Additional Table 1 All KEGG Pathways and Involved Cytokines at 1, 7, 14 and 28 Days After Sciatic Nerve Injury

Additional Table 1 All KEGG pathways 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 KEGG_PA pon04722:Neurotrophin 6 0.133274100399822 0.0000117067640775991 HRAS, NTF3, NTRK1, SORT1, 19 122 6855 17.7437446074201 0.000807445290026409 0.000807445290026409 0.0120791612630011 THWAY signaling pathway NGFR, NGF KEGG_PA pon04015:Rap1 signaling 6 0.133274100399822 0.000181658912294624 VEGFB, HRAS, PGF, VEGFA, 19 216 6855 10.0219298245614 0.012457360190217 0.00624820009733673 0.187289206649732 THWAY pathway NGFR, NGF KEGG_PA pon04060:Cytokine-cytokine 6 0.133274100399822 0.000234070325720111 VEGFB, CCL2, PPBP, VEGFA, 19 228 6855 9.49445983379501 0.0160229870120458 0.00536977858102494 0.241266133247919 THWAY receptor interaction NGFR KEGG_PA pon04014:Ras signaling 6 0.133274100399822 0.000234070325720111 VEGFB, HRAS, PGF, VEGFA, 19 228 6855 9.49445983379501 0.0160229870120458 0.00536977858102494 0.241266133247919 THWAY pathway NGFR, NGF KEGG_PA pon04062:Chemokine 5 0.111061750333185 0.00107636472177452 HRAS, CCL2, PPBP, CXCL3 19 181 6855 9.96656004652515 0.071615374437151 0.0184057969494512 1.10511137475813 THWAY signaling pathway KEGG_PA pon04151:PI3K-Akt signaling 6 0.133274100399822 0.00151994852563968 VEGFB, HRAS, PGF, VEGFA, 19 343 6855 6.31118612858677 0.0996360716213985 0.0207724638049401 1.55732375431839 THWAY pathway NGFR, NGF KEGG_PA pon04360:Axon guidance 4 0.0888494002665482 0.00395376000796968 HRAS, NRP1, SEMA4F, SEMA3A 19 125 6855 11.5452631578947 0.23917368354473 0.044536162766662 4.00541461945932 THWAY KEGG_PA pon04510:Focal adhesion 4 0.0888494002665482 0.0168857674982522 VEGFB, HRAS, PGF, VEGFA 19 212 6855 6.80734856007944 0.691201732361398 0.154533492770852 16.1152592089165 THWAY KEGG_PA pon05200:Pathways in cancer 5 0.111061750333185 0.0177324136472181 VEGFB, HRAS, PGF, NTRK1, 19 397 6855 4.54394803128728 0.709024044424823 0.142997403183119 16.8577012483735 THWAY VEGFA KEGG_PA pon05323:Rheumatoid 3 0.0666370501999111 0.024193416162877 CCL2, VEGFA 19 93 6855 11.6383701188455 0.815456677155465 0.171189259014643 22.3309460820470 THWAY arthritis KEGG_PA pon04010:MAPK signaling 4 0.0888494002665482 0.0271694232444628 HRAS, NTF3, NTRK1, NGF 19 254 6855 5.68172399502693 0.850525313728606 0.173092815906848 24.7407343544365 THWAY pathway KEGG_PA pon04668:TNF signaling 3 0.0666370501999111 0.031385585069676 CCL2, CXCL3 19 107 6855 10.115592720118 0.889232073157255 0.181292916495412 28.0391912584331 THWAY pathway KEGG_PA pon05216:Thyroid cancer 2 0.0444247001332741 0.076002368098674 HRAS, NTRK1 19 30 6855 24.0526315789473 0.995721522877716 0.365243094119777 55.7646962919834 THWAY KEGG_PA pon05205:Proteoglycans in 3 0.0666370501999111 0.090652832356961 HRAS, VEGFA, CD63 19 194 6855 5.57921866521975 0.998579796521911 0.396120837605698 62.4901175608974 THWAY cancer Day 7 KEGG_PA mmu04062:Chemokine 18 0.421545667447306 3.37806138629424E-22 CXCL1, CCL1, CCL3, CCL2, 26 196 7720 27.2684458398744 1.35122455451769E-20 1.35122455451769E-20 3.09059953735233E-19 THWAY signaling pathway CXCL2, CXCL9, CCL19, CCL5, CXCL11, CCL28, CCL4, CCL7, CCL6, CXCL10, CCL17, CCL12, CCL22, PPBP

KEGG_PA mmu04060:Cytokine-cytokine 12 0.281030444964871 7.92164438090108E-11 CCL12, CCL3, CCL2, PPBP, 26 245 7720 14.5431711145996 3.16865644833796E-09 1.58432822416898E-09 7.24753590475302E-08 THWAY receptor interaction CXCL9, CCL19, CCL5, CXCL11, CCL28, CCL4, CCL7, CXCL10

KEGG_PA mmu04668:TNF signaling 7 0.1639344262295080 0.000000982316626 CXCL1, CCL12, ICAM1, CCL2, 26 109 7720 19.06845448129850 0.000039291912393 0.000013097475674 0.0008987211337 THWAY pathway CXCL2, CCL5, CXCL10 KEGG_PA mmu04620:Toll-like receptor 6 0.1405152224824350 0.000014976130451 CCL3, CXCL9, CCL5, CXCL11, 26 101 7720 17.63899466869760 0.000598870309324 0.000149751212111 0.0137008752371 THWAY signaling pathway CCL4, CXCL10 KEGG_PA mmu05323:Rheumatoid 5 0.1170960187353630 0.000126210438947 CCL12, ICAM1, CCL3, CCL2, 26 82 7720 18.10506566604120 0.005036012719214 0.001009237610048 0.1154109857432 THWAY arthritis CCL5 KEGG_PA mmu05132:Salmonella 4 0.0936768149882903 0.00194461875812233 CXCL1, CCL3, CXCL2, CCL4 26 78 7720 15.2268244575936 0.0749065128238283 0.0128929116109968 1.7651064753274 THWAY infection KEGG_PA mmu05164:Influenza A 5 0.117096018735363 0.00204335150750468 CCL12, ICAM1, CCL2, CCL5, 26 171 7720 8.68196131354026 0.0785600596291766 0.0116201978694868 1.85398002386104 THWAY CXCL10 KEGG_PA mmu05142:Chagas disease 4 0.0936768149882903 0.00428593014101763 CCL12, CCL3, CCL2, CCL5 26 103 7720 11.530993278566 0.157857166121644 0.0212467443386188 3.85342997081349 THWAY (American trypanosomiasis) KEGG_PA mmu05144:Malaria 3 0.0702576112412178 0.0103679172383991 CCL12, ICAM1, CCL2 26 48 7720 18.5576923076923 0.340901007827084 0.0452637657124195 9.09467221396471 THWAY KEGG_PA mmu04621:NOD-like receptor 3 0.0702576112412178 0.0139330872410426 CCL12, CCL2, CCL5 26 56 7720 15.9065934065934 0.429500253333447 0.054578345129139 12.047269326728 THWAY signaling pathway KEGG_PA mmu04623:Cytosolic DNA- 3 0.0702576112412178 0.0179543772523949 CCL5, CCL4, CXCL10 26 64 7720 13.9182692307692 0.515530357931152 0.0637585387504635 15.274852114044 THWAY sensing pathway KEGG_PA mmu04064:NF-kappa B 3 0.0702576112412178 0.0388638977646735 ICAM1, CCL19, CCL4 26 97 7720 9.18318794607454 0.795169029926702 0.123773664899238 30.4177618257828 THWAY signaling pathway KEGG_PA mmu04320:Dorso-ventral axis 2 0.0468384074941451 0.078005884695285 NOTCH2, NOTCH1 26 25 7720 23.7538461538461 0.961173703580661 0.221118787765261 52.433995819716 THWAY formation Day 14 KEGG_PA rno04062:Chemokine 13 0.276536907041055 2.82312263298761E-14 CXCL1, CCL1, CCL12, HRAS, 25 177 7780 22.8564971751412 2.36877184534023E-12 2.36877184534023E-12 3.02646796512817E-11 THWAY signaling pathway CCL3, CCL2, CXCL2, CX3CL1, CCL5, CCL4, CCL7, CCL17, CXCL10

KEGG_PA rno04060:Cytokine-cytokine 13 0.276536907041055 3.12206792330392E-13 CCL3, CCL2, KITLG, IL13, 25 216 7780 18.7296296296296 2.62243560200658E-11 1.31121780100329E-11 3.35109717752857E-10 THWAY receptor interaction CX3CL1, CCL5, CCL4, CCL7, CXCL10, VEGFB, CCL12, VEGFA, NGFR

KEGG_PA rno04668:TNF signaling 8 0.17017655817911 2.48261290160627E-08 CXCL1, ICAM1, CCL12, CCL2, 25 109 7780 22.840366972477 2.08539269097585E-06 6.95131380235025E-07 2.66479904920124E-05 THWAY pathway CXCL2, CX3CL1, CCL5, CXCL10

KEGG_PA rno05323:Rheumatoid arthritis 6 0.127632418634333 0.0000066192654621606 ICAM1, CCL12, CCL3, CCL2, 25 90 7780 20.7466666666666 5.55865588496962E-04 1.38995374009964E-04 0.0071047911545552 THWAY VEGFA, CCL5 KEGG_PA rno04015:Rap1 signaling 7 0.148904488406721 0.0000378256958118386 VEGFB, HRAS, PGF, VEGFA, 25 216 7780 10.0851851851851 0.00317237589059116 0.000635281831514067 0.0405940595532228 THWAY pathway KITLG, NGFR, NGF KEGG_PA rno04014:Ras signaling 7 0.148904488406721 0.0000551557768386554 VEGFB, HRAS, PGF, VEGFA, 25 231 7780 9.430303030303 0.00462249625578636 0.000771904100274389 0.0591874917723056 THWAY pathway KITLG, NGFR, NGF KEGG_PA rno04151:PI3K-Akt signaling 7 0.148904488406721 0.000452126442798665 VEGFB, HRAS, PGF, VEGFA, 25 339 7780 6.4259587020649 0.0372747453089118 0.00541204601682054 0.484239232964611 THWAY pathway KITLG, NGFR, NGF KEGG_PA rno05164:Influenza A 5 0.106360348861944 0.0016975456477521 ICAM1, CCL12, CCL2, CCL5, 25 171 7780 9.09941520467836 0.132998872140422 0.0176811955179906 1.80714009340916 THWAY CXCL10 KEGG_PA rno05132:Salmonella infection 4 0.0850882790895554 0.00201595344737173 CXCL1, CCL3, CXCL2, CCL4 25 83 7780 14.9975903614457 0.155922539031233 0.0186582947656414 2.14278721198813 THWAY KEGG_PA rno04620:Toll-like receptor 4 0.0850882790895554 0.00314473370347221 CCL3, CCL5, CCL4, CXCL10 25 97 7780 12.8329896907216 0.232467040628111 0.0261104553920475 3.32431720851077 THWAY signaling pathway KEGG_PA rno05142:Chagas disease 4 0.0850882790895554 0.00414882281216159 CCL12, CCL3, CCL2, CCL5 25 107 7780 11.633644859813 0.294766310555928 0.031249152365064 4.36444072301321 THWAY (American trypanosomiasis) KEGG_PA rno05200:Pathways in cancer 6 0.127632418634333 0.00647755399668274 VEGFB, HRAS, PGF, NTRK1, 25 398 7780 4.69145728643216 0.420670830214307 0.044471196418093 6.73779555567276 THWAY VEGFA, KITLG KEGG_PA rno04722:Neurotrophin 4 0.0850882790895554 0.00654776977182108 HRAS, NTRK1, NGFR, NGF 25 126 7780 9.87936507936508 0.424099996307639 0.04155949325163640 6.80851988218862 THWAY signaling pathway KEGG_PA rno04621:NOD-like receptor 3 0.0638162093171665 0.0126899569866092 CCL12, CCL2, CCL5 25 56 7780 16.6714285714285 0.657942910044159 0.07376470032759650 12.8102785567147 THWAY signaling pathway KEGG_PA rno04623:Cytosolic DNA- 3 0.0638162093171665 0.0126899569866092 CCL5, CCL4, CXCL10 25 56 7780 16.6714285714285 0.657942910044159 0.07376470032759650 12.8102785567147 THWAY sensing pathway KEGG_PA rno05144:Malaria 3 0.0638162093171665 0.0140200610748502 ICAM1, CCL12, CCL2 25 59 7780 15.8237288135593 0.694565132371025 0.076022829432224 14.0628634252417 THWAY KEGG_PA rno04510:Focal adhesion 4 0.0850882790895554 0.0258449042086234 VEGFB, HRAS, PGF, VEGFA 25 210 7780 5.92761904761904 0.889143551968625 0.128439458674740 24.5019375267417 THWAY KEGG_PA rno05216:Thyroid cancer 2 0.0425441395447777 0.085849719138602 HRAS, NTRK1 25 29 7780 21.4620689655172 0.999468530739630 0.358227553100604 61.843481066324 THWAY Day 28 KEGG_PA rno04060:Cytokine-cytokine 6 0.156412930135557 0.0000535791865835298 VEGFB, CCL2, LOC103690065, 17 216 7780 12.7124183006535 0.001980519192491 0.001980519192491 0.0480993045773536 THWAY receptor interaction CCL5, THPO, EPO KEGG_PA rno04722:Neurotrophin 5 0.130344108446298 0.000102665664088439 BDNF, NTF4, NTF3, SORT1, NGF 17 126 7780 18.1605975723622 0.00379161817312123 0.00189760954755813 0.0921473513787352 THWAY signaling pathway KEGG_PA rno04640:Hematopoietic cell 3 0.0782064650677789 0.0116882169898144 LOC103690065, THPO, EPO 17 81 7780 16.9498910675381 0.352742623152968 0.134980954523153 10.0187153452771 THWAY lineage KEGG_PA rno04010:MAPK signaling 4 0.104275286757038 0.0148090127973592 BDNF, NTF4, NTF3, NGF 17 259 7780 7.06790824437883 0.424220875261268 0.128908093176859 12.538095121894 THWAY pathway KEGG_PA rno04151:PI3K-Akt signaling 4 0.104275286757038 0.0301078233268734 VEGFB, PGF, NGF, EPO 17 339 7780 5.39996529585285 0.677323096156791 0.202457975822486 24.004505836265 THWAY pathway KEGG_PA rno04630:Jak-STAT signaling 3 0.0782064650677789 0.030593358416624 LOC103690065, THPO, EPO 17 135 7780 10.1699346405228 0.683246326204708 0.174367189441609 24.3454264713799 THWAY pathway KEGG_PA rno04015:Rap1 signaling 3 0.0782064650677789 0.0713333573000699 VEGFB, PGF, NGF 17 216 7780 6.35620915032679 0.935313402504016 0.323735905414158 48.5472552845223 THWAY pathway KEGG_PA rno04014:Ras signaling 3 0.0782064650677789 0.0801730303939494 VEGFB, PGF, NGF 17 231 7780 5.94346829640947 0.954592546630919 0.320575985353642 52.7815460350622 THWAY pathway KEGG: Kyoto Encyclopedia of Genes and Genomes.