Table 1. Functional annotation of differentially methylated genes in GSC lines.

ID	Function	Count	P value	Benjaminia	Gene
GO:0032502b	Developmental process	68	1.54E-08	1.27E-05	MYOD1, DUOX1, GLI2, GDNF, CXCL12, YBX2, ACVR1C, HOOK1, OSR2, SLC2A4, OSR1, AQP11, GATA3, HLX, PAX8, PIWIL2, PIWIL3, HHIP, SRD5A2, FAM83H, CHAT, PITX2, SOX10, TBX15, GSC, RAX, SCUBE1, SIX2, ZNF141, VAX2, HOXD9, SPAG6, TFAP2A, LAMC2, NSD1, SHROOM1, IRX3, CCK, PCDHB15, FIGLA, OXTR, IGF2BP2, PRDM16, MSX2, TCP11, PCDHB16, KCNE1, GFI1, B3GNT2, WNT8A, NEFM, FOXD4, FOXD3, BGLAP, TBX3, IKZF1, TBX4, DBH, SHOX2, TNFSF11, PKP1, PSMC3, FOXE1, AVPR1A, GHSR, SMPD3, KLF4, NR5A1
GO:0031323	Regulation of cellular metabolic process	57	0.001584	0.051934	MYOD1, LPAR3, CPEB1, GLI2, GDNF, YBX2, GATA3, HLX, PAX8, ZNF578, PIWIL2, PIWIL3, FOXB1, RTEL1, PITX2, CIITA, SOX10, TBX15, GSC, RAX, SIX2, ZNF141, VAX2, GRHL2, HMGA1, GRM1, FOXR1, HOXD9, TFAP2A, ZNF710, NSD1, IRX3, IRX6, CCK, FIGLA, IGF2BP2, PRDM16, MSX2, HRH1, PRDM14, CDYL, GFI1, FOXD4, FOXD3, BGLAP, TBX3, IKZF1, TBX4, ABCG4, SHOX2, PSMC3, AVPR1A, SP5, FOXE1, GHSR, KLF4, NR5A1
GO:0045449	Regulation of transcription	45	0.002614	0.070496	MYOD1, IRX3, IRX6, FIGLA, PRDM16, GLI2, GDNF, YBX2, MSX2, PRDM14, CDYL, GATA3, HLX, PAX8, ZNF578, GFI1, FOXB1, FOXD4, FOXD3, PITX2, CIITA, SOX10, BGLAP, RAX, TBX15, GSC, IKZF1, TBX3, TBX4, SIX2, ZNF141, VAX2, ABCG4, GRHL2, HMGA1, FOXR1, HOXD9, SHOX2, FOXE1, SP5, TFAP2A, ZNF710, NSD1, KLF4, NR5A1
GO:0007399	Nervous system development	25	0.001121	0.040257	IRX3, CCK, PCDHB15, OXTR, GLI2, PRDM16, CXCL12, GDNF, HLX, PCDHB16, B3GNT2, HHIP, GFI1, NEFM, CHAT, SOX10, GSC, RAX, TBX3, IKZF1, VAX2, SHOX2, HOXD9, AVPR1A, TFAP2A

^aBenjamini-hochberg adjusted P-values;

^bGene Ontology (GO) term ID