Disease table of HOLOPROSENCEPHALY OMIM ID: PS236100

Gene-disease associations table

GeneAssociated with HOLOPROSENCEPHALY inLink to HGNCCytogenetic bandNumber of associated diseasesAssociated diseases
SIX3ClinVar, OMIM, HUMSAVARHGNC link2p213269160, PS236100, 147250
GLI2ClinVar, OMIM, HUMSAVARHGNC link2q14.22PS236100, 615849
SHHClinVar, OMIM, HUMSAVARHGNC link7q36.34PS300345, 269160, PS236100, 147250
CDONClinVar, OMIM, HUMSAVARHGNC link11q24.21PS236100
ZIC2ClinVar, OMIM, HUMSAVARHGNC link13q32.31PS236100
GAS1ClinVarHGNC link9q21.331PS236100
PTCH1ClinVar, OMIM, HUMSAVARHGNC link9q22.324605462, 109400, PS142623, PS236100
TGIF1ClinVar, OMIM, HUMSAVARHGNC link18p11.311PS236100

Download the disease annotation in CSV format

Relations among genes:

Tandem repeat annotations from DGD
Cytogenetic band analysis
By region
Shared regionNumber of genes associated with the diseaseGenes associated with the disease
9q22GAS1, PTCH1
By arm
Shared armNumber of genes associated with the diseaseGenes associated with the disease
9q2GAS1, PTCH1
By chromosome
Shared chromosomeNumber of genes associated with the diseaseGenes associated with the disease
22SIX3, GLI2
92GAS1, PTCH1
Transcription Factors (TF) annotation from TRRUST
TFassociated to this disease# regulated genesRegulated genes# regulated genes associated with this diseaseRegulated genes associated with this disease
GLI2YES14WNT2B, FOXC2, MUC5AC, BCL2, FAS, FOXL1, TNFRSF10B, FST, FOXF1, JUN, FOXA2, FOXE1, PDGFRA, H2AFX0
ZIC2YES1SLC13A40
TGIF1YES2SOX3, SERPINE10
regulated geneassociated to this disease# TFsTFs # TFs associated with this diseaseTFs associated with this disease
SIX3YES2PAX6, PROX10
GLI2YES3SMAD3, TP53, CTNNB10
SHHYES3STAT3, PAX3, SOX90
TGIF1YES2HDAC4, SOX30
Interactions from BIOGRID - physical
Gene1Gene2Direct InteractionNumber of shared interactorsShared genes in interaction
GLI2ZIC2Yes0
GLI2TGIF1No1HDAC1
ZIC2GAS1No1ELAVL1
ZIC2TGIF1No1ELAVL1
GAS1TGIF1No1ELAVL1

Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from BIOGRID - genetic
Interactions from STRING
Gene1Gene2Direct InteractionInteraction modeNumber of shared interactorsShared genes in interaction
SIX3GLI2No-2SHH, WNT1
SIX3SHHYesactivation, binding7SALL1, PITX2, PLP1, POU3F4, BMP4, WNT1, PAX6
SIX3CDONNo-1SHH
SIX3ZIC2No-1SHH
SIX3GAS1No-1SHH
SIX3PTCH1No-2SHH, BMP4
GLI2SHHYesactivation, binding29WNT2B, RUNX2, WNT5A, PTCH1, MYF5, FOXA2, GAST, WNT3A, WNT5B, JAG1, CDON, PRKCD, SMO, WNT1, GLI1, WNT16, GLI3, PTCH2, WNT7A, AKT1, MYOD1, WNT3, WNT2, ZIC2, BMP2, WNT7B, ASCL1, MAP2K1, WNT4
GLI2CDONYesactivation, binding3DHH, SHH, IHH
GLI2ZIC2Yesbinding3SHH, GLI1, GLI3
GLI2GAS1No-3DHH, SHH, IHH
GLI2PTCH1Yesactivation, binding7DHH, BMP2, SMO, IHH, GLI1, GLI3, SHH
GLI2TGIF1No-1HDAC1
SHHCDONYesactivation, binding1GLI2
SHHZIC2Yesexpression, activation, binding3GLI3, GLI2, GLI1
SHHGAS1Yesactivation, binding1FOXM1
SHHPTCH1Yesactivation14CDK1, STIL, BMP4, FGF10, SMO, TGFB2, GLI3, GLI2, GLI1, CCNB1, BMP2, UBC, GPC3, GPC5
CDONZIC2No-2SHH, GLI2
CDONGAS1No-3DHH, SHH, IHH
CDONPTCH1No-4DHH, SHH, IHH, GLI2
ZIC2GAS1No-1SHH
ZIC2PTCH1No-4SHH, GLI3, GLI2, GLI1
GAS1PTCH1No-3DHH, SHH, IHH

Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from CORUM
Interactions from CENSUS
Interactions from PDB
Interactions from manually curated literature
KEGG pathways annotation: shared terms / NET-GE enrichment

Shared terms

KEGG termKEGG term IDICNumber of genes with the same termGenes
Hedgehog signaling pathwayhsa043407.015SHH, ZIC2, PTCH1, GLI2, GAS1
Pathways in cancerhsa052003.983SHH, PTCH1, GLI2
Basal cell carcinomahsa052176.793SHH, PTCH1, GLI2

NET-GE enrichment

Term New enriched termICP valueGenes
Hedgehog signaling pathway (hsa04340) -7.010.0CDON, PTCH1, GAS1, ZIC2, GLI2, SHH
Environmental Information ProcessingNEW1.710.032SHH, ZIC2, PTCH1, GLI2, GAS1
Basal cell carcinoma (hsa05217) -6.790.003SHH, PTCH1, GLI2
Pathways in cancer (hsa05200) -3.980.027SHH, PTCH1, GLI2
Signal transductionNEW2.060.009SHH, ZIC2, PTCH1, GLI2, GAS1
Cancers: Specific typesNEW4.10.022SHH, PTCH1, GLI2
REACTOME pathways annotation: shared terms / NET-GE enrichment

Shared terms

REACTOME termREACTOME term IDICNumber of genes with the same termGenes
Signal TransductionR-HSA-1625821.786CDON, PTCH1, GAS1, GLI2, SHH, TGIF1
Hedgehog 'on' stateR-HSA-56326846.625GAS1, SHH, PTCH1, CDON, GLI2
Signaling by HedgehogR-HSA-53583515.795GAS1, SHH, PTCH1, CDON, GLI2
Ligand-receptor interactionsR-HSA-56326819.984SHH, PTCH1, CDON, GAS1
Class B/2 (Secretin family receptors)R-HSA-3730806.522SHH, PTCH1
GPCR ligand bindingR-HSA-5007924.192SHH, PTCH1
Hedgehog 'off' stateR-HSA-56107876.192PTCH1, GLI2
Signaling by GPCRR-HSA-3727902.682SHH, PTCH1

NET-GE enrichment

Term New enriched termICP valueGenes
Class B/2 (Secretin family receptors) (R-HSA-373080) -6.520.028SHH, PTCH1, GLI2
Signaling by Hedgehog (R-HSA-5358351) -5.790.0SHH, PTCH1, GLI2, GAS1, CDON
Hedgehog 'on' state (R-HSA-5632684) -6.620.0SHH, PTCH1, GLI2, GAS1, CDON
Ligand-receptor interactions (R-HSA-5632681) -9.980.0SHH, PTCH1, CDON, GAS1
CDO in myogenesis (R-HSA-375170) NEW8.120.038SHH, CDON
Myogenesis (R-HSA-525793) NEW8.120.038SHH, CDON
Signal Transduction (R-HSA-162582) -1.780.015CDON, PTCH1, GAS1, GLI2, SHH, TGIF1
GO - molecular function annotation: shared terms / NET-GE enrichment

Shared terms

GOICNumber of genes with the same GOGenes
binding (GO:0005488) 0.188CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
protein binding (GO:0005515) 0.467CDON, SIX3, PTCH1, GAS1, GLI2, SHH, TGIF1
organic cyclic compound binding (GO:0097159) 1.055TGIF1, PTCH1, ZIC2, GLI2, SIX3
transcription factor activity, sequence-specific DNA binding (GO:0003700) 2.654TGIF1, ZIC2, GLI2, SIX3
nucleic acid binding transcription factor activity (GO:0001071) 2.654TGIF1, ZIC2, GLI2, SIX3
heterocyclic compound binding (GO:1901363) 1.064TGIF1, ZIC2, GLI2, SIX3
nucleic acid binding (GO:0003676) 1.444TGIF1, ZIC2, GLI2, SIX3
DNA binding (GO:0003677) 1.924TGIF1, ZIC2, GLI2, SIX3
cation binding (GO:0043169) 1.43SHH, ZIC2, GLI2
sequence-specific double-stranded DNA binding (GO:1990837) 3.23TGIF1, GLI2, SIX3
sequence-specific DNA binding (GO:0043565) 2.793TGIF1, GLI2, SIX3
regulatory region nucleic acid binding (GO:0001067) 3.033TGIF1, GLI2, SIX3
RNA polymerase II regulatory region DNA binding (GO:0001012) 3.363TGIF1, GLI2, SIX3
ion binding (GO:0043167) 1.363SHH, ZIC2, GLI2
transcription regulatory region DNA binding (GO:0044212) 3.033TGIF1, GLI2, SIX3
macromolecular complex binding (GO:0044877) 2.613PTCH1, ZIC2, GLI2
RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977) 3.373TGIF1, GLI2, SIX3
regulatory region DNA binding (GO:0000975) 3.033TGIF1, GLI2, SIX3
transcription regulatory region sequence-specific DNA binding (GO:0000976) 3.243TGIF1, GLI2, SIX3
double-stranded DNA binding (GO:0003690) 3.093TGIF1, GLI2, SIX3
metal ion binding (GO:0046872) 1.413SHH, ZIC2, GLI2
RNA polymerase II transcription factor activity, sequence-specific DNA binding (GO:0000981) 3.293TGIF1, GLI2, SIX3
receptor binding (GO:0005102) 2.432SHH, PTCH1
transition metal ion binding (GO:0046914) 2.482SHH, GLI2
carbohydrate derivative binding (GO:0097367) 2.032SHH, PTCH1
transcription cofactor activity (GO:0003712) 3.442SIX3, TGIF1
core promoter proximal region DNA binding (GO:0001159) 3.822TGIF1, GLI2
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding (GO:0001228) 3.982SIX3, GLI2
glycosaminoglycan binding (GO:0005539) 4.422SHH, PTCH1
zinc ion binding (GO:0008270) 2.662SHH, GLI2
transcription factor activity, transcription factor binding (GO:0000989) 3.362SIX3, TGIF1
transcription factor activity, protein binding (GO:0000988) 3.352SIX3, TGIF1
core promoter proximal region sequence-specific DNA binding (GO:0000987) 3.832TGIF1, GLI2
RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978) 3.882TGIF1, GLI2
chromatin binding (GO:0003682) 3.642ZIC2, GLI2
patched binding (GO:0005113) 7.662SHH, PTCH1
transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding (GO:0000982) 3.942TGIF1, GLI2

NET-GE enrichment

Term New enriched termICP valueGenes
sequence-specific DNA binding (GO:0043565) -2.790.002SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
structure-specific DNA binding (GO:0043566) NEW4.980.012SHH, ZIC2, GLI2, SIX3
hedgehog family protein binding (GO:0097108) NEW8.640.0SHH, PTCH1
transcription regulatory region DNA binding (GO:0044212) -3.030.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
sequence-specific DNA binding transcription factor activity (GO:0003700) -2.650.014SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulatory region nucleic acid binding (GO:0001067) -3.030.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
transcription factor binding (GO:0008134) NEW3.460.006SHH, TGIF1, ZIC2, GLI2, SIX3
RNA polymerase II regulatory region DNA binding (GO:0001012) -3.360.001SHH, TGIF1, ZIC2, GLI2, SIX3
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705) NEW5.230.018SHH, SIX3, ZIC2
RNA polymerase II transcription factor binding transcription factor activity (GO:0001076) NEW4.840.027SHH, SIX3, TGIF1
transcription regulatory region sequence-specific DNA binding (GO:0000976) -3.240.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
nucleic acid binding transcription factor activity (GO:0001071) -2.650.014SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulatory region DNA binding (GO:0000975) -3.030.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
chromatin binding (GO:0003682) -3.640.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
patched binding (GO:0005113) -7.660.001SHH, PTCH1
sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981) -3.290.004SHH, TGIF1, ZIC2, GLI2, SIX3
RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977) -3.370.001SHH, TGIF1, ZIC2, GLI2, SIX3
GO - biological process annotation: shared terms / NET-GE enrichment

Shared terms

GOICNumber of genes with the same GOGenes
developmental process (GO:0032502) 1.368CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of primary metabolic process (GO:0080090) 1.088CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of metabolic process (GO:0019222) 1.028CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of macromolecule metabolic process (GO:0060255) 1.088CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of gene expression (GO:0010468) 1.378CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
cellular process (GO:0009987) 0.268CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of cellular metabolic process (GO:0031323) 1.078CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of cellular process (GO:0050794) 0.58CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
single-organism developmental process (GO:0044767) 1.498CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
biological regulation (GO:0065007) 0.398CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of biological process (GO:0050789) 0.458CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
single-organism process (GO:0044699) 0.488CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
multicellular organismal process (GO:0032501) 1.457CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of metabolic process (GO:0009892) 1.937SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
single-multicellular organism process (GO:0044707) 1.787CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of nucleobase-containing compound metabolic process (GO:0019219) 1.437CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of biosynthetic process (GO:0009889) 1.377CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
anatomical structure development (GO:0048856) 1.587CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of cellular macromolecule biosynthetic process (GO:2000112) 1.467CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of nucleic acid-templated transcription (GO:1903506) 1.557CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of macromolecule metabolic process (GO:0010605) 2.017SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of cellular biosynthetic process (GO:0031326) 1.387CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of transcription, DNA-templated (GO:0006355) 1.567CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of gene expression (GO:0010629) 2.487SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of macromolecule biosynthetic process (GO:0010556) 1.437CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
single-organism cellular process (GO:0044763) 0.657CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH
cellular developmental process (GO:0048869) 1.827CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH
regulation of RNA biosynthetic process (GO:2001141) 1.557CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of biological process (GO:0048519) 1.337SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
negative regulation of cellular metabolic process (GO:0031324) 2.017SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of RNA metabolic process (GO:0051252) 1.527CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of cellular process (GO:0048523) 1.417SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of nitrogen compound metabolic process (GO:0051171) 1.367CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of metabolic process (GO:0009893) 1.746CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
negative regulation of biosynthetic process (GO:0009890) 2.476SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of biosynthetic process (GO:0009891) 2.296CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
negative regulation of cellular biosynthetic process (GO:0031327) 2.496SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of cellular metabolic process (GO:0031325) 1.816CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
cell differentiation (GO:0030154) 2.146CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
regulation of response to stimulus (GO:0048583) 1.546CDON, SIX3, PTCH1, GAS1, GLI2, SHH
metabolic process (GO:0008152) 0.586SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of gene expression (GO:0010628) 2.356CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
regulation of signaling (GO:0023051) 1.726CDON, SIX3, PTCH1, GAS1, GLI2, SHH
regulation of cell communication (GO:0010646) 1.736CDON, SIX3, PTCH1, GAS1, GLI2, SHH
multicellular organism development (GO:0007275) 2.546SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of macromolecule metabolic process (GO:0010604) 1.816CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
regulation of signal transduction (GO:0009966) 1.846CDON, SIX3, PTCH1, GAS1, GLI2, SHH
positive regulation of cellular biosynthetic process (GO:0031328) 2.36CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
negative regulation of cellular macromolecule biosynthetic process (GO:2000113) 2.66SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
organic substance metabolic process (GO:0071704) 0.636SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of biological process (GO:0048518) 1.26CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
positive regulation of nucleic acid-templated transcription (GO:1903508) 2.566CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
positive regulation of nucleobase-containing compound metabolic process (GO:0045935) 2.356CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
negative regulation of nucleobase-containing compound metabolic process (GO:0045934) 2.556SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of nucleic acid-templated transcription (GO:1903507) 2.716SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of RNA biosynthetic process (GO:1902679) 2.76SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of transcription, DNA-templated (GO:0045892) 2.756SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of transcription, DNA-templated (GO:0045893) 2.566CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
negative regulation of nitrogen compound metabolic process (GO:0051172) 2.476SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of nitrogen compound metabolic process (GO:0051173) 2.296CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
primary metabolic process (GO:0044238) 0.696SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of RNA metabolic process (GO:0051253) 2.666SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of RNA metabolic process (GO:0051254) 2.516CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
macromolecule metabolic process (GO:0043170) 0.836SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of RNA biosynthetic process (GO:1902680) 2.546CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
positive regulation of macromolecule biosynthetic process (GO:0010557) 2.396CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
regulation of transcription from RNA polymerase II promoter (GO:0006357) 2.246CDON, SIX3, PTCH1, GLI2, SHH, TGIF1
negative regulation of macromolecule biosynthetic process (GO:0010558) 2.536SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of cellular process (GO:0048522) 1.36CDON, SIX3, PTCH1, ZIC2, GLI2, SHH
embryonic morphogenesis (GO:0048598) 3.725SHH, PTCH1, CDON, GLI2, SIX3
regulation of cell proliferation (GO:0042127) 2.415SHH, PTCH1, CDON, GLI2, SIX3
cellular response to stimulus (GO:0051716) 1.975SHH, PTCH1, TGIF1, GAS1, GLI2
cellular response to chemical stimulus (GO:0070887) 2.575SHH, TGIF1, PTCH1, GAS1, GLI2
pattern specification process (GO:0007389) 3.795SHH, PTCH1, CDON, GLI2, SIX3
regulation of developmental process (GO:0050793) 2.15SHH, PTCH1, CDON, GLI2, SIX3
response to stimulus (GO:0050896) 1.225SHH, TGIF1, PTCH1, GAS1, GLI2
cellular metabolic process (GO:0044237) 0.695SHH, TGIF1, ZIC2, GLI2, SIX3
regulation of cell differentiation (GO:0045595) 2.425SHH, PTCH1, CDON, GLI2, SIX3
animal organ development (GO:0048513) 2.535SHH, PTCH1, ZIC2, GLI2, SIX3
regulation of multicellular organismal development (GO:2000026) 2.315SHH, PTCH1, CDON, GLI2, SIX3
regionalization (GO:0003002) 4.245SHH, PTCH1, CDON, GLI2, SIX3
regulation of multicellular organismal process (GO:0051239) 1.875SHH, PTCH1, CDON, GLI2, SIX3
response to chemical (GO:0042221) 1.985SHH, TGIF1, PTCH1, GLI2, GAS1
anatomical structure morphogenesis (GO:0009653) 2.535SHH, PTCH1, CDON, GLI2, SIX3
regulation of smoothened signaling pathway (GO:0008589) 5.624SHH, PTCH1, GLI2, GAS1
RNA biosynthetic process (GO:0032774) 1.844TGIF1, ZIC2, GLI2, SIX3
nucleobase-containing compound metabolic process (GO:0006139) 1.354TGIF1, ZIC2, GLI2, SIX3
nucleic acid metabolic process (GO:0090304) 1.464TGIF1, ZIC2, GLI2, SIX3
cellular biosynthetic process (GO:0044249) 1.374TGIF1, ZIC2, GLI2, SIX3
cellular nitrogen compound metabolic process (GO:0034641) 1.224TGIF1, ZIC2, GLI2, SIX3
nitrogen compound metabolic process (GO:0006807) 1.134TGIF1, ZIC2, GLI2, SIX3
signal transduction (GO:0007165) 1.284SHH, PTCH1, CDON, GLI2
cell surface receptor signaling pathway (GO:0007166) 2.094SHH, PTCH1, CDON, GLI2
organic substance biosynthetic process (GO:1901576) 1.344TGIF1, ZIC2, GLI2, SIX3
organic cyclic compound biosynthetic process (GO:1901362) 1.664TGIF1, ZIC2, GLI2, SIX3
organic cyclic compound metabolic process (GO:1901360) 1.264TGIF1, ZIC2, GLI2, SIX3
regulation of neurogenesis (GO:0050767) 3.214SHH, CDON, GLI2, SIX3
cellular macromolecule metabolic process (GO:0044260) 0.934TGIF1, ZIC2, GLI2, SIX3
negative regulation of transcription from RNA polymerase II promoter (GO:0000122) 3.124SHH, PTCH1, TGIF1, GLI2
negative regulation of multicellular organismal process (GO:0051241) 2.844SHH, PTCH1, SIX3, GLI2
regulation of cell development (GO:0060284) 3.014SHH, CDON, GLI2, SIX3
regulation of neuron differentiation (GO:0045664) 3.394SHH, CDON, GLI2, SIX3
cellular response to organic substance (GO:0071310) 2.784TGIF1, PTCH1, GAS1, GLI2
nucleic acid-templated transcription (GO:0097659) 1.914TGIF1, ZIC2, GLI2, SIX3
tissue morphogenesis (GO:0048729) 3.874SHH, PTCH1, SIX3, GLI2
regulation of molecular function (GO:0065009) 1.784SHH, PTCH1, ZIC2, CDON
anatomical structure formation involved in morphogenesis (GO:0048646) 3.014SHH, PTCH1, CDON, GLI2
heterocycle biosynthetic process (GO:0018130) 1.74TGIF1, ZIC2, GLI2, SIX3
negative regulation of developmental process (GO:0051093) 3.174SHH, PTCH1, SIX3, GLI2
cell proliferation (GO:0008283) 3.234SHH, PTCH1, SIX3, GLI2
cellular aromatic compound metabolic process (GO:0006725) 1.34TGIF1, ZIC2, GLI2, SIX3
cellular macromolecule biosynthetic process (GO:0034645) 1.664TGIF1, ZIC2, GLI2, SIX3
negative regulation of cell differentiation (GO:0045596) 3.334SHH, PTCH1, SIX3, GLI2
biosynthetic process (GO:0009058) 1.324TGIF1, ZIC2, GLI2, SIX3
macromolecule biosynthetic process (GO:0009059) 1.614TGIF1, ZIC2, GLI2, SIX3
aromatic compound biosynthetic process (GO:0019438) 1.74TGIF1, ZIC2, GLI2, SIX3
nucleobase-containing compound biosynthetic process (GO:0034654) 1.724TGIF1, ZIC2, GLI2, SIX3
cellular nitrogen compound biosynthetic process (GO:0044271) 1.594TGIF1, ZIC2, GLI2, SIX3
response to organic substance (GO:0010033) 2.24TGIF1, PTCH1, GLI2, GAS1
heterocycle metabolic process (GO:0046483) 1.314TGIF1, ZIC2, GLI2, SIX3
RNA metabolic process (GO:0016070) 1.594TGIF1, ZIC2, GLI2, SIX3
positive regulation of cell differentiation (GO:0045597) 3.014SHH, PTCH1, CDON, GLI2
dorsal/ventral pattern formation (GO:0009953) 5.64SHH, PTCH1, SIX3, GLI2
anterior/posterior pattern specification (GO:0009952) 4.714SHH, CDON, GLI2, SIX3
smoothened signaling pathway (GO:0007224) 5.454SHH, PTCH1, CDON, GLI2
positive regulation of developmental process (GO:0051094) 2.774SHH, PTCH1, CDON, GLI2
regulation of nervous system development (GO:0051960) 3.14SHH, CDON, GLI2, SIX3
positive regulation of transcription from RNA polymerase II promoter (GO:0045944) 2.814SHH, CDON, GLI2, SIX3
transcription, DNA-templated (GO:0006351) 1.914TGIF1, ZIC2, GLI2, SIX3
system development (GO:0048731) 2.924SHH, PTCH1, ZIC2, GLI2
gland development (GO:0048732) 4.154SHH, PTCH1, SIX3, GLI2
protein localization (GO:0008104) 2.363SHH, PTCH1, SIX3
developmental growth (GO:0048589) 4.053SHH, GAS1, GLI2
cell differentiation in spinal cord (GO:0021515) 6.023SHH, PTCH1, GLI2
embryonic organ development (GO:0048568) 4.863SHH, PTCH1, GLI2
negative regulation of response to stimulus (GO:0048585) 2.523SHH, PTCH1, SIX3
spinal cord motor neuron differentiation (GO:0021522) 6.513SHH, PTCH1, GLI2
branching morphogenesis of an epithelial tube (GO:0048754) 4.933SHH, PTCH1, GLI2
movement of cell or subcellular component (GO:0006928) 2.613SHH, SIX3, GLI2
negative regulation of signaling (GO:0023057) 2.653SHH, PTCH1, SIX3
morphogenesis of a branching structure (GO:0001763) 4.713SHH, PTCH1, GLI2
negative regulation of cell communication (GO:0010648) 2.663SHH, PTCH1, SIX3
regulation of cell death (GO:0010941) 2.433SHH, GAS1, GLI2
regulation of apoptotic process (GO:0042981) 2.53SHH, GLI2, GAS1
cellular component organization or biogenesis (GO:0071840) 1.223SHH, PTCH1, GLI2
morphogenesis of an epithelium (GO:0002009) 4.083SHH, PTCH1, GLI2
regulation of localization (GO:0032879) 1.943SHH, PTCH1, GAS1
dorsal/ventral neural tube patterning (GO:0021904) 7.093SHH, PTCH1, GLI2
negative regulation of signal transduction (GO:0009968) 2.753SHH, PTCH1, SIX3
cellular macromolecule localization (GO:0070727) 3.13SHH, PTCH1, SIX3
positive regulation of multicellular organismal process (GO:0051240) 2.493SHH, CDON, GLI2
regulation of protein metabolic process (GO:0051246) 1.933SHH, CDON, GAS1
cellular component organization (GO:0016043) 1.243SHH, PTCH1, GLI2
positive regulation of neurogenesis (GO:0050769) 3.773SHH, CDON, GLI2
regulation of programmed cell death (GO:0043067) 2.493SHH, GLI2, GAS1
regulation of neural precursor cell proliferation (GO:2000177) 5.453SHH, SIX3, CDON
positive regulation of cell development (GO:0010720) 3.573SHH, CDON, GLI2
epithelial cell differentiation (GO:0030855) 3.983PTCH1, SIX3, GLI2
epithelial tube morphogenesis (GO:0060562) 5.123SHH, PTCH1, GLI2
macromolecule localization (GO:0033036) 2.343SHH, PTCH1, SIX3
central nervous system neuron differentiation (GO:0021953) 5.173SHH, PTCH1, GLI2
positive regulation of cell proliferation (GO:0008284) 3.013SHH, CDON, GLI2
organ morphogenesis (GO:0009887) 3.553SHH, PTCH1, GLI2
cellular protein localization (GO:0034613) 3.113SHH, PTCH1, SIX3
tube morphogenesis (GO:0035239) 4.353SHH, PTCH1, GLI2
neuron differentiation (GO:0030182) 4.173SHH, PTCH1, GLI2
morphogenesis of a branching epithelium (GO:0061138) 4.773SHH, PTCH1, GLI2
transport (GO:0006810) 1.513SHH, PTCH1, SIX3
tissue development (GO:0009888) 3.273SHH, PTCH1, GLI2
epithelium development (GO:0060429) 4.573SHH, PTCH1, GLI2
regulation of sequence-specific DNA binding transcription factor activity (GO:0051090) 3.833SHH, PTCH1, ZIC2
regulation of transport (GO:0051049) 2.243SHH, PTCH1, GAS1
growth (GO:0040007) 3.83SHH, GLI2, GAS1
establishment of localization (GO:0051234) 1.483SHH, PTCH1, SIX3
localization (GO:0051179) 1.43SHH, PTCH1, SIX3
cellular localization (GO:0051641) 2.323SHH, PTCH1, SIX3
regulation of cellular protein metabolic process (GO:0032268) 1.993SHH, CDON, GAS1
brain development (GO:0007420) 4.243PTCH1, SIX3, ZIC2
regulation of cell cycle (GO:0051726) 2.933PTCH1, SIX3, GAS1
positive regulation of nervous system development (GO:0051962) 3.643SHH, CDON, GLI2
embryo development (GO:0009790) 4.23SHH, PTCH1, GLI2
cell fate specification (GO:0001708) 5.573SHH, PTCH1, CDON
tube formation (GO:0035148) 4.982SHH, PTCH1
positive regulation of T cell differentiation in thymus (GO:0033089) 7.242SHH, GLI2
limb morphogenesis (GO:0035108) 5.052SHH, PTCH1
regulation of biological quality (GO:0065008) 1.682SHH, PTCH1
regulation of T cell differentiation in thymus (GO:0033081) 6.472SHH, GLI2
regulation of intracellular transport (GO:0032386) 3.582SHH, GAS1
positive regulation of response to stimulus (GO:0048584) 2.182SHH, CDON
appendage morphogenesis (GO:0035107) 5.052SHH, PTCH1
spinal cord dorsal/ventral patterning (GO:0021513) 8.122SHH, GLI2
skeletal system development (GO:0001501) 4.492SHH, GLI2
regulation of Wnt signaling pathway (GO:0030111) 3.982SHH, SIX3
cell surface receptor signaling pathway involved in cell-cell signaling (GO:1905114) 3.792SHH, GLI2
cell proliferation involved in kidney development (GO:0072111) 7.432SHH, PTCH1
neuron projection guidance (GO:0097485) 4.432SHH, GLI2
positive regulation of cell adhesion (GO:0045785) 3.792SHH, GLI2
positive regulation of signal transduction (GO:0009967) 2.52SHH, CDON
response to growth factor (GO:0070848) 4.142TGIF1, GAS1
response to mechanical stimulus (GO:0009612) 4.412PTCH1, GLI2
negative regulation of neuron differentiation (GO:0045665) 4.452SHH, SIX3
positive regulation of neuron differentiation (GO:0045666) 3.982CDON, GLI2
positive regulation of molecular function (GO:0044093) 2.232SHH, ZIC2
negative regulation of cell development (GO:0010721) 4.022SHH, SIX3
smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831) 7.782PTCH1, GLI2
regulation of striated muscle tissue development (GO:0016202) 5.092SHH, CDON
positive regulation of transport (GO:0051050) 2.92SHH, PTCH1
negative regulation of cell death (GO:0060548) 2.952SHH, GLI2
visual perception (GO:0007601) 4.412SIX3, ZIC2
sensory perception (GO:0007600) 2.932SIX3, ZIC2
establishment of protein localization (GO:0045184) 2.532PTCH1, SIX3
developmental process involved in reproduction (GO:0003006) 3.362SHH, GLI2
positive regulation of hemopoiesis (GO:1903708) 4.632SHH, GLI2
regulation of proteolysis (GO:0030162) 3.22SHH, GAS1
regulation of epithelial cell proliferation (GO:0050678) 4.062SHH, PTCH1
response to inorganic substance (GO:0010035) 3.562SHH, PTCH1
regulation of hemopoiesis (GO:1903706) 4.02SHH, GLI2
regulation of cholesterol efflux (GO:0010874) 6.732SHH, PTCH1
system process (GO:0003008) 2.32SIX3, ZIC2
hindgut morphogenesis (GO:0007442) 8.342SHH, GLI2
single organism reproductive process (GO:0044702) 2.732SHH, GLI2
response to external stimulus (GO:0009605) 2.552PTCH1, GLI2
cell motility (GO:0048870) 3.022SHH, SIX3
protein metabolic process (GO:0019538) 1.452SHH, PTCH1
kidney development (GO:0001822) 4.792SHH, GLI2
organ formation (GO:0048645) 6.732SHH, GLI2
cell development (GO:0048468) 3.282SHH, GLI2
muscle cell differentiation (GO:0042692) 5.092SHH, CDON
osteoblast development (GO:0002076) 6.842SHH, GLI2
positive regulation of striated muscle tissue development (GO:0045844) 5.692SHH, CDON
axis specification (GO:0009798) 5.422PTCH1, SIX3
epithelial cell proliferation (GO:0050673) 5.212SHH, PTCH1
negative regulation of Wnt signaling pathway (GO:0030178) 4.442SHH, SIX3
regulation of mitotic cell cycle (GO:0007346) 3.712PTCH1, GAS1
regulation of thymocyte aggregation (GO:2000398) 6.472SHH, GLI2
intracellular protein transport (GO:0006886) 3.22PTCH1, SIX3
positive regulation of thymocyte aggregation (GO:2000400) 7.242SHH, GLI2
positive regulation of immune system process (GO:0002684) 2.962SHH, GLI2
smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938) 8.342SHH, GLI2
regulation of immune system process (GO:0002682) 2.52SHH, GLI2
transcription from RNA polymerase II promoter (GO:0006366) 3.382SIX3, GLI2
regulation of skeletal muscle tissue development (GO:0048641) 5.782SHH, CDON
cell migration (GO:0016477) 3.122SHH, SIX3
mammary gland development (GO:0030879) 6.292PTCH1, GLI2
regulation of muscle tissue development (GO:1901861) 5.072SHH, CDON
positive regulation of muscle tissue development (GO:1901863) 5.672SHH, CDON
embryonic pattern specification (GO:0009880) 5.82SHH, PTCH1
sensory perception of light stimulus (GO:0050953) 4.42SIX3, ZIC2
in utero embryonic development (GO:0001701) 4.42PTCH1, GLI2
mammary gland duct morphogenesis (GO:0060603) 7.942PTCH1, GLI2
sensory organ development (GO:0007423) 4.822SHH, SIX3
cell fate commitment (GO:0045165) 4.722SHH, GAS1
protein processing (GO:0016485) 4.622SHH, PTCH1
regulation of lipid transport (GO:0032368) 5.212SHH, PTCH1
regulation of leukocyte activation (GO:0002694) 3.62SHH, GLI2
negative regulation of nervous system development (GO:0051961) 4.152SHH, SIX3
positive regulation of leukocyte activation (GO:0002696) 4.02SHH, GLI2
camera-type eye development (GO:0043010) 5.362SHH, SIX3
negative regulation of cellular protein metabolic process (GO:0032269) 2.882SHH, GAS1
regulation of cell adhesion (GO:0030155) 3.272SHH, GLI2
establishment of localization in cell (GO:0051649) 2.472PTCH1, SIX3
regulation of muscle organ development (GO:0048634) 5.072SHH, CDON
positive regulation of muscle organ development (GO:0048636) 5.692SHH, CDON
ventral midline development (GO:0007418) 8.632SHH, GLI2
positive regulation of T cell differentiation (GO:0045582) 5.522SHH, GLI2
embryo development ending in birth or egg hatching (GO:0009792) 4.352PTCH1, GLI2
axon guidance (GO:0007411) 4.442SHH, GLI2
positive regulation of cell communication (GO:0010647) 2.412SHH, CDON
response to organic cyclic compound (GO:0014070) 3.072PTCH1, GLI2
regulation of protein localization (GO:0032880) 2.882SHH, PTCH1
negative regulation of protein metabolic process (GO:0051248) 2.822SHH, GAS1
regulation of lymphocyte activation (GO:0051249) 3.732SHH, GLI2
embryonic limb morphogenesis (GO:0030326) 5.242SHH, PTCH1
regulation of cholesterol transport (GO:0032374) 6.092SHH, PTCH1
regulation of sterol transport (GO:0032371) 6.092SHH, PTCH1
negative regulation of neurogenesis (GO:0050768) 4.222SHH, SIX3
positive regulation of leukocyte cell-cell adhesion (GO:1903039) 4.352SHH, GLI2
positive regulation of lymphocyte differentiation (GO:0045621) 5.352SHH, GLI2
proteolysis (GO:0006508) 2.732SHH, PTCH1
chordate embryonic development (GO:0043009) 4.382PTCH1, GLI2
biological adhesion (GO:0022610) 2.812SHH, CDON
regulation of stem cell proliferation (GO:0072091) 5.62SHH, SIX3
regulation of leukocyte cell-cell adhesion (GO:1903037) 4.012SHH, GLI2
negative regulation of cell proliferation (GO:0008285) 3.262SHH, PTCH1
positive regulation of signaling (GO:0023056) 2.412SHH, CDON
heart development (GO:0007507) 4.242SHH, GLI2
neurological system process (GO:0050877) 2.642SIX3, ZIC2
positive regulation of T cell activation (GO:0050870) 4.392SHH, GLI2
prostate gland epithelium morphogenesis (GO:0060740) 6.732SHH, GLI2
eye development (GO:0001654) 5.072SHH, SIX3
positive regulation of skeletal muscle tissue development (GO:0048643) 6.432SHH, CDON
branching involved in ureteric bud morphogenesis (GO:0001658) 5.972SHH, PTCH1
renal system development (GO:0072001) 6.732SHH, PTCH1
embryonic digit morphogenesis (GO:0042733) 5.692SHH, GLI2
somite development (GO:0061053) 7.022SHH, PTCH1
positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091) 4.292SHH, ZIC2
cellular response to growth factor stimulus (GO:0071363) 4.272TGIF1, GAS1
protein maturation (GO:0051604) 4.482SHH, PTCH1
regulation of cell-cell adhesion (GO:0022407) 3.792SHH, GLI2
positive regulation of lymphocyte activation (GO:0051251) 4.072SHH, GLI2
cellular response to organic cyclic compound (GO:0071407) 3.932PTCH1, GLI2
response to drug (GO:0042493) 3.712PTCH1, TGIF1
positive regulation of neural precursor cell proliferation (GO:2000179) 6.092SHH, CDON
regulation of lymphocyte differentiation (GO:0045619) 4.842SHH, GLI2
protein localization to organelle (GO:0033365) 3.572SHH, SIX3
negative regulation of proteolysis (GO:0045861) 3.982SHH, GAS1
protein localization to nucleus (GO:0034504) 4.92SHH, SIX3
lung development (GO:0030324) 5.132SHH, GLI2
regulation of cellular localization (GO:0060341) 3.032SHH, GAS1
regulation of cell activation (GO:0050865) 3.532SHH, GLI2
positive regulation of cell activation (GO:0050867) 3.972SHH, GLI2
regulation of T cell activation (GO:0050863) 4.052SHH, GLI2
positive regulation of muscle cell differentiation (GO:0051149) 5.262SHH, CDON
regulation of muscle cell differentiation (GO:0051147) 4.682SHH, CDON
striated muscle cell differentiation (GO:0051146) 5.692SHH, CDON
lens development in camera-type eye (GO:0002088) 6.092SIX3, CDON
pituitary gland development (GO:0021983) 6.332SIX3, GLI2
regulation of cell division (GO:0051302) 4.882SHH, PTCH1
positive regulation of cell-cell adhesion (GO:0022409) 4.232SHH, GLI2
cell proliferation involved in metanephros development (GO:0072203) 7.782SHH, PTCH1
intracellular transport (GO:0046907) 2.672PTCH1, SIX3
negative regulation of apoptotic process (GO:0043066) 3.042SHH, GLI2
regulation of neuroblast proliferation (GO:1902692) 6.362SHH, SIX3
neural precursor cell proliferation (GO:0061351) 5.72SHH, SIX3
organic substance transport (GO:0071702) 2.152PTCH1, SIX3
negative regulation of programmed cell death (GO:0043069) 3.022SHH, GLI2
telencephalon regionalization (GO:0021978) 7.782SHH, SIX3
regulation of T cell differentiation (GO:0045580) 5.072SHH, GLI2
reproductive process (GO:0022414) 2.552SHH, GLI2
single-organism transport (GO:0044765) 2.182PTCH1, SIX3
embryonic appendage morphogenesis (GO:0035113) 5.242SHH, PTCH1
cell adhesion (GO:0007155) 2.822SHH, CDON
tube development (GO:0035295) 4.412SHH, GLI2
single-organism localization (GO:1902578) 2.092PTCH1, SIX3
locomotion (GO:0040011) 2.912SHH, SIX3
response to abiotic stimulus (GO:0009628) 2.82PTCH1, GLI2
odontogenesis of dentin-containing tooth (GO:0042475) 5.522SHH, GLI2
odontogenesis (GO:0042476) 5.192SHH, GLI2
positive regulation of leukocyte differentiation (GO:1902107) 4.852SHH, GLI2
regulation of leukocyte differentiation (GO:1902105) 4.262SHH, GLI2
hindbrain development (GO:0030902) 6.732SHH, GLI2
protein transport (GO:0015031) 2.622PTCH1, SIX3
single-organism intracellular transport (GO:1902582) 3.592PTCH1, SIX3
single-organism cellular localization (GO:1902580) 3.162PTCH1, SIX3
hindlimb morphogenesis (GO:0035137) 6.122SHH, PTCH1

NET-GE enrichment

Term New enriched termICP valueGenes
positive regulation of T cell differentiation in thymus (GO:0033089) -7.240.042SHH, GLI2
regulation of smoothened signaling pathway (GO:0008589) -5.620.0SHH, PTCH1, CDON, GAS1, GLI2
developmental growth (GO:0048589) -4.050.027SHH, GAS1, GLI2
regulation of T cell differentiation in thymus (GO:0033081) -6.470.029SHH, GLI2
negative regulation of response to stimulus (GO:0048585) -2.520.025SHH, PTCH1, TGIF1, GAS1, SIX3
regulation of response to stimulus (GO:0048583) -1.540.021CDON, SIX3, PTCH1, GAS1, GLI2, SHH, TGIF1
spinal cord dorsal/ventral patterning (GO:0021513) -8.120.003SHH, GLI2
skeletal system development (GO:0001501) -4.490.0SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH
cell proliferation involved in kidney development (GO:0072111) -7.430.007SHH, PTCH1
neuron projection guidance (GO:0097485) -4.430.0CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH
negative regulation of macromolecule metabolic process (GO:0010605) -2.010.0SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
negative regulation of signal transduction (GO:0009968) -2.750.01CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of signal transduction (GO:0009966) -1.840.002CDON, SIX3, PTCH1, GAS1, GLI2, SHH, TGIF1
determination of left/right symmetry (GO:0007368) NEW5.380.046SHH, SIX3, TGIF1
regulation of chondrocyte differentiation (GO:0032330) NEW5.920.02SHH, PTCH1, GLI2
positive regulation of neuron differentiation (GO:0045666) -3.980.005SHH, TGIF1, CDON, GLI2
positive regulation of biological process (GO:0048518) -1.20.009CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of striated muscle tissue development (GO:0016202) -5.090.022SHH, PTCH1, CDON, GLI2
spinal cord motor neuron differentiation (GO:0021522) -6.510.032SHH, PTCH1
regulation of macromolecule metabolic process (GO:0060255) -1.080.036CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
forebrain dorsal/ventral pattern formation (GO:0021798) NEW7.780.021SHH, SIX3
regionalization (GO:0003002) -4.240.0CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
regulation of RNA biosynthetic process (GO:2001141) -1.550.05CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of muscle organ development (GO:0048636) -5.690.008SHH, CDON
regulation of cholesterol efflux (GO:0010874) -6.730.022SHH, PTCH1
hindgut morphogenesis (GO:0007442) -8.340.002SHH, GLI2
single-multicellular organism process (GO:0044707) -1.780.0CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
anterior/posterior pattern specification (GO:0009952) -4.710.001SHH, TGIF1, ZIC2, CDON, SIX3
osteoblast development (GO:0002076) -6.840.022SHH, GLI2
embryonic organ morphogenesis (GO:0048562) NEW4.920.029SHH, PTCH1, GLI2, GAS1
negative regulation of metabolic process (GO:0009892) -1.930.0SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
positive regulation of striated muscle tissue development (GO:0045844) -5.690.008SHH, CDON
negative regulation of biosynthetic process (GO:0009890) -2.470.001SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of signaling (GO:0023051) -1.720.004CDON, SIX3, PTCH1, GAS1, GLI2, SHH, TGIF1
positive regulation of muscle tissue development (GO:1901863) -5.670.01SHH, CDON
negative regulation of gene expression (GO:0010629) -2.480.001SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
morphogenesis of a branching structure (GO:0001763) -4.710.032SHH, PTCH1, GLI2
axis specification (GO:0009798) -5.420.0SHH, PTCH1, ZIC2, GLI2, SIX3
developmental induction (GO:0031128) NEW6.590.003SHH, SIX3, GLI2
smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938) -8.340.002SHH, GLI2
smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831) -7.780.003PTCH1, GLI2
neural tube closure (GO:0001843) NEW5.380.003SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of skeletal muscle tissue development (GO:0048643) -6.430.006SHH, CDON
organ formation (GO:0048645) -6.730.019SHH, GLI2
anatomical structure formation involved in morphogenesis (GO:0048646) -3.010.013CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of muscle tissue development (GO:1901861) -5.070.023SHH, PTCH1, CDON, GLI2
organ morphogenesis (GO:0009887) -3.550.012CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH
negative regulation of smoothened signaling pathway (GO:0045879) NEW6.550.048SHH, PTCH1, GAS1, GLI2
tube closure (GO:0060606) NEW5.360.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
pattern specification process (GO:0007389) -3.790.0CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
mammary gland duct morphogenesis (GO:0060603) -7.940.002PTCH1, GLI2
embryonic digit morphogenesis (GO:0042733) -5.690.025SHH, GLI2, GAS1
cell fate commitment (GO:0045165) -4.720.03SHH, PTCH1, ZIC2, GAS1
dorsal/ventral pattern formation (GO:0009953) -5.60.0SIX3, PTCH1, GAS1, GLI2, SHH, TGIF1
brain development (GO:0007420) -4.240.04SHH, PTCH1, ZIC2, GLI2, SIX3
sensory organ development (GO:0007423) -4.820.007SHH, SIX3, GAS1
smoothened signaling pathway (GO:0007224) -5.450.001SHH, PTCH1, CDON, GLI2
cell-cell signaling involved in cell fate commitment (GO:0045168) NEW9.040.003SHH, SIX3, GLI2
positive regulation of mesenchymal cell proliferation (GO:0002053) NEW6.40.014SHH, PTCH1, GAS1
regulation of transcription, DNA-templated (GO:0006355) -1.560.046CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of transcription from RNA polymerase II promoter (GO:0006357) -2.240.006CDON, SIX3, PTCH1, GLI2, SHH, TGIF1
single-organism developmental process (GO:0044767) -1.490.005CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
negative regulation of macromolecule biosynthetic process (GO:0010558) -2.530.001SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of muscle organ development (GO:0048634) -5.070.025SHH, PTCH1, CDON, GLI2
tube formation (GO:0035148) -4.980.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
ventral midline development (GO:0007418) -8.630.0SHH, GLI2
negative regulation of signaling (GO:0023057) -2.650.001CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
negative regulation of cell communication (GO:0010648) -2.660.013CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
epithelial cell morphogenesis (GO:0003382) NEW6.040.022SHH, PTCH1, GLI2
neuroendocrine cell differentiation (GO:0061101) NEW7.650.029SHH, GLI2
specification of symmetry (GO:0009799) NEW5.360.048SHH, SIX3, TGIF1
axon guidance (GO:0007411) -4.440.0CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH
regulation of cell communication (GO:0010646) -1.730.005CDON, SIX3, PTCH1, GAS1, GLI2, SHH, TGIF1
regulation of neurogenesis (GO:0050767) -3.210.028SHH, TGIF1, CDON, GLI2
organ development (GO:0048513) -2.530.001SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH
epithelial tube morphogenesis (GO:0060562) -5.120.005SHH, PTCH1, CDON, GLI2
regulation of stem cell proliferation (GO:0072091) -5.60.006SHH, PTCH1, CDON, GAS1
developmental process (GO:0032502) -1.360.01CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
multicellular organismal process (GO:0032501) -1.450.001CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
tube morphogenesis (GO:0035239) -4.350.007SHH, PTCH1, CDON, GLI2
neurological system process (GO:0050877) -2.640.01CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
prostate gland epithelium morphogenesis (GO:0060740) -6.730.038SHH, GLI2
eye development (GO:0001654) -5.070.003SHH, SIX3, GAS1
hindlimb morphogenesis (GO:0035137) -6.120.018SHH, PTCH1, GLI2
branching involved in ureteric bud morphogenesis (GO:0001658) -5.970.027SHH, PTCH1, GLI2
renal system development (GO:0072001) -6.730.01SHH, PTCH1
somite development (GO:0061053) -7.020.005SHH, PTCH1
regulation of sequence-specific DNA binding transcription factor activity (GO:0051090) -3.830.048SHH, TGIF1, PTCH1, ZIC2, GLI2
response to chlorate (GO:0010157) NEW9.040.002SHH, PTCH1
negative regulation of RNA metabolic process (GO:0051253) -2.660.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
positive regulation of RNA metabolic process (GO:0051254) -2.510.049SHH, ZIC2, CDON, GLI2, SIX3
positive regulation of RNA biosynthetic process (GO:1902680) -2.540.045SHH, ZIC2, CDON, GLI2, SIX3
spinal cord ventral commissure morphogenesis (GO:0021965) NEW9.040.001PTCH1, GLI2
system development (GO:0048731) -2.920.011CDON, SIX3, PTCH1, GAS1, GLI2, SHH, TGIF1
prostatic bud formation (GO:0060513) NEW8.340.006SHH, GLI2
dorsal/ventral neural tube patterning (GO:0021904) -7.090.013SHH, GAS1
negative regulation of cellular biosynthetic process (GO:0031327) -2.490.001SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of cellular metabolic process (GO:0031324) -2.010.009SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
branching morphogenesis of an epithelial tube (GO:0048754) -4.930.018SHH, PTCH1, GLI2
positive regulation of smoothened signaling pathway (GO:0045880) NEW6.550.0GAS1, SHH, PTCH1, CDON, GLI2
positive regulation of muscle cell differentiation (GO:0051149) -5.260.045SHH, PTCH1, CDON
morphogenesis of an epithelium (GO:0002009) -4.080.037SHH, ZIC2, PTCH1, CDON, GLI2
cell proliferation involved in metanephros development (GO:0072203) -7.780.021SHH, PTCH1
negative regulation of cellular macromolecule biosynthetic process (GO:2000113) -2.60.001SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
regulation of mesenchymal cell proliferation (GO:0010464) NEW6.170.023SHH, PTCH1, GAS1
regulation of nervous system development (GO:0051960) -3.10.044SHH, TGIF1, CDON, GLI2
regulation of gene expression (GO:0010468) -1.370.005CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
embryonic morphogenesis (GO:0048598) -3.720.0CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
negative regulation of nucleobase-containing compound metabolic process (GO:0045934) -2.550.001SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
morphogenesis of a branching epithelium (GO:0061138) -4.770.027SHH, PTCH1, GLI2
negative regulation of RNA biosynthetic process (GO:1902679) -2.70.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of nitrogen compound metabolic process (GO:0051172) -2.470.001SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
cell communication (GO:0007154) NEW3.040.014CDON, SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
middle ear morphogenesis (GO:0042474) NEW6.730.003SHH, SIX3, GAS1
odontogenesis (GO:0042476) -5.190.006GAS1, SHH, CDON, GLI2
regulation of neural precursor cell proliferation (GO:2000177) -5.450.003SHH, ZIC2, CDON, GLI2
anatomical structure development (GO:0048856) -1.580.0CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
hindbrain development (GO:0030902) -6.730.017SHH, GLI2
determination of bilateral symmetry (GO:0009855) NEW5.370.047SHH, SIX3, TGIF1
negative regulation of transcription, DNA-templated (GO:0045892) -2.750.0SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
negative regulation of cellular process (GO:0048523) -1.410.037SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
positive regulation of transcription, DNA-templated (GO:0045893) -2.560.038SHH, ZIC2, CDON, GLI2, SIX3
GO - cellular component annotation: shared terms / NET-GE enrichment

Shared terms

GOICNumber of genes with the same GOGenes
cell part (GO:0044464) 0.118CDON, SIX3, PTCH1, GAS1, ZIC2, GLI2, SHH, TGIF1
intracellular part (GO:0044424) 0.286SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
intracellular organelle (GO:0043229) 0.515TGIF1, PTCH1, ZIC2, GLI2, SIX3
membrane (GO:0016020) 0.685GAS1, SHH, PTCH1, CDON, GLI2
membrane-bounded organelle (GO:0043227) 0.475TGIF1, PTCH1, ZIC2, GLI2, SIX3
organelle (GO:0043226) 0.45TGIF1, PTCH1, ZIC2, GLI2, SIX3
intracellular membrane-bounded organelle (GO:0043231) 0.65TGIF1, PTCH1, ZIC2, GLI2, SIX3
intracellular organelle part (GO:0044446) 0.814SHH, PTCH1, TGIF1, GLI2
membrane part (GO:0044425) 0.954SHH, PTCH1, CDON, GAS1
nucleus (GO:0005634) 1.074TGIF1, ZIC2, GLI2, SIX3
organelle part (GO:0044422) 0.794SHH, PTCH1, TGIF1, GLI2
plasma membrane (GO:0005886) 1.394SHH, PTCH1, CDON, GAS1
integral component of membrane (GO:0016021) 1.143PTCH1, CDON, GAS1
plasma membrane part (GO:0044459) 1.953PTCH1, CDON, GAS1
cytoplasmic part (GO:0044444) 0.823SHH, PTCH1, GLI2
intrinsic component of membrane (GO:0031224) 1.133PTCH1, CDON, GAS1
cytoplasm (GO:0005737) 1.012ZIC2, GLI2
membrane region (GO:0098589) 3.952SHH, PTCH1
cytosol (GO:0005829) 1.682SHH, GLI2
cell surface (GO:0009986) 3.442SHH, CDON
cell projection part (GO:0044463) 2.972PTCH1, GLI2
membrane microdomain (GO:0098857) 4.172SHH, PTCH1
extracellular matrix (GO:0031012) 3.812SHH, CDON
nucleoplasm (GO:0005654) 1.892TGIF1, GLI2
primary cilium (GO:0072372) 4.642PTCH1, GLI2
nuclear part (GO:0044428) 1.552TGIF1, GLI2
cilium (GO:0005929) 3.892PTCH1, GLI2
ciliary part (GO:0044441) 4.052PTCH1, GLI2
cell projection (GO:0042995) 2.472PTCH1, GLI2
intrinsic component of plasma membrane (GO:0031226) 2.532CDON, GAS1
extracellular region part (GO:0044421) 1.572SHH, CDON
membrane raft (GO:0045121) 4.182SHH, PTCH1

NET-GE enrichment

Term New enriched termICP valueGenes
primary cilium (GO:0072372) -4.640.038PTCH1, GLI2
proteinaceous extracellular matrix (GO:0005578) NEW4.010.015SHH, PTCH1, CDON, GLI2
extracellular matrix (GO:0031012) -3.810.035SHH, PTCH1, CDON, GLI2