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Table 3 SignaLink 2.0 transcription regulatory network (TRN) analysis of differentially expressed transcription factors and their up-regulated and down-regulated target genes in the perilesional cortex and the ipsilateral thalamus at 3 months after traumatic brain injury. The same targets that were up-regulated both in the perilesional cortex and ipsilateral thalamus or down-regulated both in the perilesional cortex and ipsilateral thalamus are bold fonts

From: Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury

  Perilesional cortex Ipsilateral thalamus
TF Log2FC FDR Altered targets/all targets Upregulated
TF targets
Downregulated
TF targets
Log2FC FDR Altered targets/all targets Upregulated
TF targets
Downregulated
TF targets
Cebpd 1.835 3.78E-034 1/1 IGF1 1.261 7.47E-005 1/1 IGF1
Etv4 −1.105 2.03E-008 0/1 −0.697 0.00523964 0/1
Myb 1.350 0.0042262 0/3 ns ns
Pax6 1.186 5.97E-022 91/300 ABCA1, ABL1, BMP6, BTK, CAV2, CDKL1, DAB2, DAPP1, ERBB2IP, FGFR1, FGR, FOXO1, FYB, GAB1, IL21R, ITGA8, ITGB1, MAP3K1, MET, MICAL1, MTSS1, NEDD1, NIM1, PRKD1, PTPRZ1, ROR2, SKAP2, STK10, SYK, TGFA, TICAM2, UBE2U AKT3, ARHGAP32, ATF2, BIRC6, BMPR2, CAMK1D, CHN1, CHRNA7, CNKSR2, CTNND2,DAB, DMXL2, EFNA5, EPHA7, EPHB2, ERBB4, ESRRG, GABRB3, GRB2,GRIA1, GRIA4, GRIK3, GRIN2A, ITPR1, MAGI2, MAP3K13, MAPK10, MAPK8IP3, MEF2C, MRAS, NEDD4L, NLK, NRD1, NRG1, NRG3, NUAK1, PAK7, PAM, PCSK5, PDE4D, PLCB1, PRKCA, PRKCB, PTPRG, PTPRJ, PTPRK, PTPRT, RAB14, RAP1GDS1, RGS7, ROCK2, RPS6KC1, RPTOR, SH3GL2, SNRK, SORBS2, TRIM33, TTBK2, ZFYVE9 0.779 8.41E-5 33/300 ABCA1, ATF1, BTK, DAPP1, EPHB1, ERBB2IP, ERBB4, FGF2, FGR, GAB1, GRB14, IL21R, INPP5D, ITGAM
ITGB1, PKP4, PRKCA, TCF4, TGFA
ARHGAP32, CAMK1D, CHN1, DAPK1, GRM1, MAP3K14, MAPK10, NEDD4L, NRG2, PRKCB, RAP1GDS1, SRC, STRADB, TRIO
Spi1 1.021 2.88E-011 1/3 LSP1 1.310 8.57E-006 1/3 LSP1
Tp73 1.328 0.01004339 15/54 TGFA, PTPN22, CDK1, PDGFC, NOTCH1 BDNF, RGS7, ERBB4, SNCA, PRKCE, PTPRJ, NEDD4L, KPNA1, APBB2, STAM, MYO3B ns ns 6/55 MYLK, NEDD4L RRAD, TGFA, ERBB4, PCNA
  1. Abbreviations: FDR false discovery rate, ns non-significant, TF transcription factor