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

Cebpd

IGF1

–

IGF1

–

Etv4

–

–

–

–

Myb

–

–

–

–

Pax6

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

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

LSP1

–

LSP1

–

Tp73

TGFA, PTPN22, CDK1, PDGFC, NOTCH1

BDNF, RGS7, ERBB4, SNCA, PRKCE, PTPRJ, NEDD4L, KPNA1, APBB2, STAM, MYO3B

MYLK, NEDD4L

RRAD, TGFA, ERBB4, PCNA