Table 3. Enriched transcription factor genes in CGI probe loci within each of the five transgenerational methylation maintenance categories.
| Categories | Enriched Transcription Factor Genes |
| Stochastic Hypermethylation | FOXD1, FOXF2, FOXJ2, FOXL1, FOXO1, FOXO3, HNF1A, MEF2A, MEF2C, MEF2D, NKX2-5, NKX3-1, NKX6-1, NKX6-2, POU1F1, POU2F1, POU3F2, POU6F1, SOX10, SOX11, SOX12, SOX13, SOX14, SOX15, SOX18, SOX2, SOX21, SOX3, SOX4, SOX5, SOX6, SOX8, SOX9, SRY, STAT1, STAT5A, TBP, ZNF384 |
| Stochastic Hypomethylation | ARID5B, ASCL1, HNF4A, HNF4G, LMO2, MYF5, MYF6, MYOD1, MYOG, NFIA, NFIC, NKX2-1, NR2F1, NR2F2, NR5A1, PPARG, REST, SMAD4, TAL1, TCF12, TCF3, TCF4, TFAP2A, TFAP2B, TFAP2C, TFAP4, TFCP2, UBP1, ZBTB6 |
| Random Methylation | REST |
| Heritable Low Methylation | AR, ATF2, CDX2, CEBPA, CUX1, FOXD1, FOXO3, FOXO4, HMGA1, HMGA2, HNF1A, IKZF2, LEF1, LHX3, MEF2A, MEF2C, MEF2D, NFIL3, NKX2-2, NKX2-5, NKX3-1, NKX6-1, NKX6-2, ONECUT1, ONECUT2, PAX2, PDX1, POU2F1, POU3F2, POU6F1, PRRX2, SRY, STAT4, STAT5A, TBP, TCF7, TCF7L2, TEF, ZNF384 |
| Heritable High Methylation | AHR, ARID5B, ARNT, ASCL1, ATF1, ATF2, ATF3, ATF4, ATF7, BACH1, BACH2, BHLHB2, BHLHB3, CREB1, CREM, E2F1, E2F2, E2F3, E2F4, E2F5, E2F7, EGR1, EGR2, EGR3, EGR4, ELF1, ELF2, ELK1, ELK4, EP300, ERF, ERG, ESR1, ESR2, ETS1, ETS2, ETV7, FLI1, GCM1, GTF2I, HAND1, HAND2, HES1, HIF1A, HOXA5, KLF12, LMO2, MAF, MAFB, MAFF, MAFG, MAFK, MAX, MAZ, MEIS1, MITF, MTF1, MXD1, MXD4, MXI1, MYB, MYC, MYCN, MYF5, MYF6, MYOD1, MYOG, MZF1, NFE2, NFE2L1, NFE2L2, NFE2L3, NFIA, NFIC, NHLH1, NKX2-1, NR1H2, NR1H3, NR1I2, NR1I3, NR2F1, NR2F2, NR3C1, PATZ1, PAX5, PAX6, PGR, PPARA, RARA, RARB, RARG, REST, RUNX1, RUNX2, RUNX3, RXRA, RXRB, RXRG, SMAD1, SMAD2, SMAD3, SMAD4, SMAD5, SMAD6, SMAD7, SMAD9, SP1, SP2, SP3, SP4, SREBF1, SREBF2, TAL1, TAL2, TBX5, TCF12, TCF3, TCF4, TFAP2A, TFAP2B, TFAP2C, TFAP4, TFCP2, TFDP1, TFE3, TFEB, THRA, THRB, TLX2, UBP1, USF1, USF2, VDR, YY1, ZBTB6, ZEB1, ZIC1, ZIC2, ZIC3, ZNF148 |
CGI microarray probe sequences were assessed for 459 human TFBS motifs from TRANSFAC using TFBS motif searching algorithm MATCH, with a significant individual TFBS enrichment threshold determined by Fisher's exact test and a p-value justified by Bonferroni correction of 0.05/459/5 = 2.2×10−5 (i.e., p = 0.05/459 TFBS motifs/five methylation maintenance categories) when background sets were selected as #1 in Table 2.