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Table 2 GO biological process terms enriched with a significant number of genes involved in CP

From: MicroRNA-374a, -4680, and -133b suppress cell proliferation through the regulation of genes associated with human cleft palate in cultured human palate cells

GO biological process CP genes in biological process category
GO:0045893
positive regulation of transcription, DNA-templated
WNT5A, FGF7, WNT3A, GDF6, TGFB3, PAX6, FGF10, TP63, CDH1, PAX3, TGFB1, ARNT, FOXF2, BCL3, RARA, RUNX2, FGF2, BMP4, DVL3, BMP2, LEF1, TBX1, IRF6, IRF7, FOXE1, TFAP2A, ROR2, PTCH1, WNT11, BMP7
GO:0014066
regulation of phosphatidylinositol 3-kinase signaling
FGF19, FGFR2, FGF18, FGFR1, FGF8, FGF7, FGFR3, FGF9, ERBB2, PDGFRA, FGF10, FGF1, FGF2, FGF3, FGF4
GO:0036092
phosphatidylinositol-3-phosphate biosynthetic process
FGF19, FGFR2, FGF18, FGFR1, FGF8, FGF7, FGFR3, FGF9, FGF10, FGF1, FGF2, FGF3, FGF4
GO:0046854
phosphatidylinositol phosphorylation
FGF19, FGFR2, FGF18, FGFR1, FGF8, FGF7, FGFR3, FGF9, ERBB2, PDGFRA, FGF10, FGF1, FGF2, FGF3, FGF4
GO:0008543
fibroblast growth factor receptor signaling pathway
FGF19, FGFR2, FGF18, FGFR1, FGF8, FGF7, FGFR3, FGF9, FGF10, UBB, FGF1, FGF2, FGF3, FGF4
GO:0048015
phosphatidylinositol-mediated signaling
FGF19, FGFR2, FGF18, FGFR1, FGF8, FGF7, FGFR3, FGF9, ERBB2, PDGFRA, FGF10, FGF1, FGF2, FGF3, FGF4
GO:0060021
palate development
WNT5A, SUMO1, MSX1, GABRB3, WNT3A, FOXF2, TGFB3, LEF1, TFAP2A, COL2A1, WNT11, VAX1, COL11A2
GO:0018108
peptidyl-tyrosine phosphorylation
FGFR2, FGF18, FGFR1, FGF8, FGF7, FGFR3, FGF9, RYK, ERBB2, PDGFRA, FGF10, ROR2, FGF1, FGF2, FGF3, FGF4
GO:0045944
positive regulation of transcription from RNA polymerase II promoter
FGFR2, WNT5A, NOG, TBK1, WNT3A, TGFB3, PAX6, FGF10, TP63, PAX3, GREM1, TGFB1, ARNT, JADE1, PAX9, PAX7, FOXF2, BCL3, RARA, FGF1, FGF2, FGF4, BMP4, BMP2, MAFB, LEF1, GRHL3, TBX1, MSX1, IRF7, TFAP2A, UBB, BMP7
GO:0051781
positive regulation of cell division
FGFR2, FGF8, FGF7, FGF9, TGFB3, TGFA, FGF1, FGF2, TGFB1, FGF3, FGF4
GO:0042475
odontogenesis of dentin-containing tooth
BMP4, BMP2, MSX1, JAG2, TP63, LEF1, FGF10, TBX1, BMP7, RUNX2, FGF4
GO:0050679
positive regulation of epithelial cell proliferation
FGFR2, BMP4, NOG, FGF7, FGF9, ERBB2, TGFA, FGF10, TBX1, FGF1, TGFB1
GO:0008284
positive regulation of cell proliferation
FGFR2, FGF19, FGFR1, FGF18, FGF8, FGF7, FGFR3, FGF9, WNT3A, LEF1, TBX1, GREM1, NTN1, TGFB1, PDGFRA, TGFA, RARA, FGF1, FGF2, RUNX2, FGF3, FGF4
GO:0060325
face morphogenesis
NOG, MSX1, CRISPLD1, PAX9, CRISPLD2, TGFB3, LEF1, TBX1, TGFB1
GO:0000165
MAPK cascade
FGFR2, FGF19, FGFR1, FGF18, FGF8, FGFR3, FGF7, FGF9, ERBB2, FGF10, TGFB1, PDGFRA, UBB, FGF1, FGF2, FGF3, FGF4
GO:0001837
epithelial to mesenchymal transition
FGFR2, WNT5A, BMP2, NOG, FOXF2, LEF1, WNT11, BMP7, TGFB1
GO:0042472
inner ear morphogenesis
FGFR2, FGFR1, MAFB, FGF9, WNT3A, TFAP2A, ROR2, COL2A1, TBX1, NTN1
GO:0002062
chondrocyte differentiation
BMP4, FGFR1, BMP2, FGFR3, FGF9, COL2A1, COL11A2, RUNX2, TGFB1
GO:0008285
negative regulation of cell proliferation
BMP4, BMP2, CYP1B1, JARID2, TGFB3, FGF10, BRIP1, TIMP2, TGFB1, MSX1, IRF6, ROR2, TFAP2A, NOS3, RARA, AXIN2, BMP7, FGF2
GO:0070374
positive regulation of ERK1 and ERK2 cascade
FGF19, FGFR2, BMP4, FGF18, BMP2, FGF8, FGFR3, PDGFRA, FGF10, FGF1, FGF2, TGFB1, FGF4
GO:0042060
wound healing
WNT5A, NOG, ERBB2, PDGFRA, TGFB3, TGFA, FGF10, GRHL3, FGF2, TPM1
GO:0001759
organ induction
BMP4, FGFR1, FGF8, FGF10, FGF1, FGF2
GO:0030326
embryonic limb morphogenesis
FGFR1, FGF9, TP63, LEF1, PTCH1, SP8, GREM1, BMP7
GO:0045892
negative regulation of transcription, DNA-templated
WNT5A, BMP4, BMP2, JARID2, TBX22, LEF1, TP63, GREM1, TGFB1, SUMO1, PAX9, FOXF2, FOXE1, BCL3, TFAP2A, WNT11, RARA, BMP7, RUNX2
GO:0090090
negative regulation of canonical Wnt signaling pathway
WNT5A, JADE1, DVL3, BMP2, NOG, ROR2, LEF1, WNT11, UBB, GREM1, AXIN2, MLLT3
GO:0042476
odontogenesis
FGFR2, BMP4, WNT10A, FGF8, PAX9, TGFB3, AXIN2
GO:0043547
positive regulation of GTPase activity
FGFR2, FGF19, DVL3, FGFR1, FGF18, FGF8, FGFR3, FGF7, FGF9, ERBB2, FGF10, GRHL3, ARHGAP29, PDGFRA, WNT11, AXIN2, FGF1, FGF2, FGF3, FGF4
GO:0009086
methionine biosynthetic process
MTHFD1, BHMT2, MTR, BHMT, MTRR
GO:0042487
regulation of odontogenesis of dentin-containing tooth
BMP4, WNT10A, BMP2, FGF8, RUNX2
GO:0030509
BMP signaling pathway
BMP4, BMP2, NOG, FGF8, GDF6, ROR2, LEF1, BMP7, RUNX2
GO:0001701
in utero embryonic development
FGFR2, FGFR1, BMP2, NOG, MSX1, WNT3A, TGFB3, JAG2, PTCH1, NOS3, MYH9, TPM1
GO:0043410
positive regulation of MAPK cascade
FGFR2, FGFR1, BMP2, FGFR3, RYK, FGF9, FGF10, TBX1, TIMP2
GO:0046655
folic acid metabolic process
MTHFD1, MTHFR, ALDH1L1, DHFR, SLC19A1, MTRR
GO:0042493
response to drug
DVL3, MTHFR, FGF8, CYP1A1, ASS1, SLC6A4, TGFA, CDH1, PTCH1, ABCB1, ABCA1, TIMP2, GAD1, TGFB1
GO:0010628
positive regulation of gene expression
WNT10A, BMP2, NOG, FGF8, FGF9, WNT3A, ERBB2, SLC6A4, PAX6, TFAP2A, LEF1, WNT11, TGFB1
GO:0003148
outflow tract septum morphogenesis
FGFR2, BMP4, DVL3, FGF8, TBX1, RARA
GO:0001501
skeletal system development
FGFR1, BMP2, NOG, FGFR3, TCOF1, JAG2, TP63, COL2A1, COL11A2, BMP7
GO:0001525
angiogenesis
FGFR2, FGFR1, FGF18, CYP1B1, FGF9, TGFA, FGF10, TBX1, NOS3, STAB2, FGF1, MYH9
GO:0060445
branching involved in salivary gland morphogenesis
FGFR2, FGFR1, FGF8, FGF7, BMP7
GO:0045165
cell fate commitment
FGFR2, WNT5A, WNT10A, BMP2, FGF8, ROR2, WNT11
GO:0002053
positive regulation of mesenchymal cell proliferation
FGFR2, WNT5A, FGFR1, FGF9, TP63, TBX1
GO:0031069
hair follicle morphogenesis
FGFR2, WNT10A, FGF7, FOXE1, TP63, FGF10
GO:0000122
negative regulation of transcription from RNA polymerase II promoter
BMP4, FGFR2, FGFR1, NOG, BMP2, JARID2, FGF9, TBX22, PAX6, LEF1, TP63, VAX1, TGFB1, MSX1, IRF7, FOXE1, TFAP2A, PTCH1, RARA, UBB
GO:0021983
pituitary gland development
BMP4, NOG, MSX1, PAX6, FGF10, CDH1
GO:0048701
embryonic cranial skeleton morphogenesis
FGFR2, BMP4, PDGFRA, TFAP2A, TBX1, RUNX2
GO:0001934
positive regulation of protein phosphorylation
FGF19, BMP4, DVL3, BMP2, WNT3A, ERBB2, TBX1, AXIN2, TGFB1
GO:0032355
response to estradiol
ASS1, SLC6A4, FGF10, PTCH1, RARA, BMP7, TGFB1, GSTP1
GO:0030501
positive regulation of bone mineralization
BMP4, BMP2, TGFB3, TFAP2A, BMP7, TGFB1
GO:0060395
SMAD protein signal transduction
BMP4, BMP2, GDF6, TGFB3, ROR2, BMP7, TGFB1
GO:0043066
negative regulation of apoptotic process
BMP4, WNT5A, TP63, LEF1, GREM1, MSX1, PAX7, TGFA, BCL3, TFAP2A, RARA, WNT11, UBB, GSTP1, FGF4
GO:0001657
ureteric bud development
FGFR2, BMP4, FGFR1, RARA, BMP7, TGFB1
GO:0001649
osteoblast differentiation
BMP4, BMP2, NOG, FGF9, WNT3A, LEF1, WNT11, RUNX2
GO:0071300
cellular response to retinoic acid
WNT5A, WNT3A, SLC6A4, TBX1, RARA, WNT11, ABCA1
GO:0001658
branching involved in ureteric bud morphogenesis
BMP4, BMP2, FGF8, PTCH1, GREM1, FGF2
GO:0000187
activation of MAPK activity
WNT5A, BMP2, TGFB3, TGFA, FGF10, UBB, FGF1, FGF2
GO:0048762
mesenchymal cell differentiation
FGFR2, FGFR1, BMP2, BMP7
GO:0030324
lung development
FGFR2, WNT5A, FGF18, CRISPLD2, NOS3, FGF1, FGF2
GO:0001843
neural tube closure
MTHFD1, BMP4, NOG, GRHL3, PTCH1, RARA, TGFB1
GO:0045666
positive regulation of neuron differentiation
BMP4, FGFR1, BMP2, GDF6, RARA, TIMP2, BMP7
GO:0010862
positive regulation of pathway-restricted SMAD protein phosphorylation
BMP4, BMP2, GDF6, TGFB3, BMP7, TGFB1