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Table 1 Functional annotation (biological process) and mRNA fold change of selected TSA (6 and 12 h) down- and up-regulated genes

From: Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis

Gene symbol Fold change 0 to 6 hrs TSA Fold change 0 to 12 hrs TSA F-test_p-value Function (biological process)
Inhbb -11.91 -11.93 2.33E-08 Growth
Sall1 -10.95 -16.09 1.06E-05 System development
Nanog - 9.87 -15.24 2.27E-05 Stem cell division
Gdf3 - 8.11 -12.56 9.83E-07 Growth
Lefty2 - 5.7 -16.58 6.87E-06 Development
Gli2 - 5.61 -8.38 4.34E-08 Regulation of transcription, DNA-dependent
Klf2 - 4.73 -10.39 4.48E-08 Positive regulation of transcription
Zfp42/Rex - 4.62 -5.00 1.01E-05 Regulation of transcription, DNA-dependent
Foxd3 - 4.59 -4.66 3.74E-05 Regulation of transcription, DNA-dependent
Tbx3 - 4.46 -6.10 9.29E-05 Development, cell aging, negative regulation of transcription
Eras -4.22 -5.94 3.11E-06 Small GTPase mediated signal transduction
Nr0b1 -4.11 -13.39 1.70E-06 Negative regulation of transcription
Rif1 -4.03 -3.82 1.54E-04 Response to stress, chromosome maintenance
Lefty1 -3.66 -9.11 1.13E-06 Development, cell growth
Suv39h1 -3.50 -4.87 2.38E-06 Chromatin assembly or disassembly, chromatin modification
Sall4 -3.47 -3.34 2.47E-03 Stem cell pluripotency
Utx -3.61 -2.81 1.68E-04 Chromatin modification
Pcaf -3.29 -5.15 3.79E-05 Regulation of transcription, DNA-dependent
Bmi1 -3.39 -1.80 2.39E-06 Chromatin modification, somatic stem cell division, development
Klf4 -3.02 -4.09 1.59E-06 Regulation of transcription, DNA-dependent
Fgf4 -2.95 -3.47 2.23E-06 Stem cell maintenance, regulation of cell cycle
Zic3 -2.87 -3.28 2.38E-05 Regulation of transcription
Esrrb -2.64 -4.26 2.96E-04 Regulation of transcription, DNA-dependent
Sox2 -2.43 -1.63 2.03E-04 Cell fate specification, regulation of transcription, DNA-dependent
Jmjd1a -2.20 -2.94 8.14E-08 Chromatin modification
Suz12 -2.10 -1.87 1.58E-03 Chromatin modification
Jmjd2c -2.20 -2.27 2.28E-04 Chromatin modification
Tcl1 -1.85 -3.13 1.09E-04 Regulation of transcription
Eed -1.80 -2.05 2.37E-05 Imprinting
Cbx5 -1.42 -2.21 1.76E-03 Chromatin assembly or disassembly
Pou5f1 -1.09 -1.74 6.04E-04 Stem cell maintenance
Egr1 28.37 40.75 1.53E-06 Regulation of transcription, DNA-dependent
H1f0 13.39 22.33 4.45E-06 Nucleosome assembly
Hist1h1c 12.34 17.88 1.01E-03 Nucleosome assembly, chromosome organization and biogenesis
Pdgfrb 9.78 10.77 3.98E-06 Protein tyrosine kinase signaling pathway
Fos 8.02 11.35 9.00E-07 Regulation of cell cycle, regulation of transcription, neurogenesis
Ndrg4 7.87 8.15 9.85E-06 Cell differentiation, development
Hist3h2a 5.98 11.17 7.97E-04 Nucleosome, chromosome
Creg1 4.65 5.32 2.84E-06 Regulation of transcription, DNA-dependent
Ttll1 4.47 5.13 7.84E-06 Protein modification
Nnat 4.05 8.37 1.04E-03 Development
Hoxa1 4.05 5.34 8.61E-06 Anterior/posterior pattern formation, hindbrain development
Edg3 3.88 4.82 1.53E-04 G-protein signaling, positive regulation of cell proliferation
Cacna1b 3.83 7.21 8.76E-04 Neurotransmitter secretion, regulation of heart contraction
Idb2 3.49 7.12 3.42E-04 Development, heart development, lymph gland development
Hoxb13 3.33 4.45 6.74E-06 Pattern specification, organogenesis, regulation of growth
Cacna1h 3.15 5.50 1.45E-05 Calcium ion transport
Cbx4 3.14 4.85 5.13E-05 Chromatin assembly or disassembly, chromatin modification
Sirt7 2.69 2.68 1.05E-04 Chromatin silencing, regulation of transcription, DNA-dependent
Mlf1 2.29 12.44 6.88E-05 Cell differentiation
Ctgf 2.12 9.88 6.80E-04 Ossification, angiogenesis, regulation of cell growth, cell adhesion
Cbx2 1.81 2.00 6.16E-05 Chromatin assembly or disassembly, chromatin modification
Wif1 1.41 6.33 2.38E-06 Negative regulation of Wnt receptor signaling pathway