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Additional File 2 Additional Table 2 All biological function categories and involved cytokines at 1, 7, 14 and 28 days after sciatic nerve injury List Pop Pop Category Term Count % P -value Genes total hits total Fold enrichment Bonferroni Benjamini False discovery rate Day 1 GOTERM_B GO:0021828~gonadotrophin- 3 0.0666370501999111 0.0000218920775503996 NRP2, NRP1, SEMA3A 31 3 10910 351.935483870967 0.004063691764008 0.004063691764008 0.0271097576750367 P_DIRECT releasing hormone neuronal migration to the hypothalamus GOTERM_B GO:1903375~facioacoustic 3 0.0666370501999111 0.0000218920775503996 NRP2, NRP1, SEMA3A 31 3 10910 351.935483870967 0.004063691764008 0.004063691764008 0.0271097576750367 P_DIRECT ganglion development GOTERM_B GO:0097490~sympathetic neuron 3 0.0666370501999111 0.0000437092389619988 NRP2, NRP1, SEMA3A 31 4 10910 263.951612903225 0.00809713627958896 0.00405679694050276 0.054120022480375 P_DIRECT projection extension GOTERM_B GO:0097491~sympathetic neuron 3 0.0666370501999111 0.0000437092389619988 NRP2, NRP1, SEMA3A 31 4 10910 263.951612903225 0.00809713627958896 0.00405679694050276 0.054120022480375 P_DIRECT projection guidance GOTERM_B GO:0048846~axon extension 3 0.0666370501999111 0.0000437092389619988 NRP2, NRP1, SEMA3A 31 4 10910 263.951612903225 0.00809713627958896 0.00405679694050276 0.054120022480375 P_DIRECT involved in axon guidance GOTERM_B GO:0036486~ventral trunk neural 3 0.0666370501999111 0.0000437092389619988 NRP2, NRP1, SEMA3A 31 4 10910 263.951612903225 0.00809713627958896 0.00405679694050276 0.054120022480375 P_DIRECT crest cell migration GOTERM_B GO:0061551~trigeminal ganglion 3 0.0666370501999111 0.0000727241031738213 NRP2, NRP1, SEMA3A 31 5 10910 211.16129032258 0.01343609399186 0.00449890781593431 0.0900308545265016 P_DIRECT development GOTERM_B GO:0060385~axonogenesis 3 0.0666370501999111 0.0000727241031738213 NRP1, NTRK1, SEMA3A 31 5 10910 211.16129032258 0.01343609399186 0.00449890781593431 0.0900308545265016 P_DIRECT involved in innervation GOTERM_B GO:0021612~facial nerve 3 0.0666370501999111 0.000202584492041162 NRP2, NRP1, SEMA3A 31 8 10910 131.975806451612 0.0369833068430469 0.00937689336329583 0.25060989132758 P_DIRECT structural organization GOTERM_B GO:0061549~sympathetic 3 0.0666370501999111 0.000260020435237439 NRP2, NRP1, SEMA3A 31 9 10910 117.311827956989 0.0472188927805887 0.00962737518360001 0.321556682575296 P_DIRECT ganglion development GOTERM_B GO:0048485~sympathetic nervous 3 0.0666370501999111 0.000395896466905332 NTRK1, GDNF, GFRA3 31 11 10910 95.9824046920821 0.071004443198981 0.0122001873036784 0.489210654974903 P_DIRECT system development GOTERM_B GO:0043524~negative regulation 4 0.0888494002665482 0.00128874933466054 HRAS, NRP1, NTRK1, GDNF 31 79 10910 17.8195181706819 0.213263553545273 0.0336855651103454 1.58444699743414 P_DIRECT of neuron apoptotic process GOTERM_B GO:0008284~positive regulation 5 0.111061750333185 0.00234317373235068 NTF3, PGF, FGFBP1, GDNF, TIMP1 31 207 10910 8.50085709833255 0.353603202616509 0.0530819403602919 2.86360326948454 P_DIRECT of cell proliferation GOTERM_B GO:0007169~transmembrane 3 0.0666370501999111 0.00283393786764009 NRTN, NTF3, GFRA2 31 29 10910 36.4071190211345 0.410134514916265 0.0569643531217523 3.45373729790252 P_DIRECT receptor protein tyrosine kinase signaling pathway GOTERM_B GO:0097374~sensory neuron axon 2 0.0444247001332741 0.00549223183632148 NRP2, NRP1 31 2 10910 351.935483870967 0.640977688872607 0.0973650532279958 6.59340796938245 P_DIRECT guidance GOTERM_B GO:0021649~vestibulocochlear 2 0.0444247001332741 0.00549223183632148 NRP2, NRP1 31 2 10910 351.935483870967 0.640977688872607 0.0973650532279958 6.59340796938245 P_DIRECT nerve structural organization GOTERM_B GO:1904835~dorsal root ganglion 2 0.0444247001332741 0.00549223183632148 NRP2, NRP1 31 2 10910 351.935483870967 0.640977688872607 0.0973650532279958 6.59340796938245 P_DIRECT morphogenesis GOTERM_B GO:0060326~cell chemotaxis 3 0.0666370501999111 0.00857237213512687 CCL2, CXCL3 31 51 10910 20.7020872865275 0.798372770321373 0.13547571283664 10.1137956790279 P_DIRECT GOTERM_B GO:0045743~positive regulation 2 0.0444247001332741 0.0109552992081338 FGFBP3, FGFBP1 31 4 10910 175.967741935483 0.871127221767186 0.156962747339677 12.7531783307393 P_DIRECT of fibroblast growth factor receptor signaling pathway GOTERM_B GO:0021785~branchiomotor 2 0.0444247001332741 0.0109552992081338 NRP1, SEMA3A 31 4 10910 175.967741935483 0.871127221767186 0.156962747339677 12.7531783307393 P_DIRECT neuron axon guidance GOTERM_B GO:1901166~neural crest cell 2 0.0444247001332741 0.0109552992081338 NRP2, NRP1 31 4 10910 175.967741935483 0.871127221767186 0.156962747339677 12.7531783307393 P_DIRECT migration involved in autonomic nervous system development GOTERM_B GO:0060666~dichotomous 2 0.0444247001332741 0.0136759429841461 NRP1, SEMA3A 31 5 10910 140.774193548387 0.922794111342528 0.178827025059579 15.6794135076415 P_DIRECT subdivision of terminal units involved in salivary gland branching GOTERM_B GO:0021637~trigeminal nerve 2 0.0444247001332741 0.0136759429841461 NRP1, SEMA3A 31 5 10910 140.774193548387 0.922794111342528 0.178827025059579 15.6794135076415 P_DIRECT structural organization GOTERM_B GO:1902287~semaphorin-plexin 2 0.0444247001332741 0.0136759429841461 NRP1, SEMA3A 31 5 10910 140.774193548387 0.922794111342528 0.178827025059579 15.6794135076415 P_DIRECT signaling pathway involved in axon guidance GOTERM_B GO:0048843~negative regulation 2 0.0444247001332741 0.0217945380347228 NRP1, SEMA3A 31 8 10910 87.983870967742 0.983404302097575 0.253797288356587 23.8837356756340 P_DIRECT of axon extension involved in axon guidance GOTERM_B GO:2000251~positive regulation 2 0.0444247001332741 0.0217945380347228 HRAS, NTF3 31 8 10910 87.983870967742 0.983404302097575 0.253797288356587 23.8837356756340 P_DIRECT of actin cytoskeleton GOTERM_B GO:0048011~neurotrophinreorganization TRK 2 0.0444247001332741 0.0244863527348708 NTRK1, SORT1 31 9 10910 78.207885304660 0.990059619638411 0.264650953687308 26.4375769787988 P_DIRECT receptor signaling pathway GOTERM_B GO:0007413~axonal fasciculation 2 0.0444247001332741 0.0298485173738343 NRP1, SEMA3A 31 11 10910 63.988269794721 0.996434202958489 0.296911833056561 31.2917224731595 P_DIRECT GOTERM_B GO:0070374~positive regulation 3 0.0666370501999111 0.0329195674493794 HRAS, NRP1, NTRK1 31 104 10910 10.151985111663 0.998022835205490 0.306664083717347 33.9374106028222 P_DIRECT of ERK1 and ERK2 cascade GOTERM_B GO:0002092~positive regulation 2 0.0444247001332741 0.0431295731387954 NTF3, CD63 31 16 10910 43.991935483871 0.999725411317371 0.365912728743961 42.0747642265996 P_DIRECT of receptor internalization GOTERM_B GO:0001755~neural crest cell 2 0.0444247001332741 0.0536277095192114 NRTN, GDNF 31 20 10910 35.193548387097 0.999964719483398 0.417011841653786 49.4722136417142 P_DIRECT migration GOTERM_B GO:0008625~extrinsic apoptotic 2 0.0444247001332741 0.0562347957200807 SORT1, NGF 31 21 10910 33.517665130568 0.999978879859737 0.416239318968733 51.1693531365012 P_DIRECT signaling pathway via death domain receptors GOTERM_B GO:0006955~immune response 3 0.0666370501999111 0.0613584612869078 CCL2, CXCL3 31 147 10910 7.182356813693 0.999992327142262 0.429275480987427 54.3530061767464 P_DIRECT GOTERM_B GO:0030593~neutrophil 2 0.0444247001332741 0.0717321271991667 LGALS3, PPBP 31 27 10910 26.069295101553 0.999999028959167 0.467042456880297 60.2225401364455 P_DIRECT chemotaxis GOTERM_B GO:0043547~positive regulation 2 0.0444247001332741 0.0844583930882933 HRAS, NTRK1 31 32 10910 21.995967741935 0.999999925505547 0.510117026933951 66.4736230748140 P_DIRECT of GTPase activity GOTERM_B GO:2001237~negative regulation 2 0.0444247001332741 0.0844583930882933 NRP1, LGALS3 31 32 10910 21.995967741935 0.999999925505547 0.510117026933951 66.4736230748140 P_DIRECT of extrinsic apoptotic signaling GOTERM_B GO:0001658~branchingpathway involved 2 0.0444247001332741 0.0869833285742652 PGF, GDNF 31 33 10910 21.329423264907 0.999999955430308 0.506019296058541 67.6009379285665 P_DIRECT in ureteric bud morphogenesis Day 7 GOTERM_B GO:0070098~chemokine- 17 0.398126463700234 5.9032086528679E-32 CXCL1, CCL1, CCL3, CCL2, CXCL2, 38 55 18082 147.078468899521 3.58324765229081E-29 3.58324765229081E-29 8.73243203864896E-29 P_DIRECT mediated signaling pathway CXCL9, CCL19, CCL5, CXCL11, CCL4, CCL7, CCL6, CXCL10, CCL17, CCL12, CCL22, PPBP GOTERM_B GO:0030593~neutrophil 15 0.351288056206089 1.93074409806996E-25 CXCL1, CCL1, CCL3, CCL2, LGALS3, 38 69 18082 103.443935926773 1.17196166752847E-22 5.85980833764235E-23 2.85608939338907E-22 P_DIRECT chemotaxis CXCL2, CCL19, CCL5, CCL4, CCL7, CCL6, CCL17, CCL12, CCL22, PPBP GOTERM_B GO:0060326~cell chemotaxis 14 0.327868852459016 2.0394561664195E-22 CXCL1, CCL1, CCL3, CCL2, CXCL2, 38 78 18082 85.407557354926 1.23794989301665E-19 4.12649964338884E-20 3.01690375799437E-19 P_DIRECT CXCL9, CCL19, CXCL11, CCL4, CCL28, CCL6, CXCL10, CCL12, CCL22 GOTERM_B GO:0006935~chemotaxis 15 0.351288056206089 6.1198755994179E-22 CCL1, CCL3, CCL2, CXCL2, CXCL9, 38 118 18082 60.488403211418 3.71476448884668E-19 9.28691122211670E-20 9.05294068014014E-19 P_DIRECT CCL5, CXCL11, CCL4, CCL28, CCL7, CCL6, CCL17, CXCL10, CCL12, CCL22 GOTERM_B GO:0006955~immune response 18 0.421545667447306 7.4829026804895E-22 CXCL1, CCL1, CCL3, CCL2, CXCL2, 38 272 18082 31.489551083591 4.54212192705713E-19 9.08424385411427E-20 1.10692240358899E-18 P_DIRECT CXCL9, CCL19, CCL5, CXCL11, CCL28, CCL4, CCL7, CCL6, CXCL10, CCL17, CCL12, CCL22, PPBP GOTERM_B GO:0048247~lymphocyte 11 0.257611241217798
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