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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,
Fatty acid metabolic process
6 75 E2F1, E2F7 Cell cycle,
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‚ÄČ% 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.