Using DAVID, we found that hypermethylated genes in ESC cells are mostly enriched with the regulation of cell cycle (FZR1, E2F5, BOP1, TRRAP, CDK4, JUNB, etc.), cell death (SIVA1, MCL1, YPEL3, ARF6, UBQLN1, SHF, CIAPIN1, APLP1, GPX1, CASP3, etc.), and mRNA metabolic process (SCAF1, FIP1L1, STRAP, RBM15B, CWC15, XAB2, YBX1, AUH, SF3B2, APLP1, HNRNPL, etc.); the hypomethylated genes are enriched with functions related to ATP synthesis (ATP6V1F, ATP6V1C1, ATP6V0C, ATP6V1A, ATP6V0E, ATP6V1E1, ATP5C1
, etc.) and mitochondrial ribosome (MRPL15, MRPL27, MRPL16, MRPL36, MRPL39, MRPL34, DAP3, etc.) (Excel Sheet S2).
Through coexpression network construction and analysis of node degree, we found some functional and high connected hubs varied in EC and HIP region, such as CHRM1, MAPK1, TGFBR1, LIFR, ERBB4, ERBIN, ATP5C1
, IGF1R, GJA1, TJP1, AP2M1, CDK5, FGF2, TUBB, SLC22A3, DBT, CDK13, NLN, and MIF.
These genes included succinate dehydrogenase (SDHC), cytochrome c oxidase (COX5B/ COX6B), and various genes of the ATP synthase complex (ATP5G1, ATP5C1
, ATP5J, ATP5B, ATP5A1, ATP50, and ATP5F1).
subunit of Na+/K+-gTPase FACL6 Fatty acid Coenzyme A ligase long-chain 6 ATP1B1 Beta subunit of Na+/K+ATPase MGLL Monoglyceride lipase ATP5C1
ATP synthase H+ transporting mitochondria) F1 complex PDHA2 Pyruvate dehydrogenase E1 alpha 2 ASPH Aspartylbeia-hydroxylase 1_965027 Containing a cache domain PECI Peroxisomal D3, D2-enoyl-CoA isomerase TXNIP Vitamin D-3 up-regulated protein-1 Unknown FLJ22662 Unknown MGC13269 Unknown AGTPBPt Unknown TRAP25 Unknown 1_1100083 Unknown Ctorf21 Unknown KIAA0125 Unknown HSPC053 Unknown DKFZp434G0920 Unknown 1_1151996 Unknown Myocardium (Myoc) metastatic neuroblasts.