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

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