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Table 3 Predicted upstream regulators after ONC

From: Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injury

Name

Predicted change

Activation z-score

P-value of overlap

Target molecules in dataset

ATF4

Activated

3.14

6.10E-18

AARS, ASNS, ATF3, ATF5, BCAT1, CDKN1A, CEBPB, DDIT3, GARS, HERPUD1, MTHFD2, PSAT1, SARS, SERPINF1, TNFRSF12A

IFNG

Activated

2.64

2.05E-04

BCL2, CDKN1A, CEBPB, CLIC4, CREM, DDIT3, FCGR2B, GNAO1, MMP12, SPRR1A, TAC1

P38 MAPK

Activated

2.22

2.42E-06

BBC3, CDKN1A, EGR1, HMOX1, JUN, NEDD4

TP53

Activated

2.14

6.99E-05

APBB2, ATF3, BBC3, BCL2, CDKN1A, CLIC4, CNN3, COL3A1, CSTB, HIST1H1B, HMOX1, HSP90AA1, KITLG, PARK7

ALDH2

Inhibited

-2.22

1.94E-07

ATF5, MTHFD2, PHGDH, PSAT1, SLC1A4

ACOX1

Inhibited

-2.00

1.33E-02

CDKN1A, CSTB, DDIT3, SQSTM1

  1. Data were analyzed with Fisher’s exact test. Differences were considered significant with a P-value < 0.05 and |z-score| ≥ 2. The activation z-score was used to infer the likely activation states of upstream regulators based on a comparison with a model that assigns random regulation directions. The P-value overlap, which indicates likely upstream regulators, represents the significance of the overlap between the dataset genes identified here and known targets of transcriptional regulators.