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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