Table S4. TCOF1 related genes calculated by Genedeck database involved in different biological process analysed by DAVID database List Pop Pop Fold Term P Value Genes Bonferroni Benjamini FDR Total Hits Total Enrichment GO:0010604~positive regulation of 1.67E-70 MEF2C, HRAS, THRB, STAT5A, STAT5B, SNCA, TGFB3, CASK, TLR4, TBP, CBFB, TGFB1, ZIC3, 481 857 13528 5.119556 6.48E-67 6.48E-67 3.09E-67 macromolecule metabolic process CITED2, TGFB2, APOE, GATA4, H2AFX, RARB, MLL4, CCNA2, INSR, SYK, RARG, MYO6, RXRA, PPARGC1A, IRS1, HES1, HHEX, MAPK1, EP300, HES5, JUN, SIX1, VEGFA, MAPK9, CAV1, BLM, SOX4 GO:0042127~regulation of cell 1.90E-68 NOG, HRAS, IL18, STAT5A, PTGS1, STAT5B, TGFB3, IL13, FGF10, TGFB1, TGFB2, BDNF, MYD88, 481 787 13528 5.289024 7.37E-65 3.69E-65 3.51E-65 proliferation CDKN2A, CDKN2C, APOE, CDKN2D, ILK, GATA4, RARB, CCNA2, INSR, SYK, EGFR, GTPBP4, RARG, RXRA, EFNB1, IRS1, HES1, PTHLH, HHEX, MAPK1, FGFR1OP, JUN, VEGFA, FOXG1, PDGFRB, F GO:0009891~positive regulation of 1.85E-66 MEF2C, HRAS, THRB, STAT5A, STAT5B, TGFB3, CASK, TLR4, TBP, TGFB1, ZIC3, CBFB, CITED2, 481 695 13528 5.584481 7.20E-63 2.40E-63 3.43E-63 biosynthetic process TGFB2, APOE, GATA4, RARB, MLL4, CCNA2, INSR, SYK, EGFR, RARG, MYO6, RXRA, PPARGC1A, IRS1, HES1, PTHLH, HHEX, MAPK1, EP300, HES5, JUN, SIX1, VEGFA, BLM, SOX4, ABCA1, SOX9 GO:0031328~positive regulation of 2.16E-65 MEF2C, HRAS, THRB, STAT5A, STAT5B, TGFB3, CASK, TLR4, TBP, TGFB1, ZIC3, CBFB, CITED2, 481 685 13528 5.58389 8.40E-62 2.10E-62 4.00E-62 cellular biosynthetic process APOE, GATA4, RARB, MLL4, CCNA2, INSR, SYK, EGFR, RARG, MYO6, RXRA, PPARGC1A, IRS1, HES1, PTHLH, HHEX, MAPK1, EP300, HES5, JUN, SIX1, VEGFA, BLM, SOX4, ABCA1, SOX9, SRF, GO:0051173~positive regulation of 4.29E-64 MEF2C, HRAS, THRB, STAT5A, STAT5B, TGFB3, CASK, TBP, TGFB1, ZIC3, CBFB, CITED2, APOE, 481 644 13528 5.721026 1.67E-60 3.34E-61 7.95E-61 nitrogen compound metabolic process GATA4, H2AFX, RARB, MLL4, CCNA2, INSR, EGFR, RARG, MYO6, RXRA, PPARGC1A, PTHLH, HES1, HHEX, MAPK1, EP300, HES5, JUN, SIX1, VEGFA, BLM, SOX4, ABCA1, SOX9, SRF, WT1, ARNT, GO:0010557~positive regulation of 3.04E-63 MEF2C, HRAS, THRB, STAT5A, STAT5B, TGFB3, CASK, TBP, TLR4, TGFB1, ZIC3, CBFB, CITED2, 481 654 13528 5.633549 1.18E-59 1.97E-60 5.63E-60 macromolecule biosynthetic process TGFB2, GATA4, RARB, MLL4, CCNA2, INSR, SYK, RARG, MYO6, RXRA, PPARGC1A, IRS1, HES1, HHEX, MAPK1, EP300, HES5, JUN, SIX1, VEGFA, BLM, SOX4, SOX9, SRF, WT1, ARNT, NR1H2, H GO:0045935~positive regulation of 6.05E-63 MEF2C, HRAS, THRB, STAT5A, STAT5B, TGFB3, CASK, TBP, TGFB1, ZIC3, CBFB, CITED2, APOE, 481 624 13528 5.769177 2.35E-59 3.36E-60 1.12E-59 nucleobase, nucleoside, nucleotide and GATA4, H2AFX, RARB, MLL4, INSR, CCNA2, RARG, MYO6, RXRA, PPARGC1A, PTHLH, HES1, nucleic acid metabolic process HHEX, MAPK1, EP300, HES5, JUN, SIX1, VEGFA, BLM, SOX4, ABCA1, SOX9, SRF, WT1, ARNT, NR1H2 GO:0010941~regulation of cell death 1.08E-62 MEF2C, XRCC5, HRAS, MAEA, MMP9, STAT5A, STAT5B, SNCA, TGFB3, TLR4, TGFB1, BTK, 481 815 13528 4.969279 4.20E-59 5.25E-60 2.00E-59 CITED2, TGFB2, MAP3K7, BDNF, MYD88, CDKN2A, CD44, HTRA2, CDKN2C, APOE, CDKN2D, ILK, RARB, FAS, TWIST2, EGFR, RARG, RXRA, FADD, STK4, MAPK1, JUN, VEGFA, RIPK3, MAPK9, MAPK8, TNF GO:0043067~regulation of programmed 5.13E-62 MEF2C, XRCC5, HRAS, MAEA, MMP9, STAT5A, SNCA, STAT5B, TGFB3, TLR4, TGFB1, BTK, 481 812 13528 4.953002 1.99E-58 2.21E-59 9.49E-59 cell death CITED2, TGFB2, MAP3K7, BDNF, MYD88, CDKN2A, CD44, HTRA2, CDKN2C, APOE, CDKN2D, ILK, RARB, FAS, TWIST2, EGFR, RARG, RXRA, FADD, STK4, MAPK1, JUN, VEGFA, RIPK3, MAPK9, MAPK8, TNF GO:0010628~positive regulation of gene 5.98E-61 MEF2C, THRB, STAT5A, STAT5B, TGFB3, CASK, TBP, TGFB1, ZIC3, CBFB, CITED2, GATA4, 481 581 13528 5.905711 2.32E-57 2.32E-58 1.11E-57 expression RARB, CCNA2, MLL4, MYO6, RARG, RXRA, PPARGC1A, HES1, HHEX, MAPK1, EP300, HES5, JUN, SIX1, VEGFA, MAPK9, BLM, SOX4, SOX9, SRF, WT1, ARNT, NR1H2, HOXA1, HOXA2, NKX2-1, RUNX1, R GO:0045944~positive regulation of 4.66E-59 MEF2C, THRB, STAT5A, STAT5B, TGFB3, CASK, ZIC3, TGFB1, CBFB, CITED2, GATA4, RARB, 481 371 13528 7.504985 1.81E-55 1.65E-56 8.63E-56 transcription from RNA polymerase II MYO6, RARG, RXRA, PPARGC1A, HES1, HHEX, EP300, HES5, JUN, SIX1, VEGFA, SOX9, SRF, promoter WT1, ARNT, NR1H2, HOXA1, HOXA2, NKX2-1, RUNX1, RUNX2, NKX2-5, BMP4, BMP2, MLL, MAFB, GRIN1, GO:0042981~regulation of apoptosis 4.74E-59 MEF2C, XRCC5, HRAS, MAEA, MMP9, STAT5A, SNCA, STAT5B, TGFB3, TLR4, TGFB1, BTK, 481 804 13528 4.862362 1.84E-55 1.54E-56 8.78E-56 CITED2, TGFB2, MAP3K7, BDNF, MYD88, CDKN2A, CD44, HTRA2, CDKN2C, APOE, CDKN2D, ILK, RARB, FAS, TWIST2, EGFR, RARG, RXRA, FADD, STK4, MAPK1, JUN, VEGFA, RIPK3, MAPK9, MAPK8, TNF GO:0045941~positive regulation of 1.18E-57 MEF2C, THRB, STAT5A, STAT5B, TGFB3, CASK, TBP, TGFB1, ZIC3, CBFB, CITED2, GATA4, 481 564 13528 5.834388 4.59E-54 3.53E-55 2.19E-54 transcription RARB, CCNA2, MLL4, MYO6, RARG, RXRA, PPARGC1A, HES1, HHEX, MAPK1, EP300, HES5, JUN, SIX1, VEGFA, BLM, SOX4, SOX9, SRF, WT1, ARNT, NR1H2, HOXA1, HOXA2, NKX2-1, RUNX1, RUNX2, N GO:0045893~positive regulation of 6.12E-56 MEF2C, THRB, STAT5A, STAT5B, TGFB3, CASK, ZIC3, TGFB1, CBFB, CITED2, GATA4, RARB, 481 477 13528 6.308904 2.38E-52 1.70E-53 1.13E-52 transcription, DNA-dependent MLL4, MYO6, RARG, RXRA, PPARGC1A, HES1, HHEX, EP300, HES5, JUN, SIX1, VEGFA, SOX4, SOX9, SRF, WT1, ARNT, NR1H2, HOXA1, HOXA2, NKX2-1, RUNX1, RUNX2, NKX2-5, BMP4, BMP2, MLL, GO:0051254~positive regulation of RNA 1.48E-55 MEF2C, THRB, STAT5A, STAT5B, TGFB3, CASK, ZIC3, TGFB1, CBFB, CITED2, GATA4, RARB, 481 481 13528 6.256439 5.75E-52 3.83E-53 2.74E-52 metabolic process MLL4, MYO6, RARG, RXRA, PPARGC1A, HES1, HHEX, EP300, HES5, JUN, SIX1, VEGFA, SOX4, SOX9, SRF, WT1, ARNT, NR1H2, HOXA1, HOXA2, NKX2-1, RUNX1, RUNX2, NKX2-5, BMP4, BMP2, MLL, GO:0006357~regulation of transcription 7.08E-49 MEF2C, THRB, STAT5A, STAT5B, FST, TGFB3, CASK, TGFB1, ZIC3, CBFB, CITED2, GATA1, 481 727 13528 4.681009 2.75E-45 1.72E-46 1.31E-45 from RNA polymerase II promoter GATA4, RARB, TWIST2, IKBKAP, MYO6, RARG, RXRA, RBL1, PPARGC1A, HES1, HHEX, EP300, HES5, JUN, SIX1, VEGFA, MNX1, TFAP2A, SOX9, SRF, WT1, ARNT, NR1H2, VDR, HOXA1, TAL1, HOXA2, GO:0051094~positive regulation of 1.05E-46 XRCC5, THRB, FOXA2, STAT5A, PPARG, STAT5B, FST, PAX6, TGFB3, NFKB1, GLI2, GLI3, 481 278 13528 7.789946 4.09E-43 2.41E-44 1.95E-43 developmental process TGFB1, TGFB2, AKT1, MEN1, ACVR1B, CCNE1, BDNF, ILK, GATA4, RARA, NOS3, NRG1, INSR, FGF2, SYK, LYN, DLL3, RB1, ACVR2A, CD36, JUN, FOXG1, MAPK9, NGFR, ACVR1, TNF, DRD2, CSF1, KI GO:0008284~positive regulation of cell 1.66E-43 NOG, NBN, HRAS, STAT5A, IL18, STAT5B, PAX6, IL13, FGF10, TP63, PAX3, GLI2, TGFB1, TGFB2, 481 414 13528 5.978206 6.45E-40 3.58E-41 3.08E-40 proliferation ILK, TGFA, NRG1, INSR, FGF2, MYC, CCNA2, SYK, EGFR, CDC7, LYN, CCKBR, EFNB1, CDK6, IRS1, CDK2, PTHLH, HES1, MAPK1, PRKCQ, CCND1, HIPK1, FGFR1OP, JUN, HIPK2, FOXG1, VE GO:0045597~positive regulation of cell 3.11E-43 XRCC5, THRB, FOXA2, STAT5A, PPARG, STAT5B, PAX6, TGFB3, NFKB1, GLI2, GLI3, TGFB1, 481 229 13528 8.351451 1.21E-39 6.35E-41 5.75E-40 differentiation TGFB2, AKT1, MEN1, ACVR1B, CCNE1, BDNF, ILK, RARA, NRG1, FGF2, SYK, LYN, DLL3, RB1, ACVR2A, CD36, JUN, FOXG1, MAPK9, NGFR, ACVR1, DRD2, CSF1, KITLG, KIT, SRF, ADA, ARNT, EPH GO:0043069~negative regulation of 6.57E-43 XRCC5, MEF2C, HRAS, MAEA, STAT5A, SNCA, STAT5B, TGFB3, TP63, NFKB1, PAX2, PTEN, 481 359 13528 6.424035 2.56E-39 1.28E-40 1.22E-39 programmed cell death CITED2, AKT1, MAP3K7, EDNRB, BDNF, MYD88, APOE, CDKN2D, PAX7, ILK, NOS3, FAS, NRG1, MKL1, CASP2, MYC, TERT, TWIST2, EGFR, CDK1, ESR1, TP53, ESR2, EYA1, PSEN1, HIPK2, PSEN2, VE GO:0060548~negative regulation of cell 8.23E-43 XRCC5, MEF2C, HRAS, MAEA, STAT5A, SNCA, STAT5B, TGFB3, TP63, NFKB1, PAX2, PTEN, 481 360 13528 6.406191 3.20E-39 1.52E-40 1.52E-39 death CITED2, AKT1, MAP3K7, EDNRB, BDNF, MYD88, APOE, CDKN2D, PAX7, ILK, NOS3, FAS, NRG1, MKL1, CASP2, MYC, TERT, TWIST2, EGFR, CDK1, ESR1, TP53, ESR2, EYA1, PSEN1, HIPK2, PSEN2, VE GO:0043066~negative regulation of 1.68E-40 XRCC5, MEF2C, HRAS, MAEA, STAT5A, SNCA, STAT5B, TGFB3, TP63, NFKB1, PTEN, CITED2, 481 354 13528 6.276425 6.55E-37 2.98E-38 3.12E-37 apoptosis AKT1, MAP3K7, EDNRB, BDNF, MYD88, APOE, CDKN2D, PAX7, ILK, NOS3, FAS, MKL1, NRG1, CASP2, MYC, TERT, TWIST2, EGFR, CDK1, ESR1, TP53, ESR2, EYA1, PSEN1, HIPK2, PSEN2, VEGFA, A GO:0006468~protein amino acid 1.81E-40 STAT5A, TGFB3, CASK, TGFB1, BTK, TGFB2, CSNK2A2, MAP3K7, CSNK2A1, COL4A3BP, ILK, 481 667 13528 4.469599 7.05E-37 3.07E-38 3.36E-37 phosphorylation PRKACA, INSR, MAP2K7, SYK, EGFR, IKBKAP, RET, STK4, MAPK1, CAMK4, RIPK3, PDGFRB, ROR2, MAPK9, MAPK8, MAPK7, EIF2AK3, FGFR2, FGFR1, ERBB4, STK11, ERBB3, ERBB2, NEK1, HUS1, MAP GO:0035295~tube development 5.00E-40 NOG, FOXA2, TGFB3, TP63, FGF10, PAX3, PAX2, GLI2, GLI3, ZIC3, MAP3K7, BDNF, CD44, CTGF, 481 220 13528 8.181743 1.94E-36 8.09E-38 9.25E-37 CXCR4, ILK, GATA4, CASP8, MKKS, NOS3, HHIP, RARB, FGF2, RET, MMP14, HES1, PTHLH, HHEX, EYA1, EP300, PSEN1, PSEN2, VEGFA, SIX1, FOXC2, TFAP2A, FOXC1, MED1, ACVR1, WNT5A GO:0007389~pattern specification process 1.40E-39 NOG, FOXA2, FST, PAX6, TP63, FGF10, ZEB1, GLI2, GLI3, ZIC3, CITED2, CXCR4, PAX7, GATA4, 481 267 13528 7.268191 5.44E-36 2.17E-37 2.59E-36 MKKS, HHIP, PITX2, EGR2, GSC, EFNB1, DLL3, LEF1, HES1, CTNNBIP1, ACVR2A, HHEX, EYA1, CRKL, EP300, PSEN1, HIPK1, HOXC13, HIPK2, PSEN2, FOXG1, VEGFA, SIX1, MNX1, ROR2, F GO:0010033~response to organic 1.45E-36 STAT5A, SLC6A3, PTGS1, SNCA, STAT5B, TGFB3, TLR4, AQP1, TGFB1, TGFB2, MYD88, CD44, 481 721