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Table 8 Top* TFBSs enriched in genes upregulated in GE2-HCC

From: Gene networks and transcriptional regulators associated with liver cancer development and progression

ID TRANSFAC

Gene symbol

Yes–no ratio

P

Involvement in cancer types other than HCC

Involvement in HCC

V$NKX61_01

NKX6-1

6.17

5.13E−02

Diagnostic marker [36]

Tumour promoting [37]

V$OCT_C

POU2F1

6.17

4.20 E−05

Tumour promoting [38]

Tumour promoting [39]

 

POU2F2

  

Tumour promoting [40]

Unknown

V$OCT1_Q6

POU2F1

4.28

6.61 E−05

Tumour promoting [38]

Tumour promoting [39]

V$VJUN_01

JUN

5.29

1.88 E−03

Tumour promoting [41]

Predictive biomarker [42]

V$LHX3A_01

LHX3

4.85

1.97 E−02

Tumour promoting [43]

Unknown

V$IRF_Q6

IRF1 through IRF8

4.7

4.96 E−03

Tumour suppressing [44]

Tumour suppressing [45]

V$E2F_03

E2F1

3.29

6.29 E−06

Tumour promoting [46]

Tumour promoting [47]

V$HSF2_01

HSF2

3.23

5.03 E−03

Suggested tumour inhibiting [48]

Unknown

V$SRF_Q4

SRF

2.94

7.27 E−02

Predictive marker [49]

Tumour promoting [50]

V$GABP_B

GABPA/ GABPB1

2.86

4.36 E−02

Suggested tumour promoting [51, 52]

Negative prognostic marker [53]

V$TFIIA_Q6

GTf2A1/ GTf2A2

2.82

2.67 E−02

General enhancement of transcription [25]

 –

V$AFP1_Q6

ZFHX3

2.64

6.02 E−03

Tumour suppressing [54]

 Unknown

V$PR_01

PGR

2.64

6.45 E−02

Tumour promoting [26]

Unclear [27]

V$CAAT_01

cellular and viral CCAAT-box

2.13

6.61 E−11

V$CP2_02

TFCP2

2.1

6.98 E−04

Tumour promoting [55]

Tumour promoting [55, 56]

V$NFY_01

NFYA, NFYB, NFYC

1.65

3.06 E−09

Prognostic marker [57, 58]

Unknown

V$CHX10_01

VSX2

1.61

4.73E−04

Diagnostic marker, suggested tumour inhibiting [59]

Unknown

  1. “Yes” set—promoter sequences of the genes co-regulated in the tumours. “No” set—promoter sequences of the control genes. Yes/No ratio—ratio of the frequencies of TFBSs in the “Yes” gene set and “No” gene set. Yes/No ratio > 1 indicates overrepresentation of TFBS in the co-regulated genes and suggests potential involvement of the corresponding transcription factor in regulation of the observed expression changes
  2. HCC hepatocellular carcinoma, TFBS transcription factor binding site
  3. *TFBS with Yes/No Ratio > 2.5 or Yes/No Ratio > 1.5 and P < 0.001 are included