Additional Table 6 Enriched pathways of downregulated DEGs after spinal cord injury in CRMP2KI (P < 0.05, q < 0.05) Database Description Ratio of DEGs Ratio of universe P -value P adjust q value Gene name GO neuron to neuron synapse 52/523 379/11234 1.49E-12 7.29E-10 5.98E-10 Drp2/Grik5/Tnr/Cpeb4/Cdh2/Snx27/Pde4b/Srcin1/Slitrk1/Arrb1/Add3/Cdkl5/ Neurl1a/Adgrl1/Dlg4/Pkp4/Sorbs2/Arhgap44/Pip5k1c/Ppp1r9b/Gphn/Lrrc4c/ Adam10/Ntrk2/Anks1b/Kalrn/Arhgef9/Abhd17a/Adcy1/Cnih2/Baiap2/Add1/P alm/Slc30a3/Rpl12/Dgkz/Mapk1/Map2k1/Rps18/Sptbn1/Arc/Rpl14/Atp1a1/R pl8/Nsf/Rps19/Camk2n1/Syt11/Syt1/Rps14/Nrgn/Rpl38 GO postsynaptic density 49/523 357/11234 6.77E-12 1.51E-09 1.24E-09 Drp2/Grik5/Cpeb4/Cdh2/Snx27/Pde4b/Srcin1/Slitrk1/Arrb1/Add3/Cdkl5/Neur l1a/Adgrl1/Dlg4/Pkp4/Sorbs2/Arhgap44/Pip5k1c/Ppp1r9b/Gphn/Lrrc4c/Ada m10/Ntrk2/Anks1b/Kalrn/Arhgef9/Abhd17a/Adcy1/Cnih2/Baiap2/Add1/Palm/ Rpl12/Dgkz/Mapk1/Map2k1/Rps18/Sptbn1/Arc/Rpl14/Atp1a1/Rpl8/Nsf/Rps1 9/Camk2n1/Syt11/Rps14/Nrgn/Rpl38 GO asymmetric synapse 49/523 360/11234 9.23E-12 1.51E-09 1.24E-09 Drp2/Grik5/Cpeb4/Cdh2/Snx27/Pde4b/Srcin1/Slitrk1/Arrb1/Add3/Cdkl5/Neur l1a/Adgrl1/Dlg4/Pkp4/Sorbs2/Arhgap44/Pip5k1c/Ppp1r9b/Gphn/Lrrc4c/Ada m10/Ntrk2/Anks1b/Kalrn/Arhgef9/Abhd17a/Adcy1/Cnih2/Baiap2/Add1/Palm/ Rpl12/Dgkz/Mapk1/Map2k1/Rps18/Sptbn1/Arc/Rpl14/Atp1a1/Rpl8/Nsf/Rps1 9/Camk2n1/Syt11/Rps14/Nrgn/Rpl38 GO postsynaptic specialization 50/523 382/11234 2.41E-11 2.95E-09 2.42E-09 Drp2/Grik5/Cpeb4/Cdh2/Snx27/Pde4b/Srcin1/Dlgap3/Slitrk1/Arrb1/Add3/Cdk l5/Neurl1a/Adgrl1/Dlg4/Pkp4/Sorbs2/Arhgap44/Pip5k1c/Ppp1r9b/Gphn/Lrrc4 c/Adam10/Ntrk2/Anks1b/Kalrn/Arhgef9/Abhd17a/Adcy1/Cnih2/Baiap2/Add1/ Palm/Rpl12/Dgkz/Mapk1/Map2k1/Rps18/Sptbn1/Arc/Rpl14/Atp1a1/Rpl8/Nsf /Rps19/Camk2n1/Syt11/Rps14/Nrgn/Rpl38 Reactome Nonsense Mediated Decay 23/286 85/5536 2.01E-11 1.25E-08 1.13E-08 Rpl10/Pabpc1/Rpl22/Rpl34- (NMD) independent of the ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ Exon Junction Complex (EJC) Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome SRP-dependent cotranslational 22/286 84/5536 1.13E-10 2.87E-08 2.61E-08 Rpl10/Rpl22/Rpl34- protein targeting to membrane ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome Formation of a pool of free 40S 23/286 93/5536 1.49E-10 2.87E-08 2.61E-08 Rpl10/Rpl22/Eif3f/Rpl34- subunits ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome L13a-mediated translational 24/286 103/5536 2.24E-10 2.87E-08 2.61E-08 Rpl10/Pabpc1/Rpl22/Eif3f/Rpl34- silencing of Ceruloplasmin ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ expression Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome Nonsense-Mediated Decay 24/286 104/5536 2.78E-10 2.87E-08 2.61E-08 Rpl10/Pabpc1/Rpl22/Rpl34- (NMD) ps1/Eif4a3/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/ Rps19/Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome Nonsense Mediated Decay 24/286 104/5536 2.78E-10 2.87E-08 2.61E-08 Rpl10/Pabpc1/Rpl22/Rpl34- (NMD) enhanced by the Exon ps1/Eif4a3/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/ Junction Complex (EJC) Rps19/Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome Eukaryotic Translation Initiation 24/286 111/5536 1.16E-09 9.00E-08 8.17E-08 Rpl10/Pabpc1/Rpl22/Eif3f/Rpl34- ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome Cap-dependent Translation 24/286 111/5536 1.16E-09 9.00E-08 8.17E-08 Rpl10/Pabpc1/Rpl22/Eif3f/Rpl34- Initiation ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome GTP hydrolysis and joining of 23/286 104/5536 1.64E-09 1.13E-07 1.02E-07 Rpl10/Rpl22/Eif3f/Rpl34- the 60S ribosomal subunit ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 KEGG Ribosome 25/207 118/4032 5.46E-10 1.34E-07 1.15E-07 Mrpl17/Rpl10/Rpl22/Rps12/Rpl34/Rpl34- ps1/Gm4705/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps 4x/Rps19/Rpl37a/Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27/Rps27r t GO glutamatergic synapse 52/523 456/11234 1.52E-09 1.49E-07 1.23E-07 Drp2/Grik5/Tnr/Cdh2/Il1rap/Dlgap3/Slitrk1/Ndrg1/Apba1/Tnik/Kcnc4/Cdkl5/L gi1/Adgrl1/Cacnb4/Rock2/Dlg4/Nptx1/Abi2/Arhgap44/Pip5k1c/Lrrc4c/Adam1 0/Ntrk2/Anks1b/Kalrn/Sptbn2/Scn2a/Abhd17a/Adcy1/Nptxr/Cnih2/Baiap2/Rp l22/Nrxn1/Eif4a3/Slc30a3/Dgkz/Map2k1/Slc1a2/Sptbn1/Arc/Cplx2/Rpsa/Prkar 1a/Nrn1/Ppp1ca/Syt1/Olfm1/Gpm6a/Ppp3r1/Nrgn GO synapse organization 49/516 373/11045 3.77E-11 1.51E-07 1.31E-07 Drp2/Pdgfb/Tnr/Cdh2/Nfasc/Lrrn3/Prkca/Il1rap/Dab2ip/Snx27/Srcin1/Dlgap3/ Slitrk1/Ndrg1/Asic2/Cdkl5/Lrrc24/Bdnf/Neurl1a/Adgrl1/Cacnb4/Rock2/Dlg4/ Nptx1/Abi2/Sorbs2/Arhgap44/Neurod2/Gphn/Lrrc4c/Adam10/Ntrk2/Kalrn/Sp tbn2/Arhgef9/C1qa/Abhd17a/Cacnb3/Nptxr/Baiap2/Adgrb2/Palm/Nrxn1/Was f1/Dgkz/Arc/Ptn/Zfp365/Gpm6a GO presynapse 50/523 446/11234 5.73E-09 4.68E-07 3.84E-07 Grik5/Cdh2/Rimbp2/Prkca/Pde4b/Dixdc1/Psen2/Apba1/Kcnc4/Atp8a1/Bdnf/A dgrl1/Cacnb4/Rab5c/Dlg4/Slc4a10/Arhgap44/Pip5k1c/Kcna6/Adam10/Ntrk2/ Anks1b/Kalrn/Sptbn2/Scn2a/Dnajc5/Stx7/Baiap2/Rpl22/Svop/Nrxn1/Slc30a3/ Rph3a/Cntn1/Glul/Slc17a7/Syt5/Slc1a2/Syngr1/Cplx2/Ptn/Lamp1/Trappc4/Pp p1ca/Syt11/Syt1/Gpm6a/Prkcb/Rpl26/Mt3 GO cytosolic ribosome 24/523 133/11234 9.15E-09 6.41E-07 5.26E-07 Rpl10/Rpl22/Rps12/Rack1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a /Rps3a1/Rps4x/Rps19/Rpl37a/Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/ Rps27 GO cytosolic part 34/523 249/11234 1.47E-08 8.98E-07 7.37E-07 Prkca/Sgtb/Anks1b/Rpl10/Pfkl/Baiap2/Psmd1/Rpl22/Rps12/Psmd2/Pfkp/Eif4a 3/Rack1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/R ps19/Rpl37a/Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Prkcb/Rpl38/Rpl26/Rps27 Reactome Neuronal System 34/286 252/5536 1.58E-07 9.78E-06 8.88E-06 Grik5/Epb41l2/Kcnq3/Il1rap/Dlgap3/Slitrk1/Kcnv1/Apba1/Kcnc4/Cacnb4/Cam kk1/Dlg4/Kcnab1/Kcna6/Kcnj10/Arhgef9/Dnajc5/Cacnb3/Adcy1/Camkk2/Gng 10/Kcnmb4/Nrxn1/Glul/Slc17a7/Slc1a2/Ncald/Prkar1a/Nsf/Lin7b/Syt1/Ap2s1/ Gng13/Nrgn GO cytosolic small ribosomal 13/523 52/11234 4.97E-07 2.70E-05 2.22E-05 Rps12/Rack1/Rps18/Rpsa/Rps2/Rps10/Rps27a/Rps3a1/Rps4x/Rps19/Rps28/R subunit ps14/Rps27 Reactome Major pathway of rRNA 25/286 164/5536 7.86E-07 3.75E-05 3.41E-05 Riok1/Exosc2/Dcaf13/Rpl10/Rpl22/Rpl34- processing in the nucleolus ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ and cytosol Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome rRNA processing 25/286 164/5536 7.86E-07 3.75E-05 3.41E-05 Riok1/Exosc2/Dcaf13/Rpl10/Rpl22/Rpl34- ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 Reactome rRNA processing in the nucleus 25/286 164/5536 7.86E-07 3.75E-05 3.41E-05 Riok1/Exosc2/Dcaf13/Rpl10/Rpl22/Rpl34- and cytosol ps1/Rpl12/Rps18/Rpl14/Rpsa/Rps2/Rps10/Rpl8/Rps27a/Rps3a1/Rps4x/Rps19/ Rpl35/Rps28/Rpl13a/Rpl9/Rps14/Rpl38/Rpl26/Rps27 GO regulation of synapse structure 32/516 231/11045 2.99E-08 5.98E-05 5.20E-05 Cdh2/Lrrn3/Prkca/Il1rap/Dab2ip/Snx27/Srcin1/Slitrk1/Asic2/Cdkl5/Lrrc24/Bdnf or activity /Neurl1a/Adgrl1/Nptx1/Abi2/Sorbs2/Arhgap44/Neurod2/Adam10/Ntrk2/Kalr n/Arhgef9/Abhd17a/Nptxr/Baiap2/Adgrb2/Nrxn1/Slc17a7/Arc/Ptn/Gpm6a GO regulation of synapse 31/516 223/11045 4.55E-08 6.07E-05 5.28E-05 Cdh2/Lrrn3/Prkca/Il1rap/Dab2ip/Snx27/Srcin1/Slitrk1/Asic2/Cdkl5/Lrrc24/Bdnf organization /Neurl1a/Adgrl1/Nptx1/Abi2/Sorbs2/Arhgap44/Neurod2/Adam10/Ntrk2/Kalr n/Arhgef9/Abhd17a/Nptxr/Baiap2/Adgrb2/Nrxn1/Arc/Ptn/Gpm6a GO synaptic membrane 42/523 415/11234 1.62E-06 7.96E-05 6.53E-05 Drp2/Grik5/Cpeb4/Cdh2/Dagla/Srcin1/Dlgap3/Slitrk1/Psen2/Arrb1/Apba1/Kc nc4/Neurl1a/Adgrl1/Dlg4/Pip5k1c/Ppp1r9b/Kcnj4/Gphn/Lrrc4c/Adam10/Ntrk 2/Anks1b/Scn2a/Arhgef9/Abhd17a/Adcy1/Cnih2/Baiap2/Palm/Nrxn1/Cntn1/S lc1a2/Arc/Trappc4/Camk2n1/Syt11/Lin7b/Syt1/Olfm1/Gpm6a/Nrgn GO cellular response to metal ion 20/516 108/11045 1.07E-07 0.000103091 8.97E-05 Smpd3/Cpne7/Gsk3a/Mef2a/Dlg4/Nptx1/Cpne9/Neurod2/Asph/Add1/Junb/ Nrxn1/Mapk1/Syt5/Mt2/Syt11/Id2/Syt1/Mt3/Mt1 GO cognition 31/516 234/11045 1.39E-07 0.000103091 8.97E-05 Ldlr/Cic/Tnr/Asic1/Prkca/Crhr1/Psen2/Pde8b/Atp8a1/Bdnf/Sgk1/Abi2/Kcnab1 /Tbr1/Neurod2/Ntrk2/Kalrn/Scn2a/Gatm/Rp9/Adcy1/Slc24a2/Nrxn1/Atp1a2/B rinp1/Slc17a7/Arc/Ptn/Thra/Tusc3/Grcc10 GO localization within membrane 25/516 164/11045 1.55E-07 0.000103091 8.97E-05 Grik5/Cdh2/Snx27/Cd24a/Tnik/Lgi1/Dlg4/Nptx1/Sorbs2/Arhgap44/Pip5k1c/G phn/Adam10/Anks1b/Kalrn/Arhgef9/Stx7/Nptxr/Cnih2/Nrxn1/Map2k1/Arc/Pt n/Ppp3r1/Thy1 GO modulation of chemical 44/516 410/11045 1.92E-07 0.000103091 8.97E-05 Grik5/Tnr/Asic1/Cdh2/Prkca/Crhr1/Psen2/Apba1/Kcnc4/Bdnf/Lgi1/Neurl1a/Ca synaptic transmission cnb4/Dlg4/Nptx1/Slc4a10/Neurod2/Ppp1r9b/Kcnj10/Lrrc4c/Ntrk2/Kalrn/Cacn b3/Adcy1/Nptxr/Cnih2/Baiap2/Rpl22/Slc24a2/Nrxn1/Eif4a3/Glul/Car2/Mapk1/ Syngr1/Arc/Celf4/Cplx2/Ptn/Nrn1/Syt1/Ppp3r1/Prkcb/Nrgn GO regulation of trans-synaptic 44/516 411/11045 2.06E-07 0.000103091 8.97E-05 Grik5/Tnr/Asic1/Cdh2/Prkca/Crhr1/Psen2/Apba1/Kcnc4/Bdnf/Lgi1/Neurl1a/Ca signaling cnb4/Dlg4/Nptx1/Slc4a10/Neurod2/Ppp1r9b/Kcnj10/Lrrc4c/Ntrk2/Kalrn/Cacn b3/Adcy1/Nptxr/Cnih2/Baiap2/Rpl22/Slc24a2/Nrxn1/Eif4a3/Glul/Car2/Mapk1/ Syngr1/Arc/Celf4/Cplx2/Ptn/Nrn1/Syt1/Ppp3r1/Prkcb/Nrgn GO postsynapse organization 25/516 170/11045 3.15E-07 0.000139856 0.000121681 Cdh2/Il1rap/Snx27/Srcin1/Ndrg1/Cdkl5/Rock2/Dlg4/Nptx1/Abi2/Sorbs2/Arhg ap44/Gphn/Adam10/Kalrn/Sptbn2/Arhgef9/Abhd17a/Nptxr/Baiap2/Nrxn1/Dg