Skip to main content

Advertisement

Table 8 Upstream regulators predicted by target gene expression in the atretic versus healthy dataset

From: Transcriptome profiling of granulosa cells from bovine ovarian follicles during atresia

Upstream regulator Predicted activation state Bias-corrected z-Score P value of overlap Target molecules in dataset
TP53 activated 4.272 5.78E-11 ALB, ANXA1, ANXA2, ARHGEF2, ARPC1B, ATF3, CALD1, CAV1, CFLAR, CLIC4, CNN1, COL18A1, COL1A2, COL3A1, COL4A1, CTGF, CTSH, CYR61, DKK3, DUSP1, EGR1, FBLN2, FERMT2, GADD45A, GLRX, GPX3, GSN, HMGCS1, ID1, ID3, IER3, IFI30, IGF2, IGFBP5, JUN, KRT8, LGALS3, MAP4K1, MMP23B, MPDZ, NDRG1, NOS2, NR2F1, PCDH7, PDE6A, PGFRA, PHLDA1, PIM1, PLAUR, POSTN, RAD51AP1, SAT1, SERPINE1, SGK1, SNAI2, SPP1, STAU1, STK17A, TAGLN2, TGFBR2, THBS2, TOP2A, TP53INP1, VCL, VEGFA
FOXO4 activated 2.203 5.41E-05 BCL6, CTGF, GADD45A, HMGCS1, IER3, SERPINE1, SGK1, VEGFA
CEBPB activated 2.142 1.59E-07 ALB, CEBPD, COL1A2, CPT1A, CSN2, CYP19A1, DAB2, DCN, GADD45A, GLIPR2, ID1, IFIT, M3, MGP, MMP11, NDRG4, NOS2, PDGFRA, PDK4, PLAUR, SAT1, SERPINE1, SGK1, SPP1, STAR, TMEM176A, TNFAIP6, TOP1
RXRA inhibited -2.100 3.52E-04 CEBPD, CPT1A, CYP2C9, FABP5, GCLC, GPT, IER3, LPL, MGP, MMP11, OLR1, PNMT, SAT1, SLC10A2, SPP1, STAR, VEGFA
HNF1A inhibited -2.168 4.07E-01 ALB, BCL6, C1S, CD55, COL3A1, IHH, SERPINE1, SLC10A2, SLC40A1, SLC4A2, UGT2B4
MYC inhibited -3.197 7.80E-07 ACTN1, ALB, AQP1, BCL6, CALD1, CAST, CAV1, CD9, CEBPD, CFLAR, CLIC4, COL1A2, COL3A1, COL4A1, CPT1A, CSTB, DSTN, DUSP1, FABP5, FBLN2, GADD45A, GCLC, GTF2F2, HLA-A, ID1, ID3, IER3, KLF6, LUM, NDRG1, PLAUR, PLP1, POLR3D, SGK1, SPP1, TAGLN2, TGFBR2, THBS2, TIMP1, TLN1, TSPO, VEGFA
MYCN inhibited -3.202 8.50E-03 ARPC1B, CAV1, CCNT1, CITED2, COL18A1, COL4A1, CTGF, DKK3, FGFR2, HLA-A, SDC2, SERPINE1, TAGLN
  1. The predicted activation state is inferred from the bias-corrected z-score, (+ = activated, - = inhibited). The bias-corrected z-score is computed based on the proportion of target genes present in the dataset which are directionally regulated as expected according to known effects of the regulator on the target compiled from the literature. The P value of overlap measures the statistical significance of overlap using Fisher’s exact t-test, between genes from the dataset and those known to be acted upon by an upstream regulator.