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Table 1 Summary of GRN modules

From: Gene regulation is governed by a core network in hepatocellular carcinoma

Index

Size

Main regulators

Target gene functions

1

419

RUNX3, RUNX2, POU2AF1, POU2F2, FLI1, BHLHB3, PRDM1

Immune response,

Plasma membrane,

Cell activation

2

328

HAND2, TCF4, FOXF1, FOXF2, ARID5B, FOXL1

Extracellular region,

Cell adhension

3

270

miR-150, miR-142, miR-155, miR-181a, miR-342, miR-27a, miR-146a, miR-199a, miR-214, HNF4A

Mitochondrion,

Oxidation reduction,

Mitochondrial envelope

4

152

AR, miR-127, miR-377, miR-323, miR-299, miR-221, miR-433, miR-376a, miR-136, miR-18a, miR-296, miR-154, miR-431, miR-382, miR-369, miR-200b

Oxidation reduction,

Cofactor metabolic process,

Steroid metabolic process

5

103

NR1I3, NR1I2, ESR1

Oxidation reduction,

Microsome,

Fatty acid metabolic process

6

75

E2F1, E2F7

Cell cycle,

Mitosis,

Chromosome,

Nuclear lumen

3, 4, 5

525

NR1I3,miR-150, miR-142, miR-155, miR-181a, AR, NR1I2, miR-342, miR-27a, miR-146a, HNF4A, miR-199a, miR-218, miR-214, miR-127, miR-132, ESR1, miR-377, SOX4, miR-323, miR-299, miR-221, miR-23a

Mitochondrion,

Oxidation reduction,

Cofactor binding,

  1. Regulators are sorted by the number of targets. Regulators that regulate more than 80 % of genes in each module are listed. Gene Ontology enrichment was applied by DAVID to find common functions of genes. Size of each module corresponds to the number of nodes. The detailed enrichment results can be found in Additional File 2.