Additional File 2

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

View Full Text

Details

  • File Type
    pdf
  • Upload Time
    -
  • Content Languages
    English
  • Upload User
    Anonymous/Not logged-in
  • File Pages
    19 Page
  • File Size
    -

Download

Channel Download Status
Express Download Enable

Copyright

We respect the copyrights and intellectual property rights of all users. All uploaded documents are either original works of the uploader or authorized works of the rightful owners.

  • Not to be reproduced or distributed without explicit permission.
  • Not used for commercial purposes outside of approved use cases.
  • Not used to infringe on the rights of the original creators.
  • If you believe any content infringes your copyright, please contact us immediately.

Support

For help with questions, suggestions, or problems, please contact us