcd4,Peli2,Phf21a,Pias2,Pi k3r1,Pkd1,Plagl1,Ppap2b,Ppif,Ppm1a,Ppp1r11,Psme3,Ptpn11,Purb,Qk,Rad23b,Rad51,Raf1,R ap2c,Rapgef1,Rassf2,Rbfox2,Rbm39,Rere,Rfc1,Rfwd2,Rgp1,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b ,Rps6ka3,Rptor,Rtf1,Rybp,Samd8,Setd3,Ski,Slc39a10,Smad3,Smad5,Smarca1,Smc5,Smek2, Son,Spred1,Srpk1,Stradb,Sumo3,Suz12,Tarbp2,Tbk1,Tbp,Tet3,Tnfaip1,Tollip,Trim39,Trp53inp 2,Tspyl2,Ube2g2,Ube2j1,Ube2v1,Ubn2,Usp14,Usp19,Usp25,Usp7,Usp9x,Vapb,Vegfa,Whsc1, Wibg,Wnt4,Ywhah,Ywhaq,Zer1,Zfp326,Zmynd11 GO:0051248 negative regulation of protein metabolic 4.46E-04 App,Bag5,Bcl2l1,Btg2,Caprin1,Cdk5rap3,Chordc1,Cnot1,Cnot2,Ctnnb1,Ddx3x,Dedd,Dnajb2,Dv process l1,Eif4e,Enc1,Fkbp1a,Flna,Furin,Gsk3b,Hipk3,Hsph1,Igf1,Igf1r,Insr,Itgav,Lats1,Lats2,Lrp5,Lrp6, Myadm,N4bp1,Nf2,Ogt,Pafah1b1,Paip2b,Patl1,Pcid2,Pik3r1,Ppap2b,Ppp1r11,Purb,Qk,Rapgef1 ,Rassf2,Rgp1,Rps6ka3,Ski,Smad3,Spred1,Suz12,Trim39,Ube2g2,Ube2j1,Usp14,Usp25,Vegfa, Zmynd11 GO:0015031 protein transport 4.47E-04 Ahcyl1,Ap2a1,Ap3b1,Ap3d1,Arf3,Atg4b,Chmp7,Erp29,Faf2,Gsk3b,Ipo4,Itgb1,Klc1,Kpna4,Macf 1,Mapk3,Mfn2,Myadm,Myo1c,Pafah1b1,Pan3,Pex13,Pex5,Pik3r1,Pkd1,Ppt1,Rab10,Rab14,Ra b22a,Rab4b,Rab5b,Raf1,Sec61a1,Sec62,Snx27,Srp14,Stradb,Tlk1,Tnpo3,Ube2q1,Unc119b,Vt i1b,Ywhah,Ywhaq GO:0018193 peptidyl-amino acid modification 4.47E-04 Adh5,Adrbk1,Baz2a,Brd4,Brpf3,Carm1,Ddr1,Dpy19l4,Dyrk1a,Egln2,Fkbp1a,Fkbp5,Galnt1,Gsk3 b,Hipk3,Igf1r,Ing4,Insr,Mapk3,Mapkapk3,Med24,Mknk1,Msl1,Ogt,Pias2,Pkd1,Pkdcc,Ppif,Ppig, Ppih,Rtf1,Setd3,Sgk1,Sumo3,Suz12,Tbk1,Tet3,Ube2g2,Ube2j1,Wdr82,Whsc1,Zdhhc21 GO:0016567 protein ubiquitination 4.47E-04 Amfr,Arih1,Bfar,Cdc27,Cdk8,Cul4a,Cul4b,Dtl,Enc1,Hectd1,Herc3,Kcmf1,March6,Med1,Med24, Rbbp6,Rfwd2,Rnf10,Rnf41,Rnf8,Rybp,Suz12,Tnfaip1,Ube2g2,Ube2j1,Ube2q1,Ube2v1,Ube4b, Ubr3,Ubr4,Zer1,Znrf2 GO:0007346 regulation of mitotic cell cycle 4.47E-04 App,Bcl2l1,Brd4,Cdc27,Cdk5rap3,Chmp1a,Ctnnb1,Cul4a,Cul4b,Ddx3x,Dynlt3,Eif4e,Gbf1,Igf1,I gf1r,Insr,Ints3,Lrp5,Map2k3,Mink1,Nusap1,Pafah1b1,Pcid2,Pkd1,Plrg1,Ptpn11,Smad3,Smc5,St radb,Top2b,Trim35,Ywhah Table S2_2 14

GO:0030163 protein catabolic process 5.17E-04 Amfr,Arih1,Bace1,Bfar,Cd2ap,Cdc27,Cul4a,Cul4b,Dnajb2,Dtl,Enc1,Erlin2,Faf2,Hectd1,Herc3,L npep,March6,Pdcd6ip,Ppp2r5c,Ppt1,Rbbp6,Rnf41,Rnf8,Tnfaip1,Trp53inp2,Ubap1,Ube2g2,Ube 2j1,Ube4b,Ubr3,Ubr4,Usp14,Usp19,Usp25,Usp7,Usp9x GO:0033365 protein localization to organelle 5.21E-04 Ap3b1,Ap3d1,Arl2,Diap1,Dvl1,Gbf1,Gsk3b,Hdgf,Ipo4,Kpna4,Macf1,Mapk3,Mapre1,Mfn2,Mtch2, Nras,Pacsin2,Pcm1,Pex13,Pex5,Pik3r1,Plrg1,Rab10,Sec61a1,Sec62,Srp14,Sumo3,Syne2,Tnp o3,Tollip,Vti1b GO:0006468 protein phosphorylation 5.23E-04 Adrbk1,App,Bmpr1a,Brd4,Cab39,Cdk9,Ddr1,Dyrk1a,Dyrk1b,Eif2s1,Fastk,Gsk3b,Hipk3,Igf1,Igf1 r,Insr,Itgav,Lats1,Lats2,Limk2,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,Mar k2,Med1,Mink1,Mknk1,Pik3r1,Pkd1,Pkdcc,Pskh1,Raf1,Rassf2,Rock2,Rps6ka3,Sgk1,Smad5,Sr pk1,Stradb,Tbk1,Tesk1,Tlk1 GO:0045931 positive regulation of mitotic cell cycle 5.37E-04 App,Brd4,Cul4a,Cul4b,Ddx3x,Eif4e,Igf1,Igf1r,Insr,Lrp5,Nusap1,Pafah1b1,Pcid2,Plrg1,Ptpn11,S mc5 GO:0009057 macromolecule catabolic process 5.95E-04 Amfr,Arih1,Bace1,Bfar,Cd2ap,Cdc27,Cnot1,Cnot2,Csde1,Cul4a,Cul4b,Dcp1a,Dnajb2,Dtl,Enc1, Erlin2,Faf2,Gtpbp2,Hectd1,Herc3,Lnpep,March6,Pan3,Patl1,Pdcd6ip,Ppp2r5c,Ppt1,Rbbp6,Rnf 41,Rnf8,Tnfaip1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ube4b,Ubr3,Ubr4,Usp14,Usp19,Usp25,Usp 7,Usp9x,Wibg GO:0031329 regulation of cellular catabolic process 6.02E-04 Atg13,Atg4b,Bag5,Btg2,Cdk5rap3,Cisd2,Cnot1,Dnajb2,Dvl1,Eif2s1,Furin,Gna12,Gsk3b,Igf1,Ins r,Larp1,Map1lc3b,Map2k1,Mtmr2,Mtmr3,N4bp1,Ogt,Pafah1b2,Pex13,Pkd1,Psme3,Rad23b,Rfw d2,Rgp1,Scoc,Smc5,Sumo3,Tbk1,Tmem39b,Trim39,Trp53inp2,Usp14,Usp19,Usp25,Usp7,Usp 9x,Wbp11 GO:1902589 single-organism organelle organization 6.11E-04 Actr2,Ankfy1,Arl2,Arl3,Atg4b,Atxn7l3,Baiap2,Baz2a,Bcl2l1,Brd4,Brpf3,Carm1,Cdc27,Cfl2,Chch d3,Chmp1a,Chmp7,Cisd2,Clcn3,Col4a3bp,Ctnnb1,Cul4b,Diap1,Dvl1,Dync1li2,Enah,Flna,Gbf1, Gnai3,Haus5,Ing4,Itgb1,Jmy,Kif23,Kif5b,Klc1,Lats1,Map1lc3b,Map2k1,Med24,Mfn2,Mink1,Mrp s25,Msl1,Mtch2,Ncaph,Nf2,Nusap1,Ocrl,Ogt,Pafah1b1,Pcm1,Pex13,Pex5,Phf13,Ppif,Ppp2r1a, Rad51,Raf1,Rnf8,Rock2,Rtf1,Rybp,Seh1l,Sept2,Setd3,Sgk1,Smarcd2,Smc5,Son,Stradb,Suz12 ,Syde1,Syne2,Tacc1,Tet3,Tnfaip1,Top2b,Usp7,Vamp8,Vapb,Vti1b,Wasl,Wdr82,Whsc1,Wipi2,Z yx GO:0033043 regulation of organelle organization 6.75E-04 Actr2,Arl2,Atg13,Atxn2,Baiap2,Bcl2l1,Cd2ap,Cdc27,Cdk9,Cfl2,Chmp1a,Chordc1,Cnot1,Cnot2, Crk,Ctnnb1,Eif2s1,Gsk3b,Higd1a,Hsph1,Igf1,Igf1r,Insr,Jmy,Kank1,Lats1,Lrp5,Map1lc3b,Map2k 1,Mapk3,Mapk9,Mapre1,Mark2,Mtmr3,Myadm,Nf2,Nusap1,Ogt,Pam,Pan3,Pdcd6ip,Pex13,Pik3 r1,Pkd1,Ppif,Rock2,Rtf1,Sgk1,Ski,Smad3,Smc5,Stxbp6,Tlk1,Tmem39b,Ubl5,Vat1,Vegfa,Wasl, Wbp11,Wnt4,Ywhah GO:0006511 ubiquitin-dependent protein catabolic process 6.75E-04 Amfr,Arih1,Bfar,Cd2ap,Cdc27,Cul4a,Cul4b,Dnajb2,Dtl,Erlin2,Faf2,Hectd1,Herc3,Ppp2r5c,Rbbp 6,Rnf8,Tnfaip1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ube4b,Ubr3,Ubr4,Usp14,Usp19,Usp25,Usp7, Usp9x

Table S2_2 15

GO:2000112 regulation of cellular macromolecule 8.03E-04 App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Caprin1,Carm1,Cbfa2t3,Cbx5,C biosynthetic process bx6,Cc2d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Dcp1a, Ddx3x,Ddx6,Dedd,Dnajc1,Dvl1,Dyrk1b,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc1,Erlin2,Etv6 ,Flna,Fosl2,Gatad2a,Gsk3b,Gtpbp2,Hdgf,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Jmy, Larp1,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mknk1,Mllt10,Mlxip, Mms19,Mtpn,Mxd4,Naa15,Nf2,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Paip2b,Pam,Patl1,Patz1,Pcid2, Pdcd4,Phf21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Purb,Qk,Raf1,Rbfox2,Rere,Rfc1,Rnf1 0,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rptor,Rtf1,Rybp,Setd3,Ski,Smad3,Smad5,Smarca1,Suz12,Tarb p2,Tbk1,Tbp,Tet3,Tnfaip1,Trp53inp2,Tspyl2,Ube2v1,Ubn2,Usp7,Usp9x,Vegfa,Whsc1,Wibg,Wn t4,Ywhah,Ywhaq,Zfp326,Zmynd11 GO:0051171 regulation of nitrogen compound metabolic 8.03E-04 Ahcyl1,Ap2a1,App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Caprin1,Carm1,C process bfa2t3,Cbx5,Cbx6,Cc2d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf, Ctnnb1,Cul4a,Dcp1a,Ddx3x,Ddx6,Dedd,Dnajc1,Dvl1,Dyrk1a,Dyrk1b,Eif2b2,Eif2s1,Eif4e,Eif4g1, Eif4g2,Eif5b,Enc1,Erlin2,Etv6,Fastk,Flna,Fosl2,Gabbr1,Gatad2a,Gsk3b,Gtpbp2,Hdgf,Hipk3,Hnr npa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Jmy,Larp1,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Mapk 3,Mapk9,Med1,Med24,Mknk1,Mllt10,Mlxip,Mms19,Mrap,Mtpn,Mxd4,Naa15,Nf2,Nfat5,Nfatc3,Nf e2l1,Nucks1,Ogt,Paip2b,Pam,Patl1,Patz1,Pcid2,Pdcd4,Phf21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap 2b,Ppif,Ppm1a,Purb,Qk,Rad51,Raf1,Rap2c,Rbfox2,Rbm39,Rere,Rfc1,Rnf10,Rnf41,Rnf8,Rprd1 b,Rps6ka3,Rptor,Rtf1,Rybp,Samd8,Setd3,Ski,Smad3,Smad5,Smarca1,Son,Srpk1,Suz12,Tarbp 2,Tbk1,Tbp,Tet3,Tnfaip1,Trp53inp2,Tspyl2,Ube2v1,Ubn2,Usp7,Usp9x,Vapb,Vegfa,Whsc1,Wib g,Wnt4,Ywhah,Ywhaq,Zfp326,Zmynd11 GO:0048468 cell development 8.97E-04 Acsl4,Aff4,App,Arl3,Atxn2,B4galt1,Baiap2,Bcl2l1,Bmpr1a,Btbd3,Btg2,Celf1,Cfl2,Ctnnb1,Cul4a, Cul4b,Ddx6,Diap1,Dvl1,Eif2b2,Eif4e,Enah,Fermt2,Flna,Fndc3b,Fosl2,Gak,Git1,Gsk3b,Igf1,Igf1r ,Ihh,Itgav,Itgb1,Kif5b,Lamc1,Lats1,Lats2,Lrp5,Lrp6,Map2k1,Mapk3,Mapk9,Med1,Med24,Med28 ,Mink1,Mtmr2,Myadm,Nfatc3,Nrn1,Numb,Pafah1b1,Pcm1,Pex5,Plxna1,Ptpn11,Pvrl1,Qk,Rab10 ,Raf1,Rap2c,Rapgef1,Rbfox2,Rere,Rnf8,Rock2,Rtf1,Rtn4,Sept2,Sgcb,Sgk1,Sidt2,Ski,Smad3,S mad5,Tarbp2,Top2b,Tpt1,Ube2j1,Ube4b,Usp9x,Vegfa,Wnt4 GO:0051179 localization 8.97E-04 Acsl4,Actr2,Adrbk1,Ahcyl1,Akap7,Ankfy1,Ap2a1,Ap3b1,Ap3d1,App,Arcn1,Arf3,Arl2,Arl3,Atg4b, B4galt1,Bcl2l1,Cacna2d1,Cd2ap,Chmp1a,Chmp7,Clcn3,Cnih2,Col4a3bp,Cope,Copz1,Ctnnb1, Ddr1,Ddx39,Diap1,Dvl1,Dync1li2,Dynll2,Elmo2,Erp29,Evi5,Faf2,Fermt2,Fkbp1a,Flna,Fndc3b,F urin,Gak,Gbf1,Gnai3,Gsk3b,Hdgf,Hnrnpa2b1,Hspg2,Ipo4,Itgav,Itgb1,Itpr1,Jmy,Kif1b,Kif1c,Kif5b ,Klc1,Kpna4,Lamc1,Lats1,Lats2,Lims1,Lrp5,Lrp6,Lsg1,Ly6e,Macf1,Map2k1,Mapk3,Mapkapk3, Mapre1,Mark2,Med1,Mesdc2,Mfn2,Mlxip,Mrap,Mtch2,Myadm,Myo1c,Nras,Nrbp1,Nup50,Nusap 1,Ogt,Pacsin2,Pafah1b1,Pan3,Pcm1,Pdcd6ip,Pex13,Pex5,Pik3r1,Pitpna,Pkd1,Plekha1,Plrg1,P pif,Ppt1,Ptpn11,Pvrl1,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Rabep1,Raf1,Rbfox2,Rere,Rgp1,Rh obtb3,Ric8,Rtn4,Sec61a1,Sec62,Seh1l,Serinc3,Slc12a6,Slc20a2,Slc25a22,Slc2a1,Slc35c2,Slc 39a10,Smad3,Snx27,Spns1,Srp14,Stim1,Stradb,Stxbp6,Sumo3,Syde1,Syne2,Tacc1,Tbc1d10b ,Tgoln1,Tlk1,Tmem201,Tmem33,Tnfaip1,Tnpo3,Tollip,Top2b,Ube2q1,Unc119b,Usp9x,Vamp8, Vapb,Vegfa,Vti1b,Wasl,Wipi2,Wnt4,Ywhah,Ywhaq,Zc3h11a,Zdhhc18

Table S2_2 16

GO:0019941 modification-dependent protein catabolic 1.02E-03 Amfr,Arih1,Bfar,Cd2ap,Cdc27,Cul4a,Cul4b,Dnajb2,Dtl,Erlin2,Faf2,Hectd1,Herc3,Ppp2r5c,Rbbp process 6,Rnf8,Tnfaip1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ube4b,Ubr3,Ubr4,Usp14,Usp19,Usp25,Usp7, Usp9x GO:0097191 extrinsic apoptotic signaling pathway 1.29E-03 Bcl2l1,Bcl2l2,Ddx3x,Dedd,Gsk3b,Igf1,Itgav,Mknk1,Pik3r1,Raf1,Rnf41,Rock2,Smad3 GO:0043632 modification-dependent macromolecule 1.29E-03 Amfr,Arih1,Bfar,Cd2ap,Cdc27,Cul4a,Cul4b,Dnajb2,Dtl,Erlin2,Faf2,Hectd1,Herc3,Ppp2r5c,Rbbp catabolic process 6,Rnf8,Tnfaip1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ube4b,Ubr3,Ubr4,Usp14,Usp19,Usp25,Usp7, Usp9x GO:0035556 intracellular signal transduction 1.41E-03 Amotl2,Arhgdia,Arhgef11,Arl3,Baiap2,Bcl2l1,Bcl2l2,Cab39,Ddx3x,Gna12,Gna13,Gsk3b,Igf1,Igf 1r,Ing4,Insr,Itgav,Itpr1,Jmy,Larp1,Lats1,Lats2,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9, Mapkapk3,Mark2,Med1,Mink1,Mknk1,Nfatc3,Nras,Ogt,Pi4kb,Pik3r1,Pkd1,Plekha1,Rab10,Rab1 4,Rab22a,Rab4b,Rab5b,Raf1,Ralgapb,Rap2c,Rapgef1,Rock2,Rps6ka3,Rptor,Smad3,Srpk1,Str adb,Tlk1,Tmem109,Ywhaq GO:0032880 regulation of protein localization 1.41E-03 Arhgdia,Atg13,Bcl2l1,Bmpr1a,Cd2ap,Cdk5rap3,Ctnnb1,Dnajc1,Dph3,Erp29,Fkbp1a,Flna,Gbf1, Glud1,Gsk3b,Hectd1,Hsph1,Igf1,Itgb1,Kank1,Kif5b,Kpna1,Lats1,Lrp5,Med1,Myo1c,Nf2,Numb, Ogt,Pam,Pcm1,Pfkl,Pik3r1,Pkd1,Pkdcc,Ppm1a,Ptpn11,Rab14,Ralgapb,Sept2,Sgk1,Sidt2,Sma d3,Trp53inp2,Ube2g2,Ube2j1,Ubl5,Vamp8,Vegfa,Vti1b,Wasl,Wbp11,Whsc1 GO:0009889 regulation of biosynthetic process 1.60E-03 Ap2a1,App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Caprin1,Carm1,Cbfa2t3, Cbx5,Cbx6,Cc2d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Clcn3,Cnot1,Cnot2,Cops2,Crebzf, Ctnnb1,Dcp1a,Ddx3x,Ddx6,Dedd,Dnajc1,Dvl1,Dyrk1b,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,E nc1,Erlin2,Etv6,Flna,Fnta,Fosl2,Furin,Gabbr1,Gatad2a,Gsk3b,Gtpbp2,Hdgf,Hipk3,Hnrnpa2b1,H sph1,Igf1,Igf1r,Ihh,Ing4,Insr,Itgav,Jmy,Larp1,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,M apk9,Med1,Med24,Mknk1,Mllt10,Mlxip,Mms19,Mrap,Mtpn,Mxd4,Naa15,Nf2,Nfat5,Nfatc3,Nfe2l 1,Nucks1,Ogt,Paip2b,Pam,Patl1,Patz1,Pcid2,Pdcd4,Phf21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b, Ppm1a,Purb,Qk,Raf1,Rap2c,Rbfox2,Rbm39,Rere,Rfc1,Rnf10,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rp tor,Rtf1,Rybp,Samd8,Setd3,Ski,Smad3,Smad5,Smarca1,Smek2,Suz12,Tarbp2,Tbk1,Tbp,Tet3, Tnfaip1,Trp53inp2,Tspyl2,Ube2j1,Ube2v1,Ubn2,Usp7,Usp9x,Vegfa,Whsc1,Wibg,Wnt4,Ywhah, Ywhaq,Zfp326,Zmynd11 GO:0010646 regulation of cell communication 2.45E-03 Adrbk1,Akap11,Akap7,App,Atg13,Bag5,Baiap2,Bcl2l1,Bcl2l2,Bfar,Bmpr1a,Carm1,Cdc42se2,C dk5rap3,Clstn1,Cnih2,Cnot1,Cnot2,Crk,Ctnnb1,Ddx3x,Dvl1,Dyrk1a,Eif2s1,Erp29,Fkbp1a,Flna,F nta,Furin,Gabbr1,Gclm,Git1,Glud1,Gna12,Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Igf1r,Ihh,Insr,Itgav,It gb1,Itpr1,Kank1,Kif5b,Larp1,Lats1,Lats2,Lims1,Lrp5,Lrp6,Macf1,Map1lc3b,Map2k1,Map2k3,Ma p3k3,Map3k4,Mapk3,Mapk9,Mapkap1,Med1,Mfn2,Mink1,Mtmr2,Mtmr3,Myadm,Myo1c,Nbr1,Nf 2,Nfat5,Nucks1,Numb,Ogt,Pafah1b1,Pafah1b2,Peli2,Pex13,Pfkl,Pias2,Pik3r1,Plekha1,Ppap2b, Ppif,Ppm1a,Ppp2r1a,Psme3,Ptpn11,Ptprd,Pum2,Raf1,Rapgef1,Rassf2,Ric8,Rnf41,Rptor,Scoc, Seh1l,Serinc3,Sesn1,Shoc2,Sidt2,Ski,Slc35c2,Slc39a10,Smad3,Spred1,Stradb,Suz12,Syde1,T bk1,Tmem39b,Tnfaip1,Tpt1,Trim39,Ube2v1,Vamp8,Vegfa,Wbp11,Wnt4,Zmynd11 GO:0032269 negative regulation of cellular protein 2.45E-03 App,Bag5,Bcl2l1,Btg2,Caprin1,Cdk5rap3,Chordc1,Cnot1,Cnot2,Ctnnb1,Ddx3x,Dnajb2,Dvl1,Eif4 metabolic process e,Enc1,Fkbp1a,Furin,Gsk3b,Hipk3,Hsph1,Igf1,Igf1r,Insr,Lats1,Lats2,Lrp5,Lrp6,Myadm,N4bp1, Nf2,Ogt,Pafah1b1,Paip2b,Patl1,Pcid2,Pik3r1,Ppap2b,Ppp1r11,Purb,Qk,Rapgef1,Rassf2,Rgp1, Rps6ka3,Ski,Smad3,Spred1,Suz12,Trim39,Usp14,Vegfa,Zmynd11

Table S2_2 17

GO:0031175 neuron projection development 2.74E-03 Acsl4,App,Atxn2,Baiap2,Btbd3,Btg2,Cul4b,Diap1,Dvl1,Enah,Git1,Gsk3b,Igf1r,Itgb1,Kif5b,Lamc 1,Map2k1,Mapk9,Mink1,Nrn1,Numb,Pafah1b1,Plxna1,Ptpn11,Pvrl1,Rab10,Rbfox2,Rere,Rock2 ,Rtn4,Sept2,Sgk1,Top2b,Ube4b,Usp9x,Vegfa GO:0000902 cell morphogenesis 2.77E-03 Actr2,App,Arl3,Asap1,Atxn2,Btbd3,Col4a3bp,Ctnnb1,Dvl1,Enah,Fermt2,Flna,Fndc3b,Gsk3b,Igf 1r,Ihh,Itgav,Itgb1,Kif5b,Lamc1,Lats1,Lats2,Lrp6,Map2k1,Med1,Mink1,Nrn1,Numb,Ocrl,Pacsin2, Pafah1b1,Pcm1,Plxna1,Ptpn11,Pvrl1,Rab10,Rbfox2,Rere,Rock2,Rtn4,Sept2,Sgk1,Sidt2,Stradb ,Top2b,Unc119b,Usp9x,Vegfa,Wnt4 GO:1903362 regulation of cellular protein catabolic process 2.87E-03 Bag5,Cdk5rap3,Dnajb2,Dvl1,Furin,Gna12,Gsk3b,N4bp1,Pkd1,Psme3,Rad23b,Rfwd2,Rgp1,Sm c5,Sumo3,Trim39,Usp14,Usp19,Usp25,Usp7,Usp9x GO:0043933 macromolecular complex subunit organization 3.01E-03 Actr2,Amfr,App,Atxn2,Atxn7l3,Baiap2,Baz2a,Bptf,Brd2,Brd4,Brpf3,Carm1,Celf1,Cfl2,Ctnnb1,Cu l4b,Ddx3x,Ddx6,Diap1,Dvl1,Eif3a,Enah,Fermt2,Fkbp1a,Flna,Gak,Haus5,Hira,Igf1r,Ing4,Insr,Ipo 4,Jmy,Kif23,Kif5b,Klc1,Lamc1,Lims1,Map2k1,Mapk3,Med24,Msl1,Mtmr2,Nbr1,Ogt,Pam,Patl1,P cm1,Pex5,Pfkl,Pom121,Ppp2r1a,Pum2,Rad51,Raf1,Rere,Rnf8,Rtf1,Rybp,Seh1l,Sept11,Sept2, Setd3,Sgk1,Ski,Slc2a1,Smad3,Smarca1,Smarcd2,Suz12,Tarbp2,Tet3,Tmem33,Tnfaip1,Txnl4a ,Usp7,Vamp8,Vbp1,Wasl,Wdr82,Whsc1,Wibg,Ythdc1,Zyx GO:0060255 regulation of macromolecule metabolic 3.01E-03 Ahcyl1,Ap2a1,App,Arhgef11,Atf6,Atg4b,Atxn2,Atxn7l3,Bag5,Baz2a,Bcl2l1,Bmpr1a,Bptf,Brd2,Br process d4,Btg2,Cab39,Caprin1,Carm1,Cbfa2t3,Cbx5,Cbx6,Cc2d1b,Ccnd2,Cdk5rap3,Cdk9,Chchd3,Ch d6,Chmp1a,Chordc1,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Cul4a,Cul4b,Dcp1a,Ddx39,Ddx3x,Ddx 6,Dedd,Dnajb2,Dnajc1,Dvl1,Dyrk1a,Dyrk1b,Egln2,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc1, Erlin2,Erp29,Etv6,Fastk,Fkbp1a,Flna,Fnta,Fosl2,Furin,Gatad2a,Gga3,Gna12,Gsk3b,Gtpbp2,Hd gf,Higd1a,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Itgav,Itgb1,Jmy,Larp1,Lats1,Lats2,Li ms1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Med1,Med24,Mink1,Mk nk1,Mllt10,Mlxip,Mms19,Mov10,Mtmr2,Mtpn,Mxd4,Myadm,N4bp1,Naa15,Nbr1,Nf2,Nfat5,Nfatc 3,Nfe2l1,Nras,Nucks1,Ogt,Pafah1b1,Paip2b,Pam,Patl1,Patz1,Pcid2,Pdcd4,Peli2,Phf21a,Pias2, Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Ppp1r11,Psme3,Ptpn11,Purb,Qk,Rad23b,Rad51,Raf1,Rap 2c,Rapgef1,Rassf2,Rbfox2,Rbm39,Rere,Rfc1,Rfwd2,Rgp1,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,R ps6ka3,Rptor,Rtf1,Rybp,Samd8,Setd3,Ski,Slc35c2,Slc39a10,Smad3,Smad5,Smarca1,Smc5,S on,Spred1,Srpk1,Stradb,Sumo3,Suz12,Tarbp2,Tbk1,Tbp,Tet3,Tnfaip1,Tollip,Trim39,Trp53inp2, Tspyl2,Ube2g2,Ube2j1,Ube2v1,Ubn2,Usp14,Usp19,Usp25,Usp7,Usp9x,Vapb,Vegfa,Whsc1,Wi bg,Wnt4,Ywhah,Ywhaq,Zer1,Zfp326,Zmynd11 GO:0060322 head development 3.02E-03 App,Arcn1,Atxn2,Bmpr1a,Bptf,Btbd3,Btg2,Ctnnb1,Gak,Gsk3b,Hspg2,Igf1r,Ihh,Itgb1,Lrp6,Map2 k1,Mapk3,Med1,Nf2,Numb,Pafah1b1,Pafah1b2,Pcm1,Pex13,Pex5,Plekha1,Ppt1,Ptpn11,Raf1, Rbfox2,Rere,Rtn4,Ski,Smarca1,Tacc1,Top2b,Usp9x,Wnt4 GO:0065009 regulation of molecular function 3.04E-03 Ahcyl1,Akap11,Akap7,Amfr,App,Arhgdia,Arl2,Asap1,Bag5,Bcl2l1,Brd4,Cab39,Calm1,Carm1,Cc nd2,Cdk5rap3,Cdk9,Chordc1,Cnih2,Crebzf,Crk,Ctnnb1,Dcp1a,Ddx3x,Dph3,Dvl1,Eif2b2,Erp29, Evi5,Faf2,Fkbp1a,Flna,Fnta,Furin,Gabbr1,Gbf1,Gclm,Git1,Gna13,Gsk3b,Higd1a,Hipk3,Hsph1,I gf1,Igf1r,Insr,Jmy,Lats1,Lats2,Lims1,Lrp5,Lrp6,Map1lc3b,Map2k1,Map2k3,Map3k3,Map3k4,Ma pk3,Mapk9,Mapre1,Med1,Mink1,Mtpn,Nf2,Ocrl,Ogt,Pafah1b1,Pcid2,Pias2,Pik3r1,Pkd1,Ppap2b ,Ppif,Ppp1r11,Ppt1,Psme3,Ptpn11,Raf1,Ralgapb,Rap2c,Rapgef1,Rasgef1b,Rassf2,Rgp1,Ric8, Rnf41,Rps6ka3,Rptor,Sbf1,Sept2,Ski,Slc39a10,Smad3,Spred1,Stim1,Stradb,Syde1,Tbc1d10b, Tspyl2,Ube2v1,Usp14,Usp7,Vapb,Vegfa,Wbp11,Wnt4,Ywhah,Zer1

Table S2_2 18

GO:0010498 proteasomal protein catabolic process 3.14E-03 Amfr,Bfar,Cd2ap,Cdc27,Cul4a,Dnajb2,Enc1,Erlin2,Faf2,March6,Ppp2r5c,Rnf41,Tnfaip1,Ube2g 2,Ube2j1,Ube4b,Ubr3,Usp14,Usp19,Usp25,Usp7,Usp9x GO:0022402 cell cycle process 3.42E-03 Actr2,Arl3,Bcl2l1,Brd4,Calm1,Ccnd2,Cdc25a,Cdc27,Cdk5rap3,Chmp1a,Chmp7,Ctnnb1,Dtl,Eif4 e,Flna,Gsk3b,Haus5,Ing4,Ints3,Itgb1,Jmy,Kif23,Lats1,Lats2,Map2k1,Ncaph,Nusap1,Pafah1b1, Phf13,Pkd1,Ppp2r1a,Ptpn11,Rad51,Rock2,Seh1l,Sept2,Smad3,Son,Syde1,Top2b,Wasl GO:0032989 cellular component morphogenesis 3.75E-03 Actr2,App,Arl3,Asap1,Atxn2,Bcl2l1,Btbd3,Cfl2,Col4a3bp,Ctnnb1,Dvl1,Enah,Fermt2,Flna,Fndc3 b,Gsk3b,Igf1r,Ihh,Itgav,Itgb1,Kif5b,Lamc1,Lats1,Lats2,Lrp6,Map2k1,Med1,Mink1,Mtmr2,Nrn1,N umb,Ocrl,Pacsin2,Pafah1b1,Pcm1,Plxna1,Ptpn11,Pvrl1,Rab10,Rbfox2,Rere,Rock2,Rtn4,Sept2 ,Sgk1,Sidt2,Stradb,Top2b,Unc119b,Usp9x,Vegfa,Wnt4 GO:0042177 negative regulation of protein catabolic 3.85E-03 process Bag5,Cdk5rap3,Dedd,Flna,Furin,N4bp1,Rgp1,Smad3,Trim39,Ube2g2,Ube2j1,Usp14,Usp25 GO:0051301 cell division 4.10E-03 Actr2,Arl3,Bcl2l1,Chmp1a,Chmp7,Gnai3,Kif23,Lrp6,Numb,Nusap1,Pafah1b1,Pdcd6ip,Rab10,S ept2,Son GO:0044710 single-organism metabolic process 4.43E-03 Acox1,Acsbg1,Acsl4,Adh5,Adrbk1,Agk,Ahcyl1,Alg3,Amfr,App,Asnsd1,Atg13,Atg4b,Atp5g1,Atxn 7l3,B4galt1,B4galt7,Baz2a,Brd4,Brpf3,Cab39,Carm1,Cdc27,Cdipt,Cdk9,Chpf,Chpt1,Cisd2,Cmp k1,Col4a3bp,Coq6,Cul4b,D2hgdh,Ddost,Dlst,Dnajb2,Dpm1,Dpy19l4,Dsel,Dtl,Egln2,Elovl5,Entp d4,Erlin2,Etnk1,Faf2,Fasn,Fkbp1a,Fkrp,Galnt1,Galnt7,Gclm,Glud1,Gpaa1,Gsk3b,H6pd,Hsd17b 7,Iars,Idh3a,Igf1,Ing4,Insr,Ints3,Ip6k1,Itgav,Lrp5,Man2a1,Map1lc3b,Map2k1,Map2k3,Map3k3, Map3k4,Mapk3,Mapk9,Mapkapk3,Med1,Med24,Mink1,Mms19,Mrps25,Msl1,Mtmr2,Mtmr3,Nbr1 ,Ndor1,Nfatc3,Ocrl,Ogt,Pam,Pcmt1,Pex13,Pex5,Pfas,Pfkl,Pgm2,Pi4kb,Pik3r1,Plekha1,Pmpcb, Ppap2b,Ppme1,Ppt1,Ptpn11,Qk,Rad23b,Rad51,Raf1,Rnf8,Rtf1,Rybp,Samd8,Setd3,Slc35c2,S mc5,Sptlc1,Stradb,Suz12,Tarbp2,Tet3,Tk2,Tmem55a,Tmem55b,Top2b,Trp53inp2,Ube2g2,Ub e2j1,Ube2v1,Uggt1,Usp19,Usp7,Vamp8,Wdr82,Whsc1,Wipi2,Wnt4,Ywhah GO:0035372 protein localization to microtubule 4.56E-03 Diap1,Dvl1,Gsk3b,Mapre1 GO:0010603 regulation of cytoplasmic mRNA processing 4.56E-03 body assembly Atxn2,Cnot1,Cnot2,Pan3 GO:0001701 in utero embryonic development 4.57E-03 Bcl2l1,Bmpr1a,Bptf,Brd4,Cnot1,Cnot2,Col4a3bp,Ctnnb1,Gatad2a,Gna12,Gna13,Hectd1,Ihh,Itg av,Itgb1,Lats1,Lats2,Ly6e,Man2a1,Map2k1,Med1,Mfn2,Ocrl,Pkd1,Rbbp6,Ric8,Rtf1,Smad3,Ubr 3,Usp9x,Vegfa GO:0090068 positive regulation of cell cycle process 4.57E-03 App,Brd4,Cul4a,Cul4b,Ddx3x,Igf1,Igf1r,Insr,Kif23,Lrp5,Med1,Nusap1,Pcid2,Plrg1,Rock2,Smc5, Usp19,Wnt4

Table S2_2 19

GO:0031326 regulation of cellular biosynthetic process 4.60E-03 App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Caprin1,Carm1,Cbfa2t3,Cbx5,C bx6,Cc2d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Dcp1a, Ddx3x,Ddx6,Dedd,Dnajc1,Dvl1,Dyrk1b,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2,Eif5b,Enc1,Erlin2,Etv6 ,Flna,Fosl2,Gabbr1,Gatad2a,Gsk3b,Gtpbp2,Hdgf,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,In sr,Jmy,Larp1,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mknk1,Mllt1 0,Mlxip,Mms19,Mrap,Mtpn,Mxd4,Naa15,Nf2,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Paip2b,Pam,Patl1 ,Patz1,Pcid2,Pdcd4,Phf21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Purb,Qk,Raf1,Rap2c,Rbf ox2,Rbm39,Rere,Rfc1,Rnf10,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rptor,Rtf1,Rybp,Samd8,Setd3,Ski,S mad3,Smad5,Smarca1,Smek2,Suz12,Tarbp2,Tbk1,Tbp,Tet3,Tnfaip1,Trp53inp2,Tspyl2,Ube2j1 ,Ube2v1,Ubn2,Usp7,Usp9x,Vegfa,Whsc1,Wibg,Wnt4,Ywhah,Ywhaq,Zfp326,Zmynd11 GO:0006413 translational initiation 4.68E-03 Ddx3x,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Larp1 GO:0051234 establishment of localization 4.68E-03 Acsl4,Actr2,Adrbk1,Ahcyl1,Ankfy1,Ap2a1,Ap3b1,Ap3d1,App,Arcn1,Arf3,Arl2,Arl3,Atg4b,Bcl2l1, Cacna2d1,Chmp1a,Chmp7,Clcn3,Col4a3bp,Cope,Copz1,Ctnnb1,Ddx39,Dvl1,Dynll2,Erp29,Evi 5,Faf2,Fkbp1a,Flna,Furin,Gak,Gbf1,Gnai3,Gsk3b,Hnrnpa2b1,Ipo4,Itgav,Itgb1,Itpr1,Kif1b,Kif1c, Kif5b,Klc1,Kpna4,Lims1,Lrp6,Lsg1,Ly6e,Macf1,Map2k1,Mapk3,Mapkapk3,Med1,Mfn2,Mlxip,Mt ch2,Myadm,Myo1c,Nras,Nrbp1,Nup50,Nusap1,Pacsin2,Pafah1b1,Pan3,Pcm1,Pdcd6ip,Pex13, Pex5,Pik3r1,Pitpna,Pkd1,Plekha1,Ppif,Ppt1,Pvrl1,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Rabep1 ,Raf1,Rgp1,Rhobtb3,Sec61a1,Sec62,Seh1l,Serinc3,Slc12a6,Slc20a2,Slc25a22,Slc2a1,Slc35c2 ,Slc39a10,Smad3,Snx27,Spns1,Srp14,Stim1,Stradb,Stxbp6,Syde1,Syne2,Tbc1d10b,Tgoln1,Tlk 1,Tmem201,Tnpo3,Ube2q1,Unc119b,Vamp8,Vapb,Vegfa,Vti1b,Wasl,Wnt4,Ywhah,Ywhaq,Zc3h 11a GO:0034645 cellular macromolecule biosynthetic process 4.72E-03 Atg4b,B4galt1,B4galt7,Bptf,Cdk9,Chpf,Chst8,Crebzf,Ddost,Ddx3x,Dpm1,Dpy19l4,Dtl,Dvl1,Eif2b 2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Etv6,Fkrp,Flna,Fosl2,Galnt1,Galnt7,Gpaa1,Gtpbp2,Hipk3,Iars, Igf1,Ing4,Larp1,Man2a1,Mapk3,Med1,Med24,Mrps25,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Patz1,P gm2,Pias2,Plagl1,Ppm1a,Rad51,Rbm39,Rere,Slc35c2,Smad3,Smarca1,Tbp,Tet3,Tk2,Tnfaip1, Top2b,Ube2g2,Ube2j1,Wipi2,Zdhhc18,Zdhhc21 GO:1902532 negative regulation of intracellular signal 5.07E-03 Bag5,Bcl2l1,Bcl2l2,Ddx3x,Dyrk1a,Gsk3b,Hipk3,Hsph1,Igf1,Igf1r,Itgb1,Itpr1,Kank1,Mapkap1,Mf transduction n2,Myadm,Nf2,Pafah1b1,Plekha1,Ppif,Ppm1a,Ptprd,Rapgef1,Rassf2,Spred1,Suz12,Tnfaip1,Tp t1,Zmynd11 GO:0009966 regulation of signal transduction 5.07E-03 Adrbk1,Akap11,Akap7,App,Bag5,Bcl2l1,Bcl2l2,Bfar,Bmpr1a,Carm1,Cdc42se2,Cdk5rap3,Cnih2, Cnot1,Cnot2,Crk,Ctnnb1,Ddx3x,Dvl1,Dyrk1a,Erp29,Fkbp1a,Flna,Fnta,Furin,Gclm,Git1,Gna12, Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Igf1r,Ihh,Insr,Itgav,Itgb1,Itpr1,Kank1,Lats1,Lats2,Lims1,Lrp5,Lr p6,Macf1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkap1,Med1,Mfn2,Mink1,Myadm ,Myo1c,Nbr1,Nf2,Nfat5,Nucks1,Numb,Ogt,Pafah1b1,Peli2,Pias2,Pik3r1,Plekha1,Ppap2b,Ppif,P pm1a,Ppp2r1a,Psme3,Ptpn11,Ptprd,Pum2,Raf1,Rapgef1,Rassf2,Ric8,Rnf41,Rptor,Seh1l,Serin c3,Sesn1,Shoc2,Ski,Slc35c2,Slc39a10,Smad3,Spred1,Stradb,Suz12,Tnfaip1,Tpt1,Trim39,Ube 2v1,Vegfa,Wnt4,Zmynd11 GO:0051493 regulation of cytoskeleton organization 5.48E-03 Actr2,Arl2,Baiap2,Cd2ap,Cfl2,Chmp1a,Chordc1,Crk,Ctnnb1,Hsph1,Jmy,Kank1,Lats1,Mapk3,M apre1,Mark2,Myadm,Nf2,Pam,Pdcd6ip,Pik3r1,Pkd1,Rock2,Sgk1,Smad3,Wasl,Wnt4

Table S2_2 20

GO:0007049 cell cycle 5.56E-03 Actr2,Arl3,Bcl2l1,Brd4,Calm1,Ccnd2,Cdc25a,Cdc27,Cdk5rap3,Chmp1a,Chmp7,Ctnnb1,Dtl,Eif4 e,Flna,Gsk3b,Haus5,Ing4,Ints3,Itgb1,Jmy,Kif23,Lats1,Lats2,Map2k1,Ncaph,Nusap1,Pafah1b1, Phf13,Pkd1,Ppp2r1a,Ptpn11,Rad51,Rock2,Seh1l,Sept2,Smad3,Son,Syde1,Top2b,Wasl GO:0016192 vesicle-mediated transport 5.56E-03 Adrbk1,Ankfy1,Ap2a1,Ap3b1,Ap3d1,App,Arcn1,Arl3,Chmp1a,Clcn3,Cope,Copz1,Ctnnb1,Erp29, Evi5,Flna,Gak,Gbf1,Gnai3,Itgav,Kif1b,Kif1c,Lrp6,Mapk3,Mapkapk3,Nrbp1,Pacsin2,Pdcd6ip,Ppt 1,Rab10,Rab14,Rab22a,Rab5b,Rabep1,Rgp1,Rhobtb3,Snx27,Stxbp6,Syde1,Tbc1d10b,Tgoln1, Vamp8,Vapb,Vti1b,Wasl GO:0010770 positive regulation of cell morphogenesis 5.63E-03 Baiap2,Caprin1,Ctnnb1,Flna,Gsk3b,Lims1,Map2k1,Mapk9,Myadm,Numb,Pafah1b1,Pias2,Ptprd involved in differentiation ,Sgk1,Smad3,Vegfa GO:0048519 negative regulation of biological process 5.89E-03 Acsl4,Adrbk1,Ap2a1,App,Arhgdia,Arl2,Asap1,Atxn2,B4galt1,B4galt7,Bag5,Baz2a,Bcl2l1,Bcl2l2, Bfar,Bmpr1a,Bptf,Btg2,Caprin1,Carm1,Cbfa2t3,Cbx5,Cbx6,Cc2d1b,Cd2ap,Cdk5rap3,Cdk8,Cdk 9,Chchd3,Chmp1a,Chordc1,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Cul4a,Dcbld2,Ddr1,Ddx3x,Ddx 6,Dedd,Dnajb2,Dph3,Dvl1,Dyrk1a,Eif4e,Enc1,Erlin2,Erp29,Etv6,Faf2,Fam60a,Fkbp1a,Flna,Fnd c3b,Fnta,Furin,Gabbr1,Gatad2a,Gclm,Gsk3b,Hdgf,Hectd1,Higd1a,Hipk3,Hnrnpa2b1,Hsph1,Igf 1,Igf1r,Ihh,Ing4,Insr,Ints3,Itgav,Itgb1,Itpr1,Jmy,Kank1,Lats1,Lats2,Lims1,Lrch4,Lrp5,Lrp6,Map2 k1,Mapkap1,Mapre1,Med1,Med24,Med28,Mfn2,Mov10,Mtmr2,Mtmr3,Mxd4,Myadm,N4bp1,Naa 15,Nbr1,Nf2,Nras,Numb,Ogt,Pacsin2,Pafah1b1,Paip2b,Patl1,Patz1,Pcid2,Pcm1,Pdcd4,Pex5,Pf kl,Phf21a,Pias2,Pik3r1,Pkd1,Pkdcc,Plekha1,Ppap2b,Ppif,Ppm1a,Ppp1r11,Ppt1,Psme3,Ptpn11, Ptprd,Purb,Qars,Qk,Raf1,Rap2c,Rapgef1,Rassf2,Rbfox2,Rere,Rfc1,Rgp1,Rnf10,Rnf41,Rnf8,R ock2,Rps6ka3,Rtf1,Rtn4,Rybp,Sbf1,Sgk1,Ski,Slc35c2,Slc39a10,Smad3,Son,Spred1,Srpk1,Stra db,Suz12,Tarbp2,Tbk1,Tmem109,Tnfaip1,Top2b,Tpt1,Trim35,Trim39,Trp53inp2,Tspyl2,Ube2g 2,Ube2j1,Usp14,Usp19,Usp25,Usp7,Vamp8,Vapb,Vat1,Vegfa,Whsc1,Wnt4,Ywhah,Ywhaq,Zmy nd11 GO:0009101 glycoprotein biosynthetic process 6.02E-03 B4galt1,B4galt7,Chpf,Chst8,Ddost,Dpm1,Dpy19l4,Fkrp,Galnt1,Galnt7,Igf1,Man2a1,Ogt,Slc35c2 ,Tet3,Ube2g2,Ube2j1 GO:0008213 protein alkylation 6.02E-03 Baz2a,Btg2,Carm1,N6amt1,Ogt,Pcmt1,Rtf1,Setd3,Suz12,Tet3,Wdr82,Whsc1 GO:0006479 protein methylation 6.02E-03 Baz2a,Btg2,Carm1,N6amt1,Ogt,Pcmt1,Rtf1,Setd3,Suz12,Tet3,Wdr82,Whsc1 GO:0048523 negative regulation of cellular process 6.23E-03 Adrbk1,App,Arhgdia,Asap1,Atxn2,B4galt1,B4galt7,Bag5,Baz2a,Bcl2l1,Bcl2l2,Bfar,Bmpr1a,Bptf, Btg2,Caprin1,Carm1,Cbfa2t3,Cbx5,Cbx6,Cc2d1b,Cdk5rap3,Cdk8,Cdk9,Chchd3,Chmp1a,Chor dc1,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Cul4a,Dcbld2,Ddr1,Ddx3x,Ddx6,Dedd,Dnajb2,Dph3,Dvl 1,Dyrk1a,Eif4e,Enc1,Erlin2,Erp29,Etv6,Fam60a,Fkbp1a,Flna,Fndc3b,Fnta,Furin,Gabbr1,Gatad 2a,Gclm,Gsk3b,Hdgf,Hectd1,Higd1a,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Ints3,Itgav ,Itgb1,Itpr1,Jmy,Kank1,Lats1,Lats2,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Mapkap1,Mapre1,Med1,Me d24,Med28,Mfn2,Mtmr2,Mtmr3,Mxd4,Myadm,N4bp1,Naa15,Nbr1,Nf2,Numb,Ogt,Pacsin2,Pafah 1b1,Paip2b,Patl1,Patz1,Pcid2,Pcm1,Pdcd4,Pex5,Pfkl,Phf21a,Pias2,Pik3r1,Pkd1,Pkdcc,Plekha 1,Ppap2b,Ppif,Ppm1a,Ppp1r11,Ppt1,Psme3,Ptpn11,Ptprd,Purb,Qars,Qk,Raf1,Rap2c,Rapgef1, Rassf2,Rbfox2,Rere,Rfc1,Rgp1,Rnf10,Rnf41,Rnf8,Rps6ka3,Rtf1,Rtn4,Rybp,Sgk1,Ski,Slc39a10 ,Smad3,Son,Spred1,Srpk1,Stradb,Suz12,Tmem109,Tnfaip1,Top2b,Tpt1,Trim35,Trim39,Tspyl2, Ube2g2,Ube2j1,Usp14,Usp25,Usp7,Vamp8,Vapb,Vat1,Vegfa,Whsc1,Wnt4,Ywhah,Ywhaq,Zmy nd11 GO:0007264 small GTPase mediated signal transduction 6.24E-03 Arhgdia,Arhgef11,Arl3,Baiap2,Gna12,Gna13,Nras,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Ralgap b,Rap2c,Rapgef1,Rock2,Stradb,Ywhaq Table S2_2 21

GO:0009100 glycoprotein metabolic process 6.40E-03 B4galt1,B4galt7,Chpf,Chst8,Ddost,Dpm1,Dpy19l4,Dsel,Fkrp,Galnt1,Galnt7,Igf1,Ihh,Man2a1,Og t,Slc35c2,Tet3,Ube2g2,Ube2j1 GO:0016071 mRNA metabolic process 6.40E-03 Ahcyl1,App,Celf1,Cnot1,Cnot2,Csde1,Dcp1a,Ddx39,Gtpbp2,Hnrnpa1,Hnrnpa2b1,Pan3,Patl1,Pl rg1,Qk,Son,Txnl4a,Ubl5,Wbp11,Wibg,Ythdc1 GO:0046856 phosphatidylinositol dephosphorylation 6.46E-03 Mtmr2,Mtmr3,Ocrl,Tmem55a,Tmem55b GO:0071786 endoplasmic reticulum tubular network 6.46E-03 organization Rab10,Rtn3,Rtn4,Tmem33 GO:0000904 cell morphogenesis involved in differentiation 7.16E-03 App,Btbd3,Ctnnb1,Dvl1,Enah,Fermt2,Flna,Fndc3b,Gsk3b,Igf1r,Ihh,Itgav,Itgb1,Kif5b,Lamc1,Lat s1,Lats2,Lrp6,Mink1,Nrn1,Numb,Pafah1b1,Ptpn11,Pvrl1,Rab10,Rbfox2,Rere,Rock2,Rtn4,Top2 b,Usp9x,Vegfa,Wnt4 GO:0046488 phosphatidylinositol metabolic process 7.16E-03 Cdipt,Dpm1,Gpaa1,Ip6k1,Mtmr2,Mtmr3,Ocrl,Pi4kb,Pik3r1,Tmem55a,Tmem55b GO:0050790 regulation of catalytic activity 7.17E-03 Akap11,App,Arhgdia,Arl2,Asap1,Bag5,Bcl2l1,Cab39,Calm1,Ccnd2,Cdk5rap3,Chordc1,Crk,Ctnn b1,Dcp1a,Ddx3x,Dvl1,Eif2b2,Erp29,Evi5,Faf2,Fkbp1a,Fnta,Furin,Gabbr1,Gbf1,Gclm,Git1,Gna1 3,Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Igf1r,Insr,Lats1,Lats2,Lims1,Lrp5,Lrp6,Map2k1,Map2k3,Map 3k3,Map3k4,Mapk3,Mapk9,Mink1,Nf2,Ocrl,Ogt,Pafah1b1,Pcid2,Pik3r1,Pkd1,Ppif,Ppp1r11,Ppt1 ,Psme3,Ptpn11,Raf1,Ralgapb,Rap2c,Rapgef1,Rasgef1b,Rassf2,Rgp1,Ric8,Rps6ka3,Rptor,Sbf 1,Sept2,Ski,Slc39a10,Smad3,Spred1,Stradb,Syde1,Tbc1d10b,Tspyl2,Usp14,Vapb,Vegfa,Wbp1 1,Wnt4,Zer1 GO:0009059 macromolecule biosynthetic process 7.23E-03 Atg4b,B4galt1,B4galt7,Bptf,Cdk9,Chpf,Chst8,Crebzf,Ddost,Ddx3x,Dpm1,Dpy19l4,Dtl,Dvl1,Eif2b 2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Etv6,Fkrp,Flna,Fosl2,Galnt1,Galnt7,Gpaa1,Gtpbp2,Hipk3,Iars, Igf1,Ing4,Larp1,Man2a1,Mapk3,Med1,Med24,Mrps25,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Patz1,P gm2,Pias2,Plagl1,Ppm1a,Rad51,Rbm39,Rere,Slc35c2,Smad3,Smarca1,Tbp,Tet3,Tk2,Tnfaip1, Top2b,Ube2g2,Ube2j1,Wipi2,Zdhhc18,Zdhhc21 GO:0010564 regulation of cell cycle process 7.66E-03 App,Brd4,Cdc27,Cdk5rap3,Cdk9,Chmp1a,Chordc1,Ctnnb1,Cul4a,Cul4b,Ddx3x,Git1,Igf1,Igf1r,I nsr,Kif23,Lrp5,Med1,Nusap1,Pcid2,Pdcd6ip,Pkd1,Plrg1,Ppp2r1a,Rock2,Rprd1b,Smc5,Usp19, Wnt4,Ywhah GO:0002053 positive regulation of mesenchymal cell 7.77E-03 proliferation Arhgap5,Bmpr1a,Ctnnb1,Ihh,Lrp5,Lrp6,Vegfa GO:0010605 negative regulation of macromolecule 7.77E-03 Ap2a1,App,Atxn2,Bag5,Baz2a,Bcl2l1,Bptf,Btg2,Caprin1,Cbfa2t3,Cbx5,Cbx6,Cc2d1b,Cdk5rap3, metabolic process Cdk9,Chchd3,Chmp1a,Chordc1,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Ddx3x,Dedd,Dnajb2,Dvl1, Dyrk1a,Eif4e,Enc1,Erp29,Etv6,Fkbp1a,Flna,Fnta,Furin,Gatad2a,Gsk3b,Hdgf,Hipk3,Hnrnpa2b1, Hsph1,Igf1,Igf1r,Ing4,Insr,Itgav,Lats1,Lats2,Lims1,Lrch4,Lrp5,Lrp6,Med1,Mov10,Mtmr2,Mxd4, Myadm,N4bp1,Nf2,Ogt,Pafah1b1,Paip2b,Patl1,Patz1,Pcid2,Pdcd4,Phf21a,Pias2,Pik3r1,Ppap2 b,Ppp1r11,Purb,Qk,Rapgef1,Rassf2,Rbfox2,Rere,Rfc1,Rgp1,Rnf8,Rps6ka3,Rtf1,Rybp,Ski,Slc3 5c2,Smad3,Spred1,Suz12,Tarbp2,Tbk1,Trim39,Tspyl2,Ube2g2,Ube2j1,Usp14,Usp25,Usp7,Ve gfa,Whsc1,Wnt4,Ywhaq,Zmynd11 GO:0098727 maintenance of cell number 7.86E-03 Bmpr1a,Ctnnb1,Cul4a,Ddx6,Eif4e,Igf1,Lrp5,Med24,Med28,Pcm1,Raf1,Rtf1,Ski,Tpt1

Table S2_2 22

GO:0051254 positive regulation of RNA metabolic process 7.92E-03 App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Btg2,Cdk5rap3,Cdk9,Chd6,Cnot1,Ctnnb1,Dcp1a, Ddx3x,Dvl1,Dyrk1b,Erlin2,Etv6,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Ihh,Jmy,Lrp5,Lrp6,Map2k1,Map2 k3,Mapk3,Mapk9,Med1,Med24,Mllt10,Mms19,Mtpn,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Pat z1,Pcid2,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Raf1,Rere,Rfc1,Rnf10,Rnf41,Rprd1b,Rps6k a3,Rptor,Rtf1,Setd3,Ski,Smad3,Smad5,Smarca1,Tbk1,Tbp,Tet3,Trp53inp2,Ube2v1,Vegfa,Wnt 4,Ywhah,Zfp326 GO:0045935 positive regulation of nucleobase-containing 7.96E-03 App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Btg2,Cdk5rap3,Cdk9,Chd6,Cnot1,Ctnnb1,Dcp1a, compound metabolic process Ddx3x,Dvl1,Dyrk1b,Erlin2,Etv6,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Igf1r,Ihh,Insr,Jmy,Lrp5,Lrp6,Map2 k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mllt10,Mms19,Mrap,Mtpn,Naa15,Nfat5,Nfatc3,Nfe2l1,N ucks1,Ogt,Patz1,Pcid2,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Rad51,Raf1,Rere,Rfc1,Rnf10 ,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rptor,Rtf1,Setd3,Ski,Smad3,Smad5,Smarca1,Tbk1,Tbp,Tet3,Tnf aip1,Trp53inp2,Ube2v1,Vapb,Vegfa,Whsc1,Wnt4,Ywhah,Zfp326 GO:0001967 suckling behavior 7.97E-03 App,Pex13,Phf21a,Ube2q1,Ubr3 GO:0006446 regulation of translational initiation 7.97E-03 Ddx3x,Eif2b2,Eif2s1,Eif4g1,Eif4g2,Eif5b,Mknk1,Paip2b GO:1903508 positive regulation of nucleic acid-templated 7.97E-03 App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Cdk5rap3,Cdk9,Chd6,Ctnnb1,Dcp1a,Ddx3x,Dvl1, transcription Dyrk1b,Erlin2,Etv6,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Ihh,Jmy,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,M apk9,Med1,Med24,Mllt10,Mms19,Mtpn,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Patz1,Pcid2,Pia s2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Raf1,Rere,Rfc1,Rnf10,Rnf41,Rprd1b,Rps6ka3,Rptor,Rtf 1,Setd3,Ski,Smad3,Smad5,Smarca1,Tbk1,Tbp,Tet3,Trp53inp2,Ube2v1,Vegfa,Wnt4,Ywhah,Zfp 326 GO:0045893 positive regulation of transcription, DNA- 7.97E-03 App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Cdk5rap3,Cdk9,Chd6,Ctnnb1,Dcp1a,Ddx3x,Dvl1, templated Dyrk1b,Erlin2,Etv6,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Ihh,Jmy,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,M apk9,Med1,Med24,Mllt10,Mms19,Mtpn,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Patz1,Pcid2,Pia s2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Raf1,Rere,Rfc1,Rnf10,Rnf41,Rprd1b,Rps6ka3,Rptor,Rtf 1,Setd3,Ski,Smad3,Smad5,Smarca1,Tbk1,Tbp,Tet3,Trp53inp2,Ube2v1,Vegfa,Wnt4,Ywhah,Zfp 326 GO:0022411 cellular component disassembly 8.04E-03 Atg4b,Cfl2,Cisd2,Gak,Gbf1,Kif5b,Klc1,Lamc1,Map1lc3b,Pafah1b1,Sgk1,Smarcd2,Wibg,Wipi2 GO:1902680 positive regulation of RNA biosynthetic 8.37E-03 App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Cdk5rap3,Cdk9,Chd6,Ctnnb1,Dcp1a,Ddx3x,Dvl1, process Dyrk1b,Erlin2,Etv6,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Ihh,Jmy,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,M apk9,Med1,Med24,Mllt10,Mms19,Mtpn,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Patz1,Pcid2,Pia s2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Raf1,Rere,Rfc1,Rnf10,Rnf41,Rprd1b,Rps6ka3,Rptor,Rtf 1,Setd3,Ski,Smad3,Smad5,Smarca1,Tbk1,Tbp,Tet3,Trp53inp2,Ube2v1,Vegfa,Wnt4,Ywhah,Zfp 326 GO:0051173 positive regulation of nitrogen compound 8.65E-03 metabolic process App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Btg2,Cdk5rap3,Cdk9,Chd6,Cnot1,Ctnnb1,Dcp1a, Ddx3x,Dvl1,Dyrk1b,Erlin2,Etv6,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Igf1r,Ihh,Insr,Jmy,Larp1,Lrp5,Lrp 6,Map2k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mllt10,Mms19,Mrap,Mtpn,Naa15,Nfat5,Nfatc3, Nfe2l1,Nucks1,Ogt,Patz1,Pcid2,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Rad51,Raf1,Rere,Rf c1,Rnf10,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rptor,Rtf1,Setd3,Ski,Smad3,Smad5,Smarca1,Tarbp2,T bk1,Tbp,Tet3,Tnfaip1,Trp53inp2,Ube2v1,Vapb,Vegfa,Whsc1,Wibg,Wnt4,Ywhah,Zfp326

Table S2_2 23

GO:0048583 regulation of response to stimulus 8.65E-03 Adrbk1,Akap11,Akap7,App,Atg13,Bag5,Bcl2l1,Bcl2l2,Bfar,Bmpr1a,Carm1,Cdc42se2,Cdk5rap3, Cdk9,Chordc1,Cnih2,Cnot1,Cnot2,Crk,Ctnnb1,Cul4a,Ddx3x,Dvl1,Dyrk1a,Eif2s1,Erp29,Fkbp1a, Flna,Fnta,Furin,Gclm,Git1,Gna12,Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Igf1r,Ihh,Insr,Itgav,Itgb1,Itpr 1,Kank1,Larp1,Lats1,Lats2,Lims1,Lrp5,Lrp6,Macf1,Map1lc3b,Map2k1,Map2k3,Map3k3,Map3k 4,Mapk3,Mapk9,Mapkap1,Mapkapk3,Med1,Mfn2,Mink1,Mpp1,Mtmr3,Mtpn,Myadm,Myo1c,Nbr1 ,Nf2,Nfat5,Nucks1,Numb,Ogt,Pafah1b1,Pafah1b2,Peli2,Pex13,Pias2,Pik3r1,Plekha1,Ppap2b,P pif,Ppm1a,Ppp2r1a,Psme3,Ptpn11,Ptprd,Pum2,Rad51,Raf1,Rapgef1,Rassf2,Repin1,Ric8,Rnf4 1,Rnf8,Rps6ka3,Rptor,Rtn4,Scoc,Seh1l,Serinc3,Sesn1,Shoc2,Sidt2,Ski,Slc35c2,Slc39a10,Sma d3,Spred1,Stradb,Suz12,Tarbp2,Tbk1,Tmem39b,Tnfaip1,Tpt1,Trim39,Ube2g2,Ube2j1,Ube2v1, Usp14,Usp19,Usp25,Vamp8,Vegfa,Wbp11,Whsc1,Wnt4,Zmynd11 GO:0007420 brain development 8.65E-03 App,Arcn1,Atxn2,Bmpr1a,Bptf,Btbd3,Btg2,Ctnnb1,Gak,Gsk3b,Hspg2,Igf1r,Itgb1,Lrp6,Map2k1, Med1,Nf2,Numb,Pafah1b1,Pafah1b2,Pcm1,Pex13,Pex5,Ppt1,Ptpn11,Rbfox2,Rere,Rtn4,Ski,S marca1,Tacc1,Top2b,Usp9x,Wnt4 GO:0010557 positive regulation of macromolecule 8.65E-03 App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Cdk5rap3,Cdk9,Chd6,Ctnnb1,Dcp1a,Ddx3x,Dvl1, biosynthetic process Dyrk1b,Erlin2,Etv6,Fnta,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Igf1r,Ihh,Insr,Jmy,Larp1,Lrp5,Lrp6,Map2 k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mllt10,Mms19,Mtpn,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks 1,Ogt,Patz1,Pcid2,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Raf1,Rere,Rfc1,Rnf10,Rnf41,Rprd 1b,Rps6ka3,Rptor,Rtf1,Setd3,Ski,Smad3,Smad5,Smarca1,Tarbp2,Tbk1,Tbp,Tet3,Tnfaip1,Trp5 3inp2,Ube2v1,Vegfa,Wibg,Wnt4,Ywhah,Zfp326 GO:0007059 chromosome segregation 8.65E-03 Actr2,Arl8b,Brd4,Chmp1a,Chmp7,Ddx3x,Ebna1bp2,Lats1,Mms19,Ncaph,Nusap1,Phf13,Ppp2r 1a,Seh1l,Srpk1,Syde1,Top2b GO:0070085 glycosylation 8.65E-03 Alg3,B4galt1,B4galt7,Ddost,Dpm1,Dpy19l4,Fkrp,Galnt1,Galnt7,Man2a1,Ogt,Slc35c2,Tet3,Ube2 g2,Ube2j1 GO:0060020 Bergmann glial cell differentiation 8.72E-03 Map2k1,Mapk3,Ppap2b,Ptpn11 GO:2001234 negative regulation of apoptotic signaling 8.76E-03 Bag5,Bcl2l1,Bcl2l2,Ctnnb1,Ddx3x,Gclm,Higd1a,Hsph1,Igf1,Itgav,Ppif,Psme3,Raf1,Stradb,Tpt1, pathway Vegfa,Wnt4,Zmynd11 GO:0043413 macromolecule glycosylation 9.35E-03 B4galt1,B4galt7,Ddost,Dpm1,Dpy19l4,Fkrp,Galnt1,Galnt7,Man2a1,Ogt,Slc35c2,Tet3,Ube2g2,U be2j1 GO:0006486 protein glycosylation 9.35E-03 B4galt1,B4galt7,Ddost,Dpm1,Dpy19l4,Fkrp,Galnt1,Galnt7,Man2a1,Ogt,Slc35c2,Tet3,Ube2g2,U be2j1 GO:0072599 establishment of protein localization to 9.61E-03 endoplasmic reticulum Macf1,Rab10,Sec61a1,Sec62,Srp14 GO:1904375 regulation of protein localization to cell 9.72E-03 periphery Bcl2l1,Hectd1,Itgb1,Kif5b,Numb,Pik3r1,Pkdcc,Vamp8,Vti1b GO:1903076 regulation of protein localization to plasma 9.72E-03 membrane Bcl2l1,Hectd1,Itgb1,Kif5b,Numb,Pik3r1,Pkdcc,Vamp8,Vti1b GO:0007265 Ras protein signal transduction 1.01E-02 Arhgdia,Arhgef11,Baiap2,Gna12,Gna13,Nras,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Ralgapb,Ra p2c,Rapgef1,Rock2,Stradb

Table S2_2 24

GO:0044093 positive regulation of molecular function 1.04E-02 Akap7,Amfr,App,Asap1,Brd4,Cab39,Calm1,Ccnd2,Cdk9,Ctnnb1,Ddx3x,Dph3,Eif2b2,Erp29,Evi 5,Fkbp1a,Fnta,Gbf1,Gclm,Git1,Gna13,Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Insr,Jmy,Lims1,Lrp5,Lr p6,Map1lc3b,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapre1,Med1,Mink1,Mtpn,Ocrl, Ogt,Pkd1,Ppap2b,Psme3,Ptpn11,Raf1,Ralgapb,Rapgef1,Rasgef1b,Rassf2,Rgp1,Ric8,Rnf41,R ptor,Sbf1,Ski,Slc39a10,Smad3,Stim1,Stradb,Syde1,Tbc1d10b,Ube2v1,Vapb,Vegfa,Wnt4 GO:0032990 cell part morphogenesis 1.05E-02 Actr2,App,Arl3,Asap1,Atxn2,Bcl2l1,Btbd3,Col4a3bp,Dvl1,Enah,Flna,Gsk3b,Igf1r,Itgb1,Kif5b,Ma p2k1,Mink1,Nrn1,Numb,Ocrl,Pacsin2,Pafah1b1,Pcm1,Plxna1,Ptpn11,Pvrl1,Rab10,Rbfox2,Rere ,Rock2,Rtn4,Sept2,Sgk1,Top2b,Unc119b,Usp9x,Vegfa GO:0006810 transport 1.08E-02 Acsl4,Actr2,Adrbk1,Ahcyl1,Ankfy1,Ap2a1,Ap3b1,Ap3d1,App,Arcn1,Arf3,Arl2,Arl3,Atg4b,Bcl2l1, Cacna2d1,Chmp1a,Chmp7,Clcn3,Col4a3bp,Cope,Copz1,Ctnnb1,Ddx39,Dvl1,Dynll2,Erp29,Evi 5,Faf2,Fkbp1a,Flna,Furin,Gak,Gbf1,Gnai3,Gsk3b,Hnrnpa2b1,Ipo4,Itgav,Itgb1,Itpr1,Kif1b,Kif1c, Kif5b,Klc1,Kpna4,Lrp6,Lsg1,Ly6e,Macf1,Map2k1,Mapk3,Mapkapk3,Med1,Mfn2,Mlxip,Mtch2,My adm,Myo1c,Nrbp1,Nup50,Pacsin2,Pafah1b1,Pan3,Pcm1,Pdcd6ip,Pex13,Pex5,Pik3r1,Pitpna,P kd1,Ppif,Ppt1,Pvrl1,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Rabep1,Raf1,Rgp1,Rhobtb3,Sec61a1 ,Sec62,Serinc3,Slc12a6,Slc20a2,Slc25a22,Slc2a1,Slc35c2,Slc39a10,Smad3,Snx27,Spns1,Srp 14,Stim1,Stradb,Stxbp6,Syde1,Tbc1d10b,Tgoln1,Tlk1,Tnpo3,Ube2q1,Unc119b,Vamp8,Vapb,V egfa,Vti1b,Wasl,Ywhah,Ywhaq,Zc3h11a GO:0009892 negative regulation of metabolic process 1.08E-02 Ap2a1,App,Arl2,Atxn2,Bag5,Baz2a,Bcl2l1,Bptf,Btg2,Caprin1,Cbfa2t3,Cbx5,Cbx6,Cc2d1b,Cdk5r ap3,Cdk8,Cdk9,Chchd3,Chmp1a,Chordc1,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Ddx3x,Dedd,Dn ajb2,Dvl1,Dyrk1a,Eif4e,Enc1,Erlin2,Erp29,Etv6,Faf2,Fkbp1a,Flna,Fnta,Furin,Gabbr1,Gatad2a, Gsk3b,Hdgf,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r,Ing4,Insr,Itgav,Lats1,Lats2,Lims1,Lrch4,Lrp5,Lr p6,Med1,Mov10,Mtmr2,Mtmr3,Mxd4,Myadm,N4bp1,Nf2,Ogt,Pafah1b1,Paip2b,Patl1,Patz1,Pcid 2,Pdcd4,Phf21a,Pias2,Pik3r1,Ppap2b,Ppif,Ppp1r11,Purb,Qk,Rapgef1,Rassf2,Rbfox2,Rere,Rfc 1,Rgp1,Rnf8,Rps6ka3,Rtf1,Rybp,Sbf1,Ski,Slc35c2,Smad3,Spred1,Suz12,Tarbp2,Tbk1,Trim39, Tspyl2,Ube2g2,Ube2j1,Usp14,Usp25,Usp7,Vegfa,Whsc1,Wnt4,Ywhaq,Zmynd11 GO:0016358 dendrite development 1.12E-02 Acsl4,App,Baiap2,Btbd3,Dvl1,Git1,Itgb1,Mink1,Rbfox2,Rere,Rock2 GO:0051252 regulation of RNA metabolic process 1.13E-02 Ahcyl1,App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Carm1,Cbfa2t3,Cbx5,Cb x6,Cc2d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Dcp1a, Ddx3x,Dedd,Dvl1,Dyrk1a,Dyrk1b,Erlin2,Etv6,Fastk,Flna,Fosl2,Gatad2a,Gsk3b,Hdgf,Hipk3,Hnrn pa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Jmy,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,Mapk 9,Med1,Med24,Mllt10,Mlxip,Mms19,Mtpn,Mxd4,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Pam,P atz1,Pcid2,Pdcd4,Phf21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Purb,Raf1,Rap2c,Rbfox2,R bm39,Rere,Rfc1,Rnf10,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rptor,Rtf1,Rybp,Setd3,Ski,Smad3,Smad5 ,Smarca1,Son,Srpk1,Suz12,Tarbp2,Tbk1,Tbp,Tet3,Trp53inp2,Ube2v1,Ubn2,Usp7,Usp9x,Vegf a,Whsc1,Wnt4,Ywhah,Ywhaq,Zfp326,Zmynd11 GO:0034968 histone lysine methylation 1.19E-02 Baz2a,Ogt,Rtf1,Setd3,Suz12,Tet3,Wdr82,Whsc1 GO:0048812 neuron projection morphogenesis 1.19E-02 App,Atxn2,Btbd3,Dvl1,Enah,Gsk3b,Igf1r,Itgb1,Kif5b,Map2k1,Mink1,Nrn1,Numb,Pafah1b1,Plxn a1,Ptpn11,Pvrl1,Rab10,Rbfox2,Rere,Rock2,Rtn4,Sgk1,Top2b,Usp9x,Vegfa

Table S2_2 25

GO:0044087 regulation of cellular component biogenesis 1.19E-02 Actr2,Arl2,Atxn2,Bag5,Baiap2,Chmp1a,Clstn1,Cnot1,Cnot2,Ddx3x,Dnajb2,Gsk3b,Jmy,Kank1,L ats1,Lims1,Macf1,Mapk9,Mapre1,Mtmr3,Myadm,Myo1c,Nf2,Pan3,Pdcd6ip,Pex5,Pik3r1,Ppm1a ,Pvrl1,Raf1,Rapgef1,Samd8,Sgk1,Smad3,Stxbp6,Vegfa,Wasl,Wnt4 GO:0007076 mitotic chromosome condensation 1.19E-02 Chmp1a,Ncaph,Nusap1,Phf13 GO:0006493 protein O-linked glycosylation 1.19E-02 Dpm1,Fkrp,Galnt1,Galnt7,Ogt,Slc35c2,Tet3 GO:0010606 positive regulation of cytoplasmic mRNA 1.19E-02 processing body assembly Cnot1,Cnot2,Pan3 GO:0032879 regulation of localization 1.21E-02 Acsl4,Adrbk1,Ahcyl1,Akap7,Ankfy1,Ap3d1,Arhgap5,Arhgdia,Atg13,Atxn2,B4galt1,Bcl2l1,Bmpr1 a,Cacna2d1,Cd2ap,Cdk5rap3,Clcn3,Cnih2,Ctnnb1,Diap1,Dnajc1,Dph3,Erp29,Fam60a,Fkbp1a, Flna,Furin,Gabbr1,Gbf1,Glud1,Gna12,Gna13,Gsk3b,Hectd1,Hsph1,Igf1,Igf1r,Insr,Itgav,Itgb1,Itp r1,Kank1,Kif5b,Kpna1,Lats1,Lrp5,Macf1,Map1lc3b,Map2k1,Mapk3,Mapk9,Med1,Mink1,Mpp1,M tmr2,Myadm,Myo1c,Nf2,Nfatc3,Numb,Ogt,Pacsin2,Pam,Pcm1,Pdcd6ip,Pfkl,Pik3r1,Pkd1,Pkdcc ,Plxna1,Ppap2b,Ppif,Ppm1a,Ppt1,Ptpn11,Rab10,Rab14,Rab4b,Rab5b,Ralgapb,Rap2c,Repin1, Rnf41,Rock2,Rtn4,Sept2,Sgk1,Sidt2,Smad3,Stim1,Stxbp6,Syne2,Trp53inp2,Ube2g2,Ube2j1,U bl5,Vamp8,Vegfa,Vti1b,Wasl,Wbp11,Whsc1,Wnt4,Ywhah,Ywhaq GO:0048193 Golgi vesicle transport 1.21E-02 Ankfy1,Arcn1,Arl3,Cope,Copz1,Erp29,Gbf1,Kif1c,Nrbp1,Rab10,Rab14,Stxbp6,Tgoln1,Vapb,Vti 1b GO:1903050 regulation of proteolysis involved in cellular 1.22E-02 Bag5,Dnajb2,Dvl1,Gna12,Gsk3b,N4bp1,Pkd1,Psme3,Rad23b,Rfwd2,Smc5,Sumo3,Trim39,Usp protein catabolic process 14,Usp19,Usp25,Usp7,Usp9x GO:0009893 positive regulation of metabolic process 1.22E-02 App,Arhgef11,Asap1,Atf6,Atg13,Atg4b,Atxn7l3,Bmpr1a,Bptf,Brd4,Btg2,Cab39,Ccnd2,Cdk5rap3 ,Cdk9,Chd6,Clcn3,Cnot1,Ctnnb1,Cul4a,Cul4b,Dcp1a,Ddx3x,Dnajb2,Dvl1,Dyrk1a,Dyrk1b,Egln2, Eif2b2,Eif2s1,Erlin2,Erp29,Etv6,Evi5,Fkbp1a,Fnta,Fosl2,Gbf1,Gclm,Gga3,Git1,Gna13,Gsk3b,H dgf,Higd1a,Hsph1,Igf1,Igf1r,Ihh,Insr,Itgav,Itgb1,Jmy,Larp1,Lats1,Lims1,Lrp5,Lrp6,Map2k1,Map 2k3,Map3k3,Map3k4,Mapk3,Mapk9,Med1,Med24,Mink1,Mllt10,Mms19,Mrap,Mtpn,Naa15,Nfat5 ,Nfatc3,Nfe2l1,Nucks1,Ocrl,Ogt,Pafah1b2,Patz1,Pcid2,Peli2,Pex13,Pias2,Pik3r1,Pkd1,Plagl1,P pap2b,Ppm1a,Psme3,Ptpn11,Qk,Rad51,Raf1,Ralgapb,Rap2c,Rapgef1,Rasgef1b,Rassf2,Rere, Rfc1,Rfwd2,Rgp1,Ric8,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rptor,Rtf1,Sbf1,Scoc,Setd3, Ski,Slc39a10,Smad3,Smad5,Smarca1,Smc5,Smek2,Stradb,Sumo3,Syde1,Tarbp2,Tbc1d10b,T bk1,Tbp,Tet3,Tmem39b,Tnfaip1,Tollip,Trp53inp2,Ube2v1,Vapb,Vegfa,Whsc1,Wibg,Wnt4,Ywh ah,Zfp326 GO:0051099 positive regulation of binding 1.22E-02 Amfr,Brd4,Calm1,Cdk9,Dph3,Fkbp1a,Gsk3b,Hipk3,Igf1,Map1lc3b,Mapre1,Pkd1,Ski GO:0017148 negative regulation of translation 1.24E-02 Btg2,Caprin1,Cnot1,Cnot2,Ddx3x,Eif4e,Enc1,Paip2b,Patl1,Purb,Qk GO:0000278 mitotic cell cycle 1.26E-02 Bcl2l1,Brd4,Calm1,Ccnd2,Cdc25a,Cdc27,Cdk5rap3,Chmp1a,Chmp7,Eif4e,Flna,Ints3,Itgb1,Kif2 3,Lats1,Lats2,Map2k1,Ncaph,Nusap1,Pafah1b1,Phf13,Pkd1,Ppp2r1a,Ptpn11,Seh1l,Top2b GO:0009056 catabolic process 1.26E-02 Acox1,Adh5,Amfr,Arih1,Atg13,Atg4b,Bace1,Bfar,Cd2ap,Cdc27,Cisd2,Cnot1,Cnot2,Csde1,Cul4 a,Cul4b,Dcp1a,Dnajb2,Dtl,Enc1,Entpd4,Erlin2,Faf2,Glud1,Gtpbp2,Hectd1,Herc3,Lnpep,Lrp5,M ap1lc3b,March6,Mtmr2,Nbr1,Pan3,Patl1,Pdcd6ip,Pex13,Pex5,Pfkl,Pgm2,Ppp2r5c,Ppt1,Rbbp6, Rnf41,Rnf8,Tnfaip1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ube4b,Ubr3,Ubr4,Usp14,Usp19,Usp25, Usp7,Usp9x,Vamp8,Wibg,Wipi2,Ywhah GO:0048732 gland development 1.30E-02 Arhgap5,B4galt1,Bmpr1a,Crkl,Ctnnb1,Ddr1,Gak,Igf1,Igf1r,Igf2r,Insr,Lrp5,Lrp6,Ly6e,Man2a1,Ma p2k1,Mapk3,Med1,Nfatc3,Pkd1,Plxna1,Raf1,Smad3,Vegfa,Wnt4,Zdhhc21

Table S2_2 26

GO:0010468 regulation of gene expression 1.30E-02 Ahcyl1,App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Caprin1,Carm1,Cbfa2t3, Cbx5,Cbx6,Cc2d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1 ,Dcp1a,Ddx39,Ddx3x,Ddx6,Dedd,Dnajc1,Dvl1,Dyrk1a,Dyrk1b,Eif2b2,Eif2s1,Eif4e,Eif4g1,Eif4g2 ,Eif5b,Enc1,Erlin2,Erp29,Etv6,Fastk,Flna,Fosl2,Gatad2a,Gsk3b,Gtpbp2,Hdgf,Hipk3,Hnrnpa2b1 ,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Jmy,Larp1,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Map3k4,Map k3,Mapk9,Med1,Med24,Mknk1,Mllt10,Mlxip,Mms19,Mov10,Mtpn,Mxd4,Myadm,Naa15,Nfat5,Nf atc3,Nfe2l1,Nras,Nucks1,Ogt,Paip2b,Pam,Patl1,Patz1,Pcid2,Pdcd4,Phf21a,Pias2,Pik3r1,Pkd1, Plagl1,Ppap2b,Ppm1a,Purb,Qk,Raf1,Rbfox2,Rere,Rfc1,Rnf10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6 ka3,Rptor,Rtf1,Rybp,Setd3,Ski,Slc35c2,Smad3,Smad5,Smarca1,Son,Srpk1,Suz12,Tarbp2,Tbk 1,Tbp,Tet3,Trp53inp2,Ube2v1,Ubn2,Usp7,Usp9x,Vegfa,Whsc1,Wibg,Wnt4,Ywhah,Ywhaq,Zfp3 26,Zmynd11 GO:0046578 regulation of Ras protein signal transduction 1.32E-02 Crk,Igf1,Itgb1,Kank1,Map2k1,Mapkap1,Mfn2,Ogt,Rapgef1,Shoc2,Tnfaip1 GO:1901575 organic substance catabolic process 1.32E-02 Acox1,Adh5,Amfr,Arih1,Bace1,Bfar,Cd2ap,Cdc27,Cnot1,Cnot2,Csde1,Cul4a,Cul4b,Dcp1a,Dnaj b2,Dtl,Enc1,Entpd4,Erlin2,Faf2,Glud1,Gtpbp2,Hectd1,Herc3,Lnpep,Lrp5,March6,Mtmr2,Pan3,P atl1,Pdcd6ip,Pex13,Pex5,Pfkl,Pgm2,Ppp2r5c,Ppt1,Rbbp6,Rnf41,Rnf8,Tnfaip1,Trp53inp2,Ubap 1,Ube2g2,Ube2j1,Ube4b,Ubr3,Ubr4,Usp14,Usp19,Usp25,Usp7,Usp9x,Wibg,Ywhah GO:1903047 mitotic cell cycle process 1.33E-02 Bcl2l1,Brd4,Calm1,Ccnd2,Cdc25a,Cdc27,Cdk5rap3,Chmp1a,Chmp7,Eif4e,Flna,Ints3,Itgb1,Kif2 3,Lats1,Lats2,Map2k1,Ncaph,Nusap1,Pafah1b1,Phf13,Pkd1,Ppp2r1a,Seh1l,Top2b GO:2001141 regulation of RNA biosynthetic process 1.33E-02 App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Carm1,Cbfa2t3,Cbx5,Cbx6,Cc2 d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Dcp1a,Ddx3x, Dedd,Dvl1,Dyrk1b,Erlin2,Etv6,Flna,Fosl2,Gatad2a,Gsk3b,Hdgf,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf 1r,Ihh,Ing4,Insr,Jmy,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mllt1 0,Mlxip,Mms19,Mtpn,Mxd4,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Pam,Patz1,Pcid2,Pdcd4,Ph f21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Purb,Raf1,Rap2c,Rbfox2,Rbm39,Rere,Rfc1,Rnf 10,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rptor,Rtf1,Rybp,Setd3,Ski,Smad3,Smad5,Smarca1,Suz12,Tar bp2,Tbk1,Tbp,Tet3,Trp53inp2,Ube2v1,Ubn2,Usp7,Usp9x,Vegfa,Whsc1,Wnt4,Ywhah,Ywhaq,Zf p326,Zmynd11 GO:0022008 neurogenesis 1.34E-02 Acsl4,App,Arl3,Asap1,Atxn2,Baiap2,Bmpr1a,Btbd3,Btg2,Caprin1,Carm1,Cops2,Ctnnb1,Cul4b, Ddx6,Diap1,Dvl1,Eif2b2,Eif4e,Eif4g1,Enah,Enc1,Git1,Gsk3b,Igf1,Igf1r,Ihh,Itgb1,Kank1,Kif5b,La mc1,Lrp6,Man2a1,Map2k1,Mapk3,Mapk9,Mark2,Med1,Mink1,Mtmr2,Nf2,Nrn1,Numb,Pafah1b1 ,Pcm1,Pex13,Pex5,Pias2,Plxna1,Ppap2b,Ptpn11,Ptprd,Pvrl1,Qk,Rab10,Rapgef1,Rbfox2,Rere, Rnf10,Rock2,Rtn4,Sept2,Sgk1,Ski,Smarca1,Tacc1,Top2b,Ube4b,Usp9x,Vegfa,Wnt4,Ywhah GO:0023051 regulation of signaling 1.34E-02 Adrbk1,Akap11,Akap7,App,Bag5,Baiap2,Bcl2l1,Bcl2l2,Bfar,Bmpr1a,Carm1,Cdc42se2,Cdk5rap 3,Clstn1,Cnih2,Cnot1,Cnot2,Crk,Ctnnb1,Ddx3x,Dvl1,Dyrk1a,Erp29,Fkbp1a,Flna,Fnta,Furin,Gab br1,Gclm,Git1,Glud1,Gna12,Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Igf1r,Ihh,Insr,Itgav,Itgb1,Itpr1,Kan k1,Kif5b,Lats1,Lats2,Lims1,Lrp5,Lrp6,Macf1,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9, Mapkap1,Med1,Mfn2,Mink1,Mtmr2,Myadm,Myo1c,Nbr1,Nf2,Nfat5,Nucks1,Numb,Ogt,Pafah1b1 ,Peli2,Pfkl,Pias2,Pik3r1,Plekha1,Ppap2b,Ppif,Ppm1a,Ppp2r1a,Psme3,Ptpn11,Ptprd,Pum2,Raf1 ,Rapgef1,Rassf2,Ric8,Rnf41,Rptor,Seh1l,Serinc3,Sesn1,Shoc2,Sidt2,Ski,Slc35c2,Slc39a10,Sm ad3,Spred1,Stradb,Suz12,Syde1,Tnfaip1,Tpt1,Trim39,Ube2v1,Vamp8,Vegfa,Wnt4,Zmynd11 Table S2_2 27

GO:0046839 phospholipid dephosphorylation 1.34E-02 Mtmr2,Mtmr3,Ocrl,Tmem55a,Tmem55b GO:1902580 single-organism cellular localization 1.35E-02 Actr2,Ap3b1,Ap3d1,Atg4b,Chmp1a,Chmp7,Ctnnb1,Dvl1,Fermt2,Flna,Gbf1,Ipo4,Kif1b,Kif5b,Kpn a4,Macf1,Map2k1,Mapk3,Mfn2,Myadm,Myo1c,Nusap1,Ogt,Pafah1b1,Pex13,Pex5,Pik3r1,Rab1 0,Sec61a1,Sec62,Seh1l,Srp14,Syde1,Syne2,Tnpo3,Vapb,Vti1b,Wasl,Wnt4 GO:0010638 positive regulation of organelle organization 1.45E-02 Actr2,Arl2,Atg13,Baiap2,Cdk9,Cfl2,Cnot1,Cnot2,Ctnnb1,Eif2s1,Gsk3b,Igf1,Igf1r,Insr,Jmy,Lrp5, Map2k1,Mapk3,Mapk9,Nf2,Nusap1,Ogt,Pan3,Pdcd6ip,Pex13,Ppif,Rock2,Rtf1,Smad3,Smc5,T mem39b,Ubl5,Vegfa,Wasl,Wbp11,Wnt4 GO:0051640 organelle localization 1.49E-02 Actr2,Ankfy1,Ap3b1,Ap3d1,Chmp1a,Chmp7,Ctnnb1,Dync1li2,Gbf1,Kif1b,Kif5b,Map2k1,Mfn2,N usap1,Ogt,Pafah1b1,Pcm1,Pex13,Seh1l,Syde1,Syne2,Tacc1,Tmem201,Wasl GO:0048009 insulin-like growth factor receptor signaling 1.49E-02 pathway Gigyf1,Igf1,Igf1r,Pik3r1 GO:1904293 negative regulation of ERAD pathway 1.49E-02 Ube2g2,Ube2j1,Usp14,Usp25 GO:0060439 trachea morphogenesis 1.49E-02 Ctnnb1,Lrp6,Map2k1,Mapk3 GO:0010628 positive regulation of gene expression 1.49E-02 App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Btg2,Cdk5rap3,Cdk9,Chd6,Cnot1,Ctnnb1,Dcp1a, Ddx3x,Dvl1,Dyrk1b,Erlin2,Erp29,Etv6,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Ihh,Jmy,Larp1,Lims1,Lrp5, Lrp6,Map2k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mllt10,Mms19,Mtpn,Naa15,Nfat5,Nfatc3,Nfe 2l1,Nucks1,Ogt,Patz1,Pcid2,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Qk,Raf1,Rere,Rfc1,Rnf1 0,Rnf41,Rock2,Rprd1b,Rps6ka3,Rptor,Rtf1,Setd3,Ski,Smad3,Smad5,Smarca1,Tarbp2,Tbk1,T bp,Tet3,Trp53inp2,Ube2v1,Vegfa,Wibg,Wnt4,Ywhah,Zfp326 GO:0010604 positive regulation of macromolecule 1.50E-02 App,Arhgef11,Atf6,Atg4b,Atxn7l3,Bmpr1a,Bptf,Brd4,Btg2,Cab39,Ccnd2,Cdk5rap3,Cdk9,Chd6, metabolic process Cnot1,Ctnnb1,Cul4a,Cul4b,Dcp1a,Ddx3x,Dnajb2,Dvl1,Dyrk1a,Dyrk1b,Egln2,Erlin2,Erp29,Etv6, Fkbp1a,Fnta,Fosl2,Gga3,Gsk3b,Hdgf,Higd1a,Hsph1,Igf1,Igf1r,Ihh,Insr,Itgav,Itgb1,Jmy,Larp1,La ts1,Lims1,Lrp5,Lrp6,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Med1,Med24,Mink1,Mllt1 0,Mms19,Mtpn,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Patz1,Pcid2,Peli2,Pias2,Pik3r1,Pkd1,Pl agl1,Ppap2b,Ppm1a,Psme3,Ptpn11,Qk,Rad51,Raf1,Rap2c,Rassf2,Rere,Rfc1,Rfwd2,Rnf10,Rnf 41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rptor,Rtf1,Setd3,Ski,Slc39a10,Smad3,Smad5,Smarca1,Smc5 ,Stradb,Sumo3,Tarbp2,Tbk1,Tbp,Tet3,Tnfaip1,Tollip,Trp53inp2,Ube2v1,Vapb,Vegfa,Whsc1,Wi bg,Wnt4,Ywhah,Zfp326 GO:0070972 protein localization to endoplasmic reticulum 1.52E-02 Gbf1,Macf1,Rab10,Sec61a1,Sec62,Srp14 GO:1903729 regulation of plasma membrane organization 1.52E-02 Bcl2l1,Hectd1,Itgb1,Kif5b,Numb,Pik3r1,Pkdcc,Vamp8,Vti1b GO:0019827 stem cell maintenance 1.55E-02 Bmpr1a,Ctnnb1,Cul4a,Ddx6,Eif4e,Lrp5,Med24,Med28,Pcm1,Raf1,Rtf1,Ski,Tpt1 GO:0044249 cellular biosynthetic process 1.57E-02 Agk,Asnsd1,Atg4b,B4galt1,B4galt7,Bptf,Cdipt,Cdk9,Chpf,Chpt1,Chst8,Cmpk1,Coq6,Crebzf,Dd ost,Ddx3x,Dpm1,Dpy19l4,Dtl,Dvl1,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Elovl5,Etnk1,Etv6,Fas n,Fkrp,Flna,Fosl2,Furin,Galnt1,Galnt7,Gclm,Glud1,Gpaa1,Gtpbp2,Hipk3,Iars,Igf1,Ing4,Larp1,M an2a1,Mapk3,Med1,Med24,Mrps25,Mtap,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Patz1,Pfas,Pgm2,Pi as2,Pik3r1,Plagl1,Ppm1a,Qk,Rad51,Rbm39,Rere,Samd8,Slc35c2,Smad3,Smarca1,Sms,Sptlc1 ,Tbp,Tet3,Tk2,Tnfaip1,Top2b,Ube2g2,Ube2j1,Wipi2,Wnt4,Zdhhc18,Zdhhc21 GO:0010464 regulation of mesenchymal cell proliferation 1.58E-02 Arhgap5,Bmpr1a,Ctnnb1,Ihh,Lrp5,Lrp6,Vegfa

Table S2_2 28

GO:0031324 negative regulation of cellular metabolic 1.58E-02 process App,Atxn2,Bag5,Baz2a,Bcl2l1,Bptf,Btg2,Caprin1,Cbfa2t3,Cbx5,Cbx6,Cc2d1b,Cdk5rap3,Cdk8, Cdk9,Chchd3,Chmp1a,Chordc1,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Ddx3x,Dedd,Dnajb2,Dvl1, Dyrk1a,Eif4e,Enc1,Erlin2,Etv6,Fkbp1a,Flna,Furin,Gabbr1,Gatad2a,Gsk3b,Hdgf,Hipk3,Hnrnpa2 b1,Hsph1,Igf1,Igf1r,Ing4,Insr,Itgav,Lats1,Lats2,Lims1,Lrch4,Lrp5,Lrp6,Med1,Mtmr2,Mtmr3,Mxd 4,Myadm,N4bp1,Nf2,Ogt,Pafah1b1,Paip2b,Patl1,Patz1,Pcid2,Pdcd4,Phf21a,Pias2,Pik3r1,Ppap 2b,Ppif,Ppp1r11,Purb,Qk,Rapgef1,Rassf2,Rbfox2,Rere,Rfc1,Rgp1,Rnf8,Rps6ka3,Rtf1,Rybp,Sk i,Smad3,Spred1,Suz12,Trim39,Tspyl2,Usp14,Usp7,Vegfa,Whsc1,Wnt4,Ywhaq,Zmynd11 GO:1903506 regulation of nucleic acid-templated 1.61E-02 App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Carm1,Cbfa2t3,Cbx5,Cbx6,Cc2 transcription d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Dcp1a,Ddx3x, Dedd,Dvl1,Dyrk1b,Erlin2,Etv6,Flna,Fosl2,Gatad2a,Gsk3b,Hdgf,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf 1r,Ihh,Ing4,Insr,Jmy,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mllt1 0,Mlxip,Mms19,Mtpn,Mxd4,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Pam,Patz1,Pcid2,Pdcd4,Ph f21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Purb,Raf1,Rap2c,Rbfox2,Rbm39,Rere,Rfc1,Rnf 10,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rptor,Rtf1,Rybp,Setd3,Ski,Smad3,Smad5,Smarca1,Suz12,Tb k1,Tbp,Tet3,Trp53inp2,Ube2v1,Ubn2,Usp7,Usp9x,Vegfa,Whsc1,Wnt4,Ywhah,Ywhaq,Zfp326,Z mynd11 GO:0048646 anatomical structure formation involved in 1.61E-02 Actr2,Atxn2,B4galt1,Bmpr1a,Cfl2,Cnot1,Cnot2,Ctnnb1,Dvl1,Dyrk1b,Enah,Fkbp1a,Flna,Gatad2a morphogenesis ,Gna13,Gsk3b,Hectd1,Ihh,Itgav,Itgb1,Lats1,Lats2,Lrp5,Lrp6,Macf1,Map2k1,Mapk3,Med1,Mfn2, Mtmr2,Nf2,Nfatc3,Nup50,Ocrl,Pafah1b1,Pcm1,Pkd1,Pnpla6,Ptpn11,Pvrl1,Rock2,Rtf1,Rtn4,Sep t2,Ski,Smad3,Stim1,Vegfa,Wnt4 GO:0006644 phospholipid metabolic process 1.61E-02 Cdipt,Chpt1,Dpm1,Etnk1,Gpaa1,Ip6k1,Mtmr2,Mtmr3,Ocrl,Pi4kb,Pik3r1,Ppap2b,Samd8,Sptlc1, Tmem55a,Tmem55b GO:0016571 histone methylation 1.61E-02 Baz2a,Carm1,Ogt,Rtf1,Setd3,Suz12,Tet3,Wdr82,Whsc1 GO:0032886 regulation of microtubule-based process 1.61E-02 Arl2,Chmp1a,Chordc1,Ctnnb1,Diap1,Gsk3b,Hsph1,Macf1,Mapre1,Pdcd6ip,Pkd1,Rock2,Sgk1,T acc1 GO:0001933 negative regulation of protein phosphorylation 1.62E-02 Cdk5rap3,Chordc1,Dvl1,Fkbp1a,Gsk3b,Hipk3,Hsph1,Igf1,Igf1r,Insr,Lats1,Lats2,Lrp5,Lrp6,Myad m,Nf2,Ogt,Pafah1b1,Ppap2b,Rapgef1,Rassf2,Smad3,Spred1,Suz12,Zmynd11 GO:0048858 cell projection morphogenesis 1.62E-02 Actr2,App,Arl3,Asap1,Atxn2,Btbd3,Dvl1,Enah,Flna,Gsk3b,Igf1r,Itgb1,Kif5b,Map2k1,Mink1,Nrn1, Numb,Ocrl,Pacsin2,Pafah1b1,Pcm1,Plxna1,Ptpn11,Pvrl1,Rab10,Rbfox2,Rere,Rock2,Rtn4,Sept 2,Sgk1,Top2b,Unc119b,Usp9x,Vegfa GO:0044248 cellular catabolic process 1.69E-02 Acox1,Adh5,Amfr,Arih1,Atg13,Atg4b,Bfar,Cd2ap,Cdc27,Cisd2,Cnot1,Cnot2,Csde1,Cul4a,Cul4b ,Dcp1a,Dnajb2,Dtl,Enc1,Entpd4,Erlin2,Faf2,Glud1,Gtpbp2,Hectd1,Herc3,Map1lc3b,March6,Nbr 1,Pan3,Patl1,Pdcd6ip,Pex13,Pex5,Ppp2r5c,Ppt1,Rbbp6,Rnf41,Rnf8,Tnfaip1,Trp53inp2,Ubap1, Ube2g2,Ube2j1,Ube4b,Ubr3,Ubr4,Usp14,Usp19,Usp25,Usp7,Usp9x,Vamp8,Wibg,Wipi2 GO:0043161 proteasome-mediated ubiquitin-dependent 1.73E-02 Amfr,Bfar,Cd2ap,Cdc27,Cul4a,Dnajb2,Erlin2,Faf2,Ppp2r5c,Tnfaip1,Ube2g2,Ube2j1,Ube4b,Ubr protein catabolic process 3,Usp14,Usp19,Usp25,Usp7,Usp9x GO:0034976 response to endoplasmic reticulum stress 1.74E-02 Amfr,Atf6,Col4a3bp,Dnajb2,Erlin2,Faf2,Gsk3b,Itpr1,Pdia6,Pik3r1,Ube2g2,Ube2j1,Ube4b,Usp19 ,Vapb

Table S2_2 29

GO:0009653 anatomical structure morphogenesis 1.79E-02 Actr2,App,Arhgap12,Arl3,Asap1,Atxn2,B4galt1,Bcl2l1,Bmpr1a,Btbd3,Carm1,Cfl2,Cnot1,Cnot2, Col4a3bp,Crkl,Ctnnb1,Ddr1,Dvl1,Dyrk1b,Enah,Fermt2,Fkbp1a,Flna,Fndc3b,Gak,Gatad2a,Gna 12,Gna13,Gsk3b,Hectd1,Hira,Hspg2,Igf1,Igf1r,Ihh,Insr,Itgav,Itgb1,Kif5b,Lamc1,Lats1,Lats2,Lrig 1,Lrp5,Lrp6,Ly6e,Macf1,Man2a1,Map2k1,Mapk3,Med1,Mfn2,Mink1,Mtmr2,Nf2,Nfatc3,Nrn1,Nu mb,Nup50,Ocrl,Pacsin2,Pafah1b1,Pcm1,Pkd1,Pkdcc,Plekha1,Plxna1,Pnpla6,Ppap2b,Ptpn11,P vrl1,Qk,Rab10,Rbfox2,Rere,Ric8,Rock2,Rtf1,Rtn4,Sept2,Sgk1,Sidt2,Ski,Smad3,Smad5,Stim1, Stradb,Top2b,Ube4b,Unc119b,Usp9x,Vegfa,Whsc1,Wnt4 GO:1901576 organic substance biosynthetic process 1.83E-02 Acsl4,Agk,Asnsd1,Atg4b,B4galt1,B4galt7,Bptf,Cdipt,Cdk9,Chpf,Chpt1,Chst8,Cmpk1,Coq6,Creb zf,Ddost,Ddx3x,Dpm1,Dpy19l4,Dtl,Dvl1,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Elovl5,Etnk1,Etv 6,Fasn,Fkrp,Flna,Fosl2,Furin,Galnt1,Galnt7,Gclm,Glud1,Gpaa1,Gtpbp2,Hipk3,Hsd17b7,Iars,Igf 1,Ing4,Ip6k1,Larp1,Man2a1,Mapk3,Med1,Med24,Mrps25,Mtap,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt ,Patz1,Pfas,Pgm2,Pias2,Pik3r1,Plagl1,Ppm1a,Qk,Rad51,Rbm39,Rere,Samd8,Slc35c2,Smad3, Smarca1,Sms,Sptlc1,Tbp,Tet3,Tk2,Tnfaip1,Top2b,Ube2g2,Ube2j1,Wipi2,Wnt4,Zdhhc18,Zdhhc 21 GO:0034249 negative regulation of cellular amide metabolic 1.84E-02 process Btg2,Caprin1,Cnot1,Cnot2,Ddx3x,Eif4e,Enc1,Paip2b,Patl1,Purb,Qk GO:0070371 ERK1 and ERK2 cascade 1.84E-02 Igf1,Itgav,Map2k1,Mapk3,Med1 GO:0072698 protein localization to microtubule cytoskeleton 1.84E-02 Diap1,Dvl1,Gsk3b,Mapre1,Pcm1 GO:0021932 hindbrain radial glia guided cell migration 1.85E-02 Itgb1,Lrp6,Rbfox2,Rere GO:0006355 regulation of transcription, DNA-templated 1.86E-02 App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Carm1,Cbfa2t3,Cbx5,Cbx6,Cc2 d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Dcp1a,Ddx3x, Dedd,Dvl1,Dyrk1b,Erlin2,Etv6,Flna,Fosl2,Gatad2a,Gsk3b,Hdgf,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf 1r,Ihh,Ing4,Insr,Jmy,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mllt1 0,Mlxip,Mms19,Mtpn,Mxd4,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Pam,Patz1,Pcid2,Pdcd4,Ph f21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Purb,Raf1,Rbfox2,Rere,Rfc1,Rnf10,Rnf41,Rnf8, Rprd1b,Rps6ka3,Rptor,Rtf1,Rybp,Setd3,Ski,Smad3,Smad5,Smarca1,Suz12,Tbk1,Tbp,Tet3,Tr p53inp2,Ube2v1,Ubn2,Usp7,Usp9x,Vegfa,Whsc1,Wnt4,Ywhah,Ywhaq,Zfp326,Zmynd11 GO:0009058 biosynthetic process 1.92E-02 Acsl4,Agk,Asnsd1,Atg4b,B4galt1,B4galt7,Bptf,Cdipt,Cdk9,Chpf,Chpt1,Chst8,Cmpk1,Coq6,Creb zf,Ddost,Ddx3x,Dpm1,Dpy19l4,Dtl,Dvl1,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Elovl5,Etnk1,Etv 6,Fasn,Fkrp,Flna,Fosl2,Furin,Galnt1,Galnt7,Gbf1,Gclm,Glud1,Gpaa1,Gtpbp2,Hipk3,Hsd17b7,Ia rs,Igf1,Ing4,Ip6k1,Larp1,Man2a1,Mapk3,Med1,Med24,Mms19,Mrps25,Mtap,Nfat5,Nfatc3,Nfe2l 1,Nucks1,Ogt,Patz1,Pfas,Pgm2,Pias2,Pik3r1,Plagl1,Ppm1a,Qk,Rad51,Rbm39,Rere,Samd8,Slc 35c2,Smad3,Smarca1,Sms,Sptlc1,Tbp,Tet3,Tk2,Tnfaip1,Top2b,Ube2g2,Ube2j1,Wipi2,Wnt4,Z dhhc18,Zdhhc21 GO:0030705 cytoskeleton-dependent intracellular transport 1.95E-02 Ap3b1,Ap3d1,App,Arl3,Kif1b,Kif1c,Kif5b,Klc1,Map2k1,Pafah1b1,Pcm1 GO:0009968 negative regulation of signal transduction 1.95E-02 Adrbk1,Bag5,Bcl2l1,Bcl2l2,Bfar,Cnot1,Cnot2,Ctnnb1,Ddx3x,Dyrk1a,Gclm,Gsk3b,Higd1a,Hipk3, Hsph1,Igf1,Igf1r,Ihh,Itgav,Itgb1,Itpr1,Kank1,Lats1,Lats2,Lrp6,Mapkap1,Mfn2,Myadm,Nf2,Numb, Pafah1b1,Pias2,Plekha1,Ppif,Ppm1a,Psme3,Ptprd,Raf1,Rapgef1,Rassf2,Ski,Spred1,Stradb,Su z12,Tnfaip1,Tpt1,Vegfa,Wnt4,Zmynd11 Table S2_2 30

GO:1902531 regulation of intracellular signal transduction 2.01E-02 Akap11,Akap7,Bag5,Bcl2l1,Bcl2l2,Cdk5rap3,Crk,Ctnnb1,Ddx3x,Dyrk1a,Erp29,Fkbp1a,Flna,Gn a12,Gsk3b,Hipk3,Hsph1,Igf1,Igf1r,Insr,Itgav,Itgb1,Itpr1,Kank1,Map2k1,Map2k3,Map3k3,Map3k 4,Mapk3,Mapk9,Mapkap1,Mfn2,Mink1,Myadm,Nbr1,Nf2,Nfat5,Ogt,Pafah1b1,Peli2,Plekha1,Ppif ,Ppm1a,Ptpn11,Ptprd,Pum2,Raf1,Rapgef1,Rassf2,Rnf41,Rptor,Seh1l,Serinc3,Sesn1,Shoc2,Sp red1,Stradb,Suz12,Tnfaip1,Tpt1,Ube2v1,Vegfa,Zmynd11 GO:0048666 neuron development 2.01E-02 Acsl4,App,Arl3,Atxn2,Baiap2,Btbd3,Btg2,Cul4b,Diap1,Dvl1,Enah,Git1,Gsk3b,Igf1r,Ihh,Itgb1,Kif5 b,Lamc1,Map2k1,Mapk9,Mink1,Mtmr2,Nrn1,Numb,Pafah1b1,Plxna1,Ptpn11,Pvrl1,Rab10,Rbfo x2,Rere,Rock2,Rtn4,Sept2,Sgk1,Top2b,Ube4b,Usp9x,Vegfa GO:0006508 proteolysis 2.02E-02 Amfr,Arih1,Atg4b,Atxn7l3,Bace1,Bfar,Capns1,Cd2ap,Cdc27,Chst8,Cops7a,Cops7b,Cul4a,Cul4 b,Dnajb2,Dtl,Enc1,Erlin2,Faf2,Fkrp,Furin,Hectd1,Herc3,Lnpep,Mapk9,March6,Otud4,Pappa,Pd cd6ip,Pmpcb,Ppp2r5c,Rbbp6,Rnf41,Rnf8,Smad3,Tnfaip1,Trp53inp2,Ubap1,Ube2g2,Ube2j1,Ub e4b,Ubr3,Ubr4,Usp12,Usp14,Usp19,Usp25,Usp7,Usp9x GO:0051701 interaction with host 2.03E-02 Adrbk1,Bcl2l1,Insr,Itgav,Pvrl1,Smad3,Vamp8,Vapb GO:0018022 peptidyl-lysine methylation 2.03E-02 Baz2a,Ogt,Rtf1,Setd3,Suz12,Tet3,Wdr82,Whsc1 GO:1903008 organelle disassembly 2.09E-02 Atg4b,Cisd2,Gbf1,Kif5b,Klc1,Map1lc3b,Wipi2 GO:0006605 protein targeting 2.12E-02 Ap3b1,Atg4b,Ipo4,Kpna4,Macf1,Mapk3,Mfn2,Myadm,Myo1c,Pan3,Pex13,Pex5,Pik3r1,Sec61a1 ,Sec62,Srp14,Tnpo3,Vti1b,Ywhaq GO:0080134 regulation of response to stress 2.12E-02 Atg13,Bag5,Bcl2l1,Bfar,Bmpr1a,Cdk9,Chordc1,Cul4a,Dyrk1a,Eif2s1,Erp29,Hipk3,Hsph1,Igf1r,K ank1,Larp1,Map1lc3b,Map2k1,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,Med1,Mink1,Mtmr3, Nbr1,Ogt,Pafah1b1,Pafah1b2,Pex13,Pik3r1,Ppap2b,Pum2,Rad51,Rassf2,Rnf8,Rps6ka3,Rtn4, Scoc,Serinc3,Smad3,Spred1,Tarbp2,Tbk1,Tmem39b,Tpt1,Ube2g2,Ube2j1,Usp14,Usp19,Usp2 5,Vamp8,Vegfa,Wbp11,Whsc1,Wnt4,Zmynd11 GO:0030258 lipid modification 2.12E-02 Acox1,Agk,Ip6k1,Mtmr2,Mtmr3,Ocrl,Pex13,Pex5,Pi4kb,Pik3r1,Tmem55a,Tmem55b GO:1903828 negative regulation of cellular protein 2.12E-02 localization Bcl2l1,Gsk3b,Hectd1,Hsph1,Numb,Ogt,Pkd1,Pkdcc,Ppm1a,Trp53inp2,Ube2g2,Ube2j1 GO:0061136 regulation of proteasomal protein catabolic 2.12E-02 Bag5,Dnajb2,Dvl1,Gna12,Gsk3b,N4bp1,Pkd1,Psme3,Rad23b,Rfwd2,Smc5,Usp14,Usp19,Usp2 process 5,Usp7,Usp9x GO:0019219 regulation of nucleobase-containing compound 2.12E-02 Ahcyl1,App,Arhgef11,Atf6,Atxn7l3,Baz2a,Bmpr1a,Bptf,Brd2,Brd4,Btg2,Carm1,Cbfa2t3,Cbx5,Cb metabolic process x6,Cc2d1b,Cdk5rap3,Cdk9,Chchd3,Chd6,Chmp1a,Cnot1,Cnot2,Cops2,Crebzf,Ctnnb1,Cul4a,D cp1a,Ddx3x,Dedd,Dvl1,Dyrk1a,Dyrk1b,Erlin2,Etv6,Fastk,Flna,Fosl2,Gabbr1,Gatad2a,Gsk3b,Hd gf,Hipk3,Hnrnpa2b1,Hsph1,Igf1,Igf1r,Ihh,Ing4,Insr,Jmy,Lims1,Lrch4,Lrp5,Lrp6,Map2k1,Map2k3 ,Mapk3,Mapk9,Med1,Med24,Mllt10,Mlxip,Mms19,Mrap,Mtpn,Mxd4,Naa15,Nf2,Nfat5,Nfatc3,Nfe 2l1,Nucks1,Ogt,Pam,Patz1,Pcid2,Pdcd4,Phf21a,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppif,Ppm1a, Purb,Rad51,Raf1,Rap2c,Rbfox2,Rbm39,Rere,Rfc1,Rnf10,Rnf41,Rnf8,Rprd1b,Rps6ka3,Rptor, Rtf1,Rybp,Setd3,Ski,Smad3,Smad5,Smarca1,Son,Srpk1,Suz12,Tarbp2,Tbk1,Tbp,Tet3,Tnfaip1 ,Trp53inp2,Tspyl2,Ube2v1,Ubn2,Usp7,Usp9x,Vapb,Vegfa,Whsc1,Wnt4,Ywhah,Ywhaq,Zfp326, Zmynd11 GO:0048699 generation of neurons 2.23E-02 Acsl4,App,Arl3,Asap1,Atxn2,Baiap2,Bmpr1a,Btbd3,Btg2,Caprin1,Carm1,Cops2,Ctnnb1,Cul4b, Ddx6,Diap1,Dvl1,Eif4e,Eif4g1,Enah,Enc1,Git1,Gsk3b,Igf1r,Ihh,Itgb1,Kank1,Kif5b,Lamc1,Lrp6, Man2a1,Map2k1,Mapk9,Mark2,Med1,Mink1,Mtmr2,Nf2,Nrn1,Numb,Pafah1b1,Pcm1,Pex13,Pe x5,Pias2,Plxna1,Ptpn11,Ptprd,Pvrl1,Qk,Rab10,Rapgef1,Rbfox2,Rere,Rnf10,Rock2,Rtn4,Sept2, Sgk1,Ski,Smarca1,Top2b,Ube4b,Usp9x,Vegfa,Wnt4,Ywhah Table S2_2 31

GO:0007369 gastrulation 2.26E-02 Bmpr1a,Ctnnb1,Dvl1,Hira,Itgav,Lrp5,Lrp6,Macf1,Nf2,Ppap2b,Ric8,Rtf1,Smad3 GO:0051056 regulation of small GTPase mediated signal 2.30E-02 transduction Crk,Igf1,Itgb1,Kank1,Map2k1,Mapkap1,Mfn2,Ogt,Rapgef1,Shoc2,Tnfaip1 GO:0045047 protein targeting to ER 2.30E-02 Macf1,Sec61a1,Sec62,Srp14 GO:0033554 cellular response to stress 2.30E-02 Amfr,Atf6,Atg13,Atg4b,Bcl2l1,Bcl2l2,Btg2,Cdk5rap3,Cdk9,Chd6,Cisd2,Col4a3bp,Cul4b,Ddx39, Ddx3x,Dnajb2,Dtl,Eif2s1,Erlin2,Faf2,Gsk3b,Higd1a,Ing4,Ints3,Itpr1,Jmy,Map1lc3b,Map2k1,Map 2k3,Mapk3,Mapk9,Mink1,Mms19,Nbr1,Pdia6,Pex13,Pik3r1,Plekha1,Ppif,Ptpn11,Rad23b,Rad5 1,Rnf8,Seh1l,Sgk1,Slc12a6,Slc2a1,Smc5,Stradb,Tmem109,Tmem39b,Trp53inp2,Ube2g2,Ube 2j1,Ube2v1,Ube4b,Usp19,Usp7,Vamp8,Vapb,Vegfa,Wipi2,Wnt4 GO:2001233 regulation of apoptotic signaling pathway 2.31E-02 Bag5,Bcl2l1,Bcl2l2,Ctnnb1,Ddx3x,Erp29,Gclm,Gsk3b,Higd1a,Hsph1,Igf1,Itgav,Mapk9,Ppif,Ppp 2r1a,Psme3,Raf1,Serinc3,Smad3,Stradb,Tpt1,Trim39,Vegfa,Wnt4,Zmynd11 GO:0042326 negative regulation of phosphorylation 2.32E-02 Cdk5rap3,Chordc1,Dvl1,Fkbp1a,Gsk3b,Hipk3,Hsph1,Igf1,Igf1r,Insr,Lats1,Lats2,Lrp5,Lrp6,Myad m,Nf2,Ogt,Pafah1b1,Ppap2b,Ppif,Rapgef1,Rassf2,Smad3,Spred1,Suz12,Zmynd11 GO:0045859 regulation of protein kinase activity 2.33E-02 App,Cab39,Ccnd2,Cdk5rap3,Chordc1,Dvl1,Erp29,Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Igf1r,Insr,La ts1,Lats2,Lrp5,Lrp6,Map2k1,Map2k3,Map3k3,Map3k4,Mink1,Nf2,Pkd1,Ptpn11,Raf1,Rap2c,Ra ssf2,Rptor,Spred1,Stradb,Tspyl2,Vapb,Vegfa GO:0048864 stem cell development 2.33E-02 Bmpr1a,Ctnnb1,Cul4a,Ddx6,Eif4e,Flna,Gsk3b,Lrp5,Lrp6,Mapk3,Med24,Med28,Pcm1,Raf1,Rtf1 ,Rtn4,Ski,Tpt1 GO:0031400 negative regulation of protein modification 2.36E-02 Bag5,Cdk5rap3,Chordc1,Ctnnb1,Dnajb2,Dvl1,Fkbp1a,Gsk3b,Hipk3,Hsph1,Igf1,Igf1r,Insr,Lats1, process Lats2,Lrp5,Lrp6,Myadm,N4bp1,Nf2,Ogt,Pafah1b1,Ppap2b,Ppp1r11,Rapgef1,Rassf2,Ski,Smad 3,Spred1,Suz12,Trim39,Zmynd11 GO:0009792 embryo development ending in birth or egg 2.36E-02 Acsl4,Bcl2l1,Bmpr1a,Bptf,Brd4,Cnot1,Cnot2,Col4a3bp,Ctnnb1,Dvl1,Enah,Gatad2a,Gna12,Gna hatching 13,Hectd1,Hspg2,Ihh,Itgav,Itgb1,Lats1,Lats2,Lims1,Lrp6,Ly6e,Man2a1,Map2k1,Med1,Mfn2,Nu p50,Ocrl,Pkd1,Rbbp6,Ric8,Rock2,Rtf1,Ski,Smad3,Ubr3,Usp9x,Vegfa GO:0061024 membrane organization 2.36E-02 Ankfy1,Ap3d1,Atg4b,Bcl2l1,Chchd3,Clcn3,Dvl1,Fermt2,Flna,Gbf1,Gnai3,Itgb1,Macf1,Map1lc3b, Mfn2,Mtch2,Myadm,Myo1c,Pacsin2,Pafah1b1,Pdcd6ip,Pex5,Ppif,Ppt1,Ptprd,Rab10,Sec61a1,S ec62,Sgcb,Syne2,Vamp8,Vapb,Vti1b,Wasl,Wnt4 GO:1900182 positive regulation of protein localization to 2.38E-02 nucleus Bmpr1a,Cd2ap,Cdk5rap3,Flna,Igf1,Kank1,Kpna1,Med1,Ogt,Pik3r1,Smad3 GO:0045070 positive regulation of viral genome replication 2.39E-02 Ddx3x,Ppih,Srpk1,Tarbp2,Vapb GO:0014010 Schwann cell proliferation 2.39E-02 Ctnnb1,Nf2 GO:0046048 UDP metabolic process 2.39E-02 Cmpk1,Entpd4 GO:0061324 canonical Wnt signaling pathway involved in 2.39E-02 positive regulation of cardiac outflow tract cell proliferation Ctnnb1,Lrp6 GO:0021691 cerebellar Purkinje cell layer maturation 2.39E-02 Arcn1,Rere GO:0009193 pyrimidine ribonucleoside diphosphate 2.39E-02 metabolic process Cmpk1,Entpd4 GO:1901963 regulation of cell proliferation involved in 2.39E-02 outflow tract morphogenesis Ctnnb1,Lrp6 GO:0035617 stress granule disassembly 2.39E-02 Kif5b,Klc1

Table S2_2 32

GO:0051276 chromosome organization 2.39E-02 Atxn7l3,Baz2a,Bptf,Brd2,Brd4,Brpf3,Carm1,Chmp1a,Chmp7,Ctnnb1,Cul4b,Ddx3x,Hira,Ing4,Ipo 4,Lats1,Med24,Msl1,Ncaph,Nusap1,Ogt,Phf13,Ppp2r1a,Rad23b,Rad51,Rere,Rnf8,Rtf1,Rybp,S eh1l,Setd3,Smarca1,Smarcd2,Smc5,Suz12,Syde1,Tet3,Top2b,Usp7,Wdr82,Whsc1 GO:0048813 dendrite morphogenesis 2.39E-02 Btbd3,Dvl1,Itgb1,Mink1,Rbfox2,Rere,Rock2 GO:1903829 positive regulation of cellular protein 2.44E-02 Atg13,Bmpr1a,Cd2ap,Cdk5rap3,Flna,Gsk3b,Igf1,Itgb1,Kank1,Kif5b,Kpna1,Med1,Myo1c,Ogt,Pc localization m1,Pik3r1,Ppm1a,Smad3,Ubl5,Vegfa,Wbp11 GO:0030030 cell projection organization 2.48E-02 Acsl4,Actr2,App,Arl3,Asap1,Atxn2,Baiap2,Btbd3,Btg2,Cul4b,Diap1,Dvl1,Enah,Flna,Git1,Gsk3b,I gf1r,Itgb1,Kif5b,Lamc1,Map2k1,Mapk9,Mink1,Mtmr2,Nrn1,Numb,Ocrl,Pacsin2,Pafah1b1,Pcm1, Plekha1,Plxna1,Ptpn11,Pvrl1,Rab10,Rbfox2,Rere,Rock2,Rtn4,Sept2,Sgk1,Top2b,Ube4b,Unc1 19b,Usp9x,Vegfa GO:0006650 glycerophospholipid metabolic process 2.48E-02 Cdipt,Chpt1,Dpm1,Etnk1,Gpaa1,Ip6k1,Mtmr2,Mtmr3,Ocrl,Pi4kb,Pik3r1,Tmem55a,Tmem55b GO:0010648 negative regulation of cell communication 2.49E-02 Adrbk1,Bag5,Bcl2l1,Bcl2l2,Bfar,Cnot1,Cnot2,Ctnnb1,Ddx3x,Dyrk1a,Gabbr1,Gclm,Gsk3b,Higd1 a,Hipk3,Hsph1,Igf1,Igf1r,Ihh,Itgav,Itgb1,Itpr1,Kank1,Lats1,Lats2,Lrp6,Mapkap1,Mfn2,Mtmr2,Mt mr3,Myadm,Nf2,Numb,Pafah1b1,Pfkl,Pias2,Plekha1,Ppif,Ppm1a,Psme3,Ptpn11,Ptprd,Raf1,Ra pgef1,Rassf2,Ski,Spred1,Stradb,Suz12,Tnfaip1,Tpt1,Vegfa,Wnt4,Zmynd11 GO:0000290 deadenylation-dependent decapping of 2.49E-02 nuclear-transcribed mRNA Dcp1a,Pan3,Patl1 GO:0006620 posttranslational protein targeting to 2.49E-02 membrane Macf1,Sec61a1,Sec62 GO:0060440 trachea formation 2.49E-02 Ctnnb1,Map2k1,Mapk3 GO:0008088 axon cargo transport 2.52E-02 Ap3b1,Ap3d1,App,Kif1b,Klc1,Pafah1b1 GO:0010656 negative regulation of muscle cell apoptotic 2.52E-02 process Gsk3b,Igf1,Igf1r,Lrp6,Pik3r1,Qk GO:0032784 regulation of DNA-templated transcription, 2.52E-02 elongation Brd4,Map2k1,Rnf8,Rtf1,Zfp326,Zmynd11 GO:0006457 protein folding 2.55E-02 Cdc37l1,Chordc1,Dnaja2,Dnajb2,Dnajc1,Erp29,Fkbp1a,Fkbp5,Hsph1,Mesdc2,Pdia6 GO:0009895 negative regulation of catabolic process 2.57E-02 Bag5,Cdk5rap3,Dedd,Flna,Furin,Mtmr2,Mtmr3,N4bp1,Rgp1,Smad3,Trim39,Ube2g2,Ube2j1,Us p14,Usp25 GO:0045667 regulation of osteoblast differentiation 2.57E-02 Bmpr1a,Ctnnb1,Fndc3b,Igf1,Lrp5,Nbr1,Pias2,Rassf2,Ski,Smad3,Smad5,Wnt4 GO:0009891 positive regulation of biosynthetic process 2.57E-02 App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Cdk5rap3,Cdk9,Chd6,Clcn3,Ctnnb1,Dcp1a,Ddx3 x,Dvl1,Dyrk1b,Erlin2,Etv6,Fnta,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Igf1r,Ihh,Insr,Jmy,Larp1,Lrp5,Lrp6 ,Map2k1,Map2k3,Mapk3,Mapk9,Med1,Med24,Mllt10,Mms19,Mrap,Mtpn,Naa15,Nfat5,Nfatc3,Nf e2l1,Nucks1,Ogt,Patz1,Pcid2,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Raf1,Rere,Rfc1,Rnf10, Rnf41,Rprd1b,Rps6ka3,Rptor,Rtf1,Setd3,Ski,Smad3,Smad5,Smarca1,Smek2,Tarbp2,Tbk1,Tb p,Tet3,Tnfaip1,Trp53inp2,Ube2v1,Vegfa,Wibg,Wnt4,Ywhah,Zfp326 GO:0060444 branching involved in mammary gland duct 2.67E-02 morphogenesis Ddr1,Lrp5,Lrp6,Med1,Wnt4 GO:0051568 histone H3-K4 methylation 2.67E-02 Ogt,Rtf1,Setd3,Tet3,Wdr82 GO:0044380 protein localization to cytoskeleton 2.67E-02 Diap1,Dvl1,Gsk3b,Mapre1,Pcm1 GO:0016032 viral process 2.72E-02 Adrbk1,Bcl2l1,Ddx6,Insr,Itgav,Pdcd6ip,Pvrl1,Smad3,Vamp8,Vapb

Table S2_2 33

GO:0030154 cell differentiation 2.76E-02 Acsl4,Aff4,Ap3d1,App,Arl3,Asap1,Atxn2,B4galt1,Baiap2,Bcl2l1,Bmpr1a,Btbd3,Btg2,Caprin1,Car m1,Cbfa2t3,Celf1,Cfl2,Cnot1,Cnot2,Cops2,Ctnnb1,Cul4a,Cul4b,Ddx6,Diap1,Dvl1,Dyrk1b,Eif2b 2,Eif4e,Eif4g1,Enah,Enc1,Etv6,Fasn,Fermt2,Flna,Fndc3b,Fosl2,Gabbr1,Gak,Git1,Gna12,Gna1 3,Gsk3b,Hectd1,Hira,Hspg2,Iars,Igf1,Igf1r,Ihh,Itgav,Itgb1,Kank1,Kif5b,Lamc1,Lats1,Lats2,Lrp5, Lrp6,Man2a1,Map2k1,Map3k4,Mapk3,Mapk9,Mark2,Med1,Med24,Med28,Mink1,Mrap,Mtmr2,M yadm,Nf2,Nfatc3,Nfe2l1,Nrn1,Numb,Pafah1b1,Patz1,Pcm1,Pex13,Pex5,Pias2,Pik3r1,Plagl1,Pl ekha1,Plxna1,Ppap2b,Prrc2c,Ptpn11,Ptprd,Purb,Pvrl1,Qk,Rab10,Raf1,Rap2c,Rapgef1,Rbfox2, Rere,Rnf10,Rnf8,Rock2,Rpl22,Rtf1,Rtn4,Sept2,Sgcb,Sgk1,Sidt2,Ski,Smad3,Smad5,Smarca1, Stim1,Tacc1,Tarbp2,Top2b,Tpt1,Trp53inp2,Ube2j1,Ube4b,Usp9x,Vegfa,Wnt4,Ywhah GO:0031325 positive regulation of cellular metabolic 2.80E-02 App,Arhgef11,Atf6,Atg13,Atg4b,Atxn7l3,Bmpr1a,Bptf,Brd4,Btg2,Cab39,Ccnd2,Cdk5rap3,Cdk9, process Chd6,Clcn3,Cnot1,Ctnnb1,Dcp1a,Ddx3x,Dnajb2,Dvl1,Dyrk1a,Dyrk1b,Eif2s1,Erlin2,Erp29,Etv6, Fkbp1a,Fnta,Fosl2,Gsk3b,Hdgf,Higd1a,Hsph1,Igf1,Igf1r,Ihh,Insr,Itgav,Itgb1,Jmy,Larp1,Lats1,Lr p5,Lrp6,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Med1,Med24,Mink1,Mllt10,Mms19,Mr ap,Mtpn,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks1,Ogt,Pafah1b2,Patz1,Pcid2,Peli2,Pex13,Pias2,Pik3 r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Psme3,Ptpn11,Rad51,Raf1,Rap2c,Rassf2,Rere,Rfc1,Rfwd2,Rn f10,Rnf41,Rnf8,Rock2,Rprd1b,Rps6ka3,Rptor,Rtf1,Scoc,Setd3,Ski,Slc39a10,Smad3,Smad5,S marca1,Smc5,Smek2,Stradb,Sumo3,Tarbp2,Tbk1,Tbp,Tet3,Tmem39b,Tnfaip1,Tollip,Trp53inp 2,Ube2v1,Vapb,Vegfa,Whsc1,Wibg,Wnt4,Ywhah,Zfp326 GO:0050775 positive regulation of dendrite morphogenesis 2.80E-02 Baiap2,Caprin1,Numb,Pias2,Ptprd,Sgk1 GO:0051865 protein autoubiquitination 2.80E-02 Amfr,Bfar,Hectd1,Rnf10,Rnf41,Rnf8,Ube4b GO:0051961 negative regulation of nervous system 3.00E-02 App,Asap1,Bmpr1a,Carm1,Ctnnb1,Ddx6,Eif4e,Gsk3b,Itgb1,Kank1,Lrp6,Med1,Mtmr2,Pafah1b1 development ,Pcm1,Rnf10,Rtn4,Ski,Ywhah GO:0007017 microtubule-based process 3.05E-02 Actr2,Ap3b1,Ap3d1,App,Arl2,Arl3,Ctnnb1,Dvl1,Dync1li2,Flna,Haus5,Kif1b,Kif1c,Kif23,Kif5b,Klc1 ,Map2k1,Nusap1,Pafah1b1,Pcm1,Pex13,Ppp2r1a,Rock2,Seh1l,Sgk1,Son,Tacc1,Vbp1 GO:0000819 sister chromatid segregation 3.05E-02 Chmp1a,Chmp7,Lats1,Ncaph,Nusap1,Phf13,Ppp2r1a,Seh1l,Top2b GO:1900180 regulation of protein localization to nucleus 3.05E-02 Bmpr1a,Cd2ap,Cdk5rap3,Flna,Gsk3b,Igf1,Kank1,Kpna1,Med1,Nf2,Ogt,Pik3r1,Pkd1,Ppm1a,S mad3 GO:0071702 organic substance transport 3.05E-02 Acsl4,Ahcyl1,Ap2a1,Ap3b1,Ap3d1,Arf3,Arl2,Atg4b,Chmp7,Col4a3bp,Ddx39,Erp29,Faf2,Gsk3b, Hnrnpa2b1,Ipo4,Itgb1,Klc1,Kpna4,Lrp6,Ly6e,Macf1,Mapk3,Mfn2,Myadm,Myo1c,Pafah1b1,Pan 3,Pex13,Pex5,Pik3r1,Pitpna,Pkd1,Ppt1,Rab10,Rab14,Rab22a,Rab4b,Rab5b,Raf1,Sec61a1,Se c62,Serinc3,Slc25a22,Slc2a1,Slc35c2,Snx27,Spns1,Srp14,Stradb,Tlk1,Tnpo3,Ube2q1,Unc119 b,Vti1b,Ywhah,Ywhaq,Zc3h11a GO:0043009 chordate embryonic development 3.05E-02 Bcl2l1,Bmpr1a,Bptf,Brd4,Cnot1,Cnot2,Col4a3bp,Ctnnb1,Dvl1,Enah,Gatad2a,Gna12,Gna13,He ctd1,Hspg2,Ihh,Itgav,Itgb1,Lats1,Lats2,Lims1,Lrp6,Ly6e,Man2a1,Map2k1,Med1,Mfn2,Nup50,O crl,Pkd1,Rbbp6,Ric8,Rock2,Rtf1,Ski,Smad3,Ubr3,Usp9x,Vegfa GO:0023057 negative regulation of signaling 3.05E-02 Adrbk1,Bag5,Bcl2l1,Bcl2l2,Bfar,Cnot1,Cnot2,Ctnnb1,Ddx3x,Dyrk1a,Gabbr1,Gclm,Gsk3b,Higd1 a,Hipk3,Hsph1,Igf1,Igf1r,Ihh,Itgav,Itgb1,Itpr1,Kank1,Lats1,Lats2,Lrp6,Mapkap1,Mfn2,Mtmr2,My adm,Nf2,Numb,Pafah1b1,Pfkl,Pias2,Plekha1,Ppif,Ppm1a,Psme3,Ptpn11,Ptprd,Raf1,Rapgef1,R assf2,Ski,Spred1,Stradb,Suz12,Tnfaip1,Tpt1,Vegfa,Wnt4,Zmynd11 GO:0097190 apoptotic signaling pathway 3.05E-02 Bcl2l1,Bcl2l2,Ddx3x,Dedd,Dido1,Gsk3b,Igf1,Itgav,Itpr1,Jmy,Mapk9,Mknk1,Pik3r1,Raf1,Rnf41,R ock2,Smad3,Tmem109,Ube4b Table S2_2 34

GO:0072594 establishment of protein localization to 3.05E-02 Ap3b1,Ipo4,Kpna4,Macf1,Mapk3,Mfn2,Nras,Pex13,Pex5,Pik3r1,Rab10,Sec61a1,Sec62,Srp14, organelle Tnpo3,Vti1b GO:0071496 cellular response to external stimulus 3.18E-02 Arhgdia,Atg13,Atg4b,Chmp1a,Cisd2,Ctnnb1,Gsk3b,Higd1a,Map1lc3b,Nbr1,Rptor,Seh1l,Slc2a1 ,Trp53inp2,Vamp8,Wipi2,Wnt4 GO:0048869 cellular developmental process 3.18E-02 Acsl4,Actr2,Aff4,Ap3d1,App,Arl3,Asap1,Atxn2,B4galt1,Baiap2,Bcl2l1,Bmpr1a,Btbd3,Btg2,Capri n1,Carm1,Cbfa2t3,Celf1,Cfl2,Cnot1,Cnot2,Col4a3bp,Cops2,Ctnnb1,Cul4a,Cul4b,Ddx6,Diap1,D vl1,Dyrk1b,Eif2b2,Eif4e,Eif4g1,Enah,Enc1,Etv6,Fasn,Fermt2,Flna,Fndc3b,Fosl2,Gabbr1,Gak,G it1,Gna12,Gna13,Gsk3b,Hectd1,Hira,Hspg2,Iars,Igf1,Igf1r,Ihh,Itgav,Itgb1,Kank1,Kif5b,Lamc1,L ats1,Lats2,Lrp5,Lrp6,Man2a1,Map2k1,Map3k4,Mapk3,Mapk9,Mark2,Med1,Med24,Med28,Mink 1,Mrap,Mtmr2,Myadm,Nf2,Nfatc3,Nfe2l1,Nrn1,Numb,Ocrl,Pacsin2,Pafah1b1,Patz1,Pcm1,Pex1 3,Pex5,Pias2,Pik3r1,Plagl1,Plekha1,Plxna1,Ppap2b,Prrc2c,Ptpn11,Ptprd,Purb,Pvrl1,Qk,Rab10, Raf1,Rap2c,Rapgef1,Rbfox2,Rere,Rnf10,Rnf8,Rock2,Rpl22,Rtf1,Rtn4,Sept2,Sgcb,Sgk1,Sidt2, Ski,Smad3,Smad5,Smarca1,Stim1,Stradb,Tacc1,Tarbp2,Top2b,Tpt1,Trp53inp2,Ube2j1,Ube4b, Unc119b,Usp9x,Vegfa,Wnt4,Ywhah GO:0031328 positive regulation of cellular biosynthetic 3.19E-02 App,Arhgef11,Atf6,Atxn7l3,Bmpr1a,Bptf,Brd4,Cdk5rap3,Cdk9,Chd6,Ctnnb1,Dcp1a,Ddx3x,Dvl1, process Dyrk1b,Erlin2,Etv6,Fosl2,Gsk3b,Hdgf,Hsph1,Igf1,Igf1r,Ihh,Insr,Jmy,Larp1,Lrp5,Lrp6,Map2k1,M ap2k3,Mapk3,Mapk9,Med1,Med24,Mllt10,Mms19,Mrap,Mtpn,Naa15,Nfat5,Nfatc3,Nfe2l1,Nucks 1,Ogt,Patz1,Pcid2,Pias2,Pik3r1,Pkd1,Plagl1,Ppap2b,Ppm1a,Raf1,Rere,Rfc1,Rnf10,Rnf41,Rprd 1b,Rps6ka3,Rptor,Rtf1,Setd3,Ski,Smad3,Smad5,Smarca1,Smek2,Tarbp2,Tbk1,Tbp,Tet3,Tnfai p1,Trp53inp2,Ube2v1,Vegfa,Wibg,Wnt4,Ywhah,Zfp326 GO:0010970 microtubule-based transport 3.24E-02 Ap3b1,Ap3d1,App,Arl3,Kif1b,Kif5b,Klc1,Map2k1,Pafah1b1,Pcm1 GO:0023014 signal transduction by protein phosphorylation 3.28E-02 Cab39,Igf1,Insr,Itgav,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,Med1,Mink1, Raf1,Stradb GO:0040007 growth 3.32E-02 App,Bcl2l1,Bmpr1a,Brd4,Ctnnb1,Dvl1,Igf1,Ihh,Itgav,Itgb1,Lrp6,Ly6e,Med1,Mtpn,Pkdcc,Plekha1, Plxna1,Ptpn11,Rbbp6,Rptor,Rtf1,Sec61a1,Smad3,Tarbp2,Usp9x,Vegfa GO:0031017 exocrine pancreas development 3.43E-02 Igf1,Igf1r,Insr GO:0034392 negative regulation of smooth muscle cell 3.43E-02 apoptotic process Gsk3b,Igf1,Lrp6 GO:0044802 single-organism membrane organization 3.43E-02 Ankfy1,Ap3d1,Atg4b,Bcl2l1,Chchd3,Dvl1,Fermt2,Flna,Gbf1,Gnai3,Itgb1,Macf1,Mfn2,Mtch2,Mya dm,Myo1c,Pacsin2,Pafah1b1,Pex5,Ppif,Ppt1,Ptprd,Rab10,Sec61a1,Sec62,Syne2,Vamp8,Vapb ,Vti1b,Wasl,Wnt4 GO:0097192 extrinsic apoptotic signaling pathway in 3.43E-02 absence of ligand Bcl2l1,Bcl2l2,Gsk3b,Igf1,Itgav,Mknk1 GO:0038034 signal transduction in absence of ligand 3.43E-02 Bcl2l1,Bcl2l2,Gsk3b,Igf1,Itgav,Mknk1 GO:0034243 regulation of transcription elongation from RNA 3.48E-02 polymerase II promoter Brd4,Map2k1,Rnf8,Rtf1,Zmynd11 GO:0006892 post-Golgi vesicle-mediated transport 3.48E-02 Ankfy1,Arl3,Gbf1,Rab10,Rab14,Stxbp6,Tgoln1,Vti1b GO:0051338 regulation of transferase activity 3.62E-02 App,Bag5,Cab39,Ccnd2,Cdk5rap3,Chordc1,Ctnnb1,Dvl1,Erp29,Gsk3b,Higd1a,Hipk3,Hsph1,Igf 1,Igf1r,Insr,Lats1,Lats2,Lrp5,Lrp6,Map2k1,Map2k3,Map3k3,Map3k4,Mink1,Nf2,Pik3r1,Pkd1,Pt pn11,Raf1,Rap2c,Rassf2,Rptor,Spred1,Stradb,Tspyl2,Vapb,Vegfa,Zer1 GO:0007266 Rho protein signal transduction 3.63E-02 Arhgdia,Arhgef11,Baiap2,Gna12,Gna13,Rock2,Stradb

Table S2_2 35

GO:0009896 positive regulation of catabolic process 3.70E-02 Atg13,Atg4b,Btg2,Cnot1,Cul4a,Cul4b,Dnajb2,Dvl1,Egln2,Eif2s1,Gga3,Gsk3b,Igf1,Insr,Larp1,M ap2k1,Pafah1b2,Pex13,Rfwd2,Scoc,Smc5,Sumo3,Tbk1,Tmem39b,Trp53inp2 GO:0048585 negative regulation of response to stimulus 3.70E-02 Adrbk1,Bag5,Bcl2l1,Bcl2l2,Bfar,Cnot1,Cnot2,Ctnnb1,Ddx3x,Dvl1,Dyrk1a,Gclm,Gsk3b,Higd1a,H ipk3,Hsph1,Igf1,Igf1r,Ihh,Itgav,Itgb1,Itpr1,Kank1,Lats1,Lats2,Lrp6,Mapkap1,Mfn2,Mtmr3,Myad m,Nf2,Numb,Ogt,Pafah1b1,Pias2,Plekha1,Ppif,Ppm1a,Psme3,Ptprd,Raf1,Rapgef1,Rassf2,Rtn 4,Ski,Smad3,Spred1,Stradb,Suz12,Tarbp2,Tnfaip1,Tpt1,Ube2g2,Ube2j1,Usp14,Usp25,Vegfa, Wnt4,Zmynd11 GO:0021543 pallium development 3.82E-02 Btbd3,Btg2,Ctnnb1,Gsk3b,Lrp6,Nf2,Pafah1b1,Pex13,Pex5,Rtn4,Tacc1,Usp9x GO:0021535 cell migration in hindbrain 3.83E-02 Itgb1,Lrp6,Rbfox2,Rere GO:0009950 dorsal/ventral axis specification 3.83E-02 Bmpr1a,Ctnnb1,Lrp5,Lrp6 GO:0044764 multi-organism cellular process 3.84E-02 Adrbk1,Bcl2l1,Ddx6,Insr,Itgav,Pdcd6ip,Pvrl1,Smad3,Vamp8,Vapb GO:0031399 regulation of protein modification process 3.86E-02 App,Bag5,Bmpr1a,Cab39,Ccnd2,Cdk5rap3,Cdk9,Chordc1,Ctnnb1,Dnajb2,Dvl1,Dyrk1a,Erp29,F kbp1a,Fnta,Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Igf1r,Insr,Itgav,Itgb1,Lats1,Lats2,Lrp5,Lrp6,Map2k 1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mink1,Myadm,N4bp1,Nbr1,Nf2,Nras,Ogt,Pafah1b1, Peli2,Pik3r1,Pkd1,Ppap2b,Ppp1r11,Ptpn11,Rad51,Raf1,Rap2c,Rapgef1,Rassf2,Rnf41,Rock2, Rptor,Rtf1,Ski,Slc39a10,Smad3,Spred1,Stradb,Sumo3,Suz12,Tollip,Trim39,Tspyl2,Vapb,Vegfa ,Zer1,Zmynd11 GO:0031333 negative regulation of protein complex 3.88E-02 assembly Ddx3x,Gsk3b,Kank1,Mapre1,Myadm,Pex5,Ppm1a,Raf1,Sgk1 GO:0010660 regulation of muscle cell apoptotic process 3.92E-02 Gsk3b,Igf1,Igf1r,Lrp6,Pdcd4,Pik3r1,Qk GO:0043549 regulation of kinase activity 3.92E-02 App,Cab39,Ccnd2,Cdk5rap3,Chordc1,Dvl1,Erp29,Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Igf1r,Insr,La ts1,Lats2,Lrp5,Lrp6,Map2k1,Map2k3,Map3k3,Map3k4,Mink1,Nf2,Pik3r1,Pkd1,Ptpn11,Raf1,Ra p2c,Rassf2,Rptor,Spred1,Stradb,Tspyl2,Vapb,Vegfa GO:0000288 nuclear-transcribed mRNA catabolic process, 3.92E-02 deadenylation-dependent decay Cnot1,Cnot2,Dcp1a,Pan3,Patl1 GO:0051647 nucleus localization 3.92E-02 Pafah1b1,Pcm1,Syne2,Tacc1,Tmem201 GO:0000956 nuclear-transcribed mRNA catabolic process 3.99E-02 Cnot1,Cnot2,Csde1,Dcp1a,Gtpbp2,Pan3,Patl1,Wibg GO:0001952 regulation of cell-matrix adhesion 4.12E-02 Ddr1,Gsk3b,Lims1,Macf1,Mink1,Pik3r1,Smad3,Vegfa,Wnt4 GO:0030182 neuron differentiation 4.14E-02 Acsl4,App,Arl3,Atxn2,Baiap2,Btbd3,Btg2,Cops2,Cul4b,Diap1,Dvl1,Enah,Git1,Gsk3b,Igf1r,Ihh,Itg b1,Kif5b,Lamc1,Lrp6,Map2k1,Mapk9,Mink1,Mtmr2,Nrn1,Numb,Pafah1b1,Pex5,Plxna1,Ptpn11, Ptprd,Pvrl1,Rab10,Rbfox2,Rere,Rock2,Rtn4,Sept2,Sgk1,Smarca1,Top2b,Ube4b,Usp9x,Vegfa, Wnt4 GO:0071826 ribonucleoprotein complex subunit 4.14E-02 organization Atxn2,Celf1,Ddx3x,Ddx6,Eif3a,Kif5b,Klc1,Patl1,Pum2,Tarbp2,Txnl4a,Ythdc1 GO:0001932 regulation of protein phosphorylation 4.14E-02 App,Bmpr1a,Cab39,Ccnd2,Cdk5rap3,Cdk9,Chordc1,Ctnnb1,Dvl1,Erp29,Fkbp1a,Gsk3b,Higd1a ,Hipk3,Hsph1,Igf1,Igf1r,Insr,Itgav,Itgb1,Lats1,Lats2,Lrp5,Lrp6,Map2k1,Map2k3,Map3k3,Map3k 4,Mapk3,Mapk9,Mink1,Myadm,Nbr1,Nf2,Nras,Ogt,Pafah1b1,Peli2,Pik3r1,Pkd1,Ppap2b,Ptpn11, Rad51,Raf1,Rap2c,Rapgef1,Rassf2,Rnf41,Rock2,Rptor,Smad3,Spred1,Stradb,Suz12,Tspyl2,V apb,Vegfa,Zmynd11 GO:0007167 enzyme linked receptor protein signaling 4.15E-02 Akap7,Baiap2,Bmpr1a,Crk,Dcp1a,Ddr1,Fermt2,Fkbp1a,Gigyf1,Git1,Igf1,Igf1r,Insr,Lnpep,Mapk3 pathway ,Myo1c,Pdap1,Pik3r1,Plekha1,Ptpn11,Rab14,Raf1,Rapgef1,Rassf2,Ski,Smad3,Smad5,Usp9x, Vegfa,Zyx Table S2_2 36

GO:0071822 protein complex subunit organization 4.16E-02 Actr2,Amfr,App,Baiap2,Brd2,Cfl2,Ctnnb1,Diap1,Dvl1,Enah,Fermt2,Fkbp1a,Flna,Gak,Haus5,Hir a,Igf1r,Insr,Ipo4,Jmy,Kif23,Lamc1,Lims1,Map2k1,Mapk3,Med24,Mtmr2,Nbr1,Ogt,Pam,Pcm1,P ex5,Pfkl,Pom121,Ppp2r1a,Rad51,Raf1,Rnf8,Seh1l,Sept11,Sept2,Sgk1,Ski,Slc2a1,Smad3,Sma rcd2,Tmem33,Tnfaip1,Vamp8,Vbp1,Wasl,Wibg,Zyx GO:0016197 endosomal transport 4.24E-02 Ankfy1,Ap3d1,Chmp7,Evi5,Flna,Gbf1,Rab10,Rab14,Rab5b,Rgp1,Rhobtb3,Snx27,Tbc1d10b,Tg oln1,Vti1b GO:0051129 negative regulation of cellular component 4.24E-02 Asap1,Atxn2,Bcl2l1,Carm1,Ddx3x,Dnajb2,Gsk3b,Hectd1,Higd1a,Igf1,Itgb1,Kank1,Mapre1,Mtmr organization 2,Mtmr3,Myadm,Numb,Ogt,Pacsin2,Pafah1b1,Pex5,Pkdcc,Ppif,Ppm1a,Raf1,Rtn4,Sgk1,Ski,Vat 1,Ywhah GO:0018205 peptidyl-lysine modification 4.42E-02 Baz2a,Brd4,Brpf3,Ing4,Med24,Msl1,Ogt,Pias2,Rtf1,Setd3,Sumo3,Suz12,Tet3,Wdr82,Whsc1 GO:0071900 regulation of protein serine/threonine kinase 4.42E-02 Cab39,Ccnd2,Cdk5rap3,Chordc1,Erp29,Gsk3b,Higd1a,Hipk3,Igf1,Insr,Lats1,Lats2,Lrp5,Lrp6,M activity ap2k1,Map2k3,Map3k3,Map3k4,Pkd1,Ptpn11,Rptor,Spred1,Vegfa GO:0048667 cell morphogenesis involved in neuron 4.42E-02 App,Btbd3,Dvl1,Enah,Gsk3b,Igf1r,Itgb1,Kif5b,Mink1,Nrn1,Numb,Pafah1b1,Ptpn11,Pvrl1,Rab10 differentiation ,Rbfox2,Rere,Rock2,Rtn4,Top2b,Usp9x,Vegfa GO:1904376 negative regulation of protein localization to 4.42E-02 cell periphery Bcl2l1,Hectd1,Numb,Pkdcc GO:1903077 negative regulation of protein localization to 4.42E-02 plasma membrane Bcl2l1,Hectd1,Numb,Pkdcc GO:0090201 negative regulation of release of cytochrome c 4.42E-02 from mitochondria Bcl2l1,Higd1a,Igf1,Ppif GO:0034391 regulation of smooth muscle cell apoptotic 4.42E-02 process Gsk3b,Igf1,Lrp6,Pdcd4 GO:0048754 branching morphogenesis of an epithelial tube 4.42E-02 B4galt1,Ctnnb1,Ddr1,Gna13,Igf1,Ihh,Lrp5,Lrp6,Med1,Nfatc3,Pkd1,Vegfa,Wnt4 GO:0043414 macromolecule methylation 4.42E-02 Baz2a,Btg2,Carm1,Gatad2a,N6amt1,Ogt,Pcmt1,Rtf1,Setd3,Suz12,Tet3,Wdr82,Whsc1 GO:0043066 negative regulation of apoptotic process 4.42E-02 Bag5,Bcl2l1,Bcl2l2,Bfar,Btg2,Ctnnb1,Ddx3x,Flna,Fnta,Gclm,Gsk3b,Higd1a,Hipk3,Hsph1,Igf1,Ig f1r,Ihh,Itgav,Itgb1,Lims1,Lrp6,Med1,Naa15,Pcid2,Pdcd4,Pik3r1,Ppif,Ppt1,Psme3,Qars,Qk,Raf1 ,Rps6ka3,Sgk1,Slc39a10,Smad3,Son,Stradb,Tpt1,Vegfa,Wnt4,Ywhah,Zmynd11 GO:0090031 positive regulation of steroid hormone 4.42E-02 biosynthetic process Igf1,Igf1r,Wnt4 GO:0034641 cellular nitrogen compound metabolic process 4.42E-02 Agk,Ahcyl1,App,Asnsd1,Atp5g1,Bace1,Baz2a,Bptf,Cdk9,Celf1,Chpt1,Chst8,Cmpk1,Cnot1,Cnot 2,Col4a3bp,Crebzf,Csde1,Cul4b,Dcp1a,Ddx39,Ddx3x,Ddx6,Dhx16,Dlst,Dpm1,Dtl,Dvl1,Ebna1b p2,Eif2b2,Eif2s1,Eif3a,Eif4e,Eif4g2,Eif5b,Entpd4,Etv6,Flna,Fosl2,Furin,Gatad2a,Gclm,Gsk3b,G tpbp2,H6pd,Hipk3,Hnrnpa1,Hnrnpa2b1,Iars,Idh3a,Ing4,Ints3,Larp1,Mapk3,Med1,Med24,Mms1 9,Mov10,Mrps25,Mtap,Nfat5,Nfatc3,Nfe2l1,Nop56,Nucks1,Pam,Pan3,Patl1,Patz1,Pcmt1,Pfas, Pfkl,Pias2,Plagl1,Plrg1,Pmpcb,Qk,Rad23b,Rad51,Rbm39,Rere,Rnf8,Samd8,Smad3,Smarca1, Smc5,Sms,Son,Sptlc1,Tarbp2,Tbp,Tet3,Tk2,Tnfaip1,Top2b,Txnl4a,Ube2v1,Ubl5,Uggt1,Usp7, Wbp11,Wibg,Ythdc1,Zfp326 GO:0046580 negative regulation of Ras protein signal 4.45E-02 transduction Itgb1,Kank1,Mapkap1,Mfn2,Rapgef1,Tnfaip1 GO:0060324 face development 4.45E-02 Lrp6,Map2k1,Mapk3,Plekha1,Ptpn11,Raf1,Ski

Table S2_2 37

GO:0006913 nucleocytoplasmic transport 4.45E-02 Ahcyl1,Ddx39,Gsk3b,Ipo4,Kpna4,Lsg1,Mapk3,Mlxip,Nup50,Pik3r1,Pkd1,Stradb,Tnpo3,Zc3h11 a GO:0070646 protein modification by small protein removal 4.63E-02 Atxn7l3,Cops7a,Cops7b,Otud4,Usp12,Usp14,Usp19,Usp25,Usp7,Usp9x GO:0031669 cellular response to nutrient levels 4.66E-02 Atg13,Atg4b,Chmp1a,Cisd2,Higd1a,Map1lc3b,Nbr1,Rptor,Seh1l,Slc2a1,Trp53inp2,Vamp8,Wipi 2,Wnt4 GO:0000165 MAPK cascade 4.81E-02 Igf1,Itgav,Map2k1,Map2k3,Map3k3,Map3k4,Mapk3,Mapk9,Mapkapk3,Med1,Mink1,Raf1,Stradb GO:0001763 morphogenesis of a branching structure 4.83E-02 B4galt1,Ctnnb1,Ddr1,Gna13,Igf1,Ihh,Lrp5,Lrp6,Med1,Nfatc3,Pkd1,Plxna1,Rere,Vegfa,Wnt4 GO:0030433 ER-associated ubiquitin-dependent protein 4.83E-02 catabolic process Amfr,Dnajb2,Erlin2,Faf2,Ube2g2,Ube2j1,Usp19 GO:0006612 protein targeting to membrane 4.83E-02 Atg4b,Macf1,Myadm,Myo1c,Pex5,Sec61a1,Sec62 GO:0030518 intracellular steroid hormone receptor signaling 4.89E-02 pathway Carm1,Med1,Med24,Pias2,Rbfox2,Ywhah GO:0051058 negative regulation of small GTPase mediated 4.89E-02 signal transduction Itgb1,Kank1,Mapkap1,Mfn2,Rapgef1,Tnfaip1 GO:0061316 canonical Wnt signaling pathway involved in 4.90E-02 heart development Ctnnb1,Lrp6 GO:0044340 canonical Wnt signaling pathway involved in 4.90E-02 regulation of cell proliferation Ctnnb1,Lrp6 GO:0021699 cerebellar cortex maturation 4.90E-02 Arcn1,Rere GO:0001827 inner cell mass cell fate commitment 4.90E-02 Lats1,Lats2 GO:0001828 inner cell mass cellular morphogenesis 4.90E-02 Lats1,Lats2 GO:1904193 negative regulation of cholangiocyte apoptotic 4.90E-02 process Igf1,Igf1r GO:2000645 negative regulation of receptor catabolic 4.90E-02 process Furin,Mtmr2 GO:0032911 negative regulation of transforming growth 4.90E-02 factor beta1 production Cd2ap,Furin GO:0070966 nuclear-transcribed mRNA catabolic process, 4.90E-02 no-go decay Csde1,Gtpbp2 GO:0016560 protein import into peroxisome matrix, docking 4.90E-02 Pex13,Pex5 GO:1904192 regulation of cholangiocyte apoptotic process 4.90E-02 Igf1,Igf1r

Table S2_2