Gene Page: SHH

Summary ?
GeneID6469
SymbolSHH
SynonymsHHG1|HLP3|HPE3|MCOPCB5|SMMCI|TPT|TPTPS
Descriptionsonic hedgehog
ReferenceMIM:600725|HGNC:HGNC:10848|HPRD:02838|
Gene typeprotein-coding
Map location7q36
Pascal p-value0.502
Fetal beta-0.021
DMG3 (# studies)
eGenePutamen basal ganglia
Meta

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 3
DMG:Nishioka_2013Genome-wide DNA methylation analysisThe authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. 3
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 3
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 8 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg117429097155601876SHH5.047E-4-0.3240.047DMG:Wockner_2014
cg005774647155604780SHH-0.0260.93DMG:Nishioka_2013
cg058204487155605094SHH1.24E-8-0.0185.03E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs127196647154998349SHHENSG00000164690.31.61749E-60.04606618gtex_brain_putamen_basal
rs49605807154998951SHHENSG00000164690.31.27595E-60.04606016gtex_brain_putamen_basal
rs49605817154998952SHHENSG00000164690.31.27415E-60.04606015gtex_brain_putamen_basal

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
KIAA14680.870.89
INPP5F0.870.89
PCYOX10.860.90
KIAA03170.860.90
MAPRE20.860.90
UBE2Z0.860.89
UGCG0.850.88
RTN40.850.88
RABGEF10.850.87
CLASP20.850.88
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.31-0.69-0.71
MT-CO2-0.68-0.71
FXYD1-0.68-0.68
AF347015.21-0.67-0.71
AF347015.8-0.67-0.70
AF347015.33-0.67-0.67
AF347015.2-0.66-0.68
MT-CYB-0.65-0.67
AC021016.1-0.65-0.69
AF347015.27-0.65-0.67

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005113patched bindingIEA-
GO:0005515protein bindingISS-
GO:0008233peptidase activityIEA-
GO:0043237laminin-1 bindingISS-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007411axon guidanceISSaxon (GO term level: 13)-
GO:0048663neuron fate commitmentISSneuron (GO term level: 9)-
GO:0021978telencephalon regionalizationIEABrain (GO term level: 10)-
GO:0060020Bergmann glial cell differentiationIEAastrocyte, Glial (GO term level: 6)-
GO:0030902hindbrain developmentISSBrain (GO term level: 8)-
GO:0030901midbrain developmentISSBrain (GO term level: 8)-
GO:0030900forebrain developmentISSBrain (GO term level: 8)-
GO:0014003oligodendrocyte developmentIEAaxon, oligodendrocyte, Glial (GO term level: 10)-
GO:0001755neural crest cell migrationISS-
GO:0001570vasculogenesisISS-
GO:0001569patterning of blood vesselsISS-
GO:0001658ureteric bud branchingISS-
GO:0001656metanephros developmentISS-
GO:0001708cell fate specificationISS-
GO:0002052positive regulation of neuroblast proliferationIEA-
GO:0002076osteoblast developmentIEA-
GO:0007267cell-cell signalingISS-
GO:0007228positive regulation of hh target transcription factor activityIEA-
GO:0009952anterior/posterior pattern formationIEA-
GO:0009887organ morphogenesisISS-
GO:0007165signal transductionISS-
GO:0007507heart developmentISS-
GO:0007442hindgut morphogenesisIEA-
GO:0007435salivary gland morphogenesisISS-
GO:0007418ventral midline developmentTAS8896572 
GO:0007389pattern specification processISS-
GO:0008209androgen metabolic processISS-
GO:0030850prostate gland developmentISS-
GO:0031069hair follicle morphogenesisIEA-
GO:0016539intein-mediated protein splicingIEA-
GO:0042475odontogenesis of dentine-containing toothIEA-
GO:0051146striated muscle cell differentiationIEA-
GO:0021940positive regulation of granule cell precursor proliferationIEA-
GO:0021938smoothened signaling pathway involved in regulation of granule cell precursor cell proliferationIEA-
GO:0042733embryonic digit morphogenesisISS-
GO:0042130negative regulation of T cell proliferationIEA-
GO:0030539male genitalia developmentISS-
GO:0043010camera-type eye developmentIEA-
GO:0032435negative regulation of proteasomal ubiquitin-dependent protein catabolic processIEA-
GO:0030162regulation of proteolysisISS-
GO:0030336negative regulation of cell migrationISS-
GO:0030324lung developmentISS-
GO:0021513spinal cord dorsal/ventral patterningIEA-
GO:0045944positive regulation of transcription from RNA polymerase II promoterIEA-
GO:0045596negative regulation of cell differentiationISS-
GO:0046639negative regulation of alpha-beta T cell differentiationIEA-
GO:0048568embryonic organ developmentIEA-
GO:0048589developmental growthIEA-
GO:0048598embryonic morphogenesisIEA-
GO:0045445myoblast differentiationIEA-
GO:0045449regulation of transcriptionIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-
GO:0005615extracellular spaceISS-
GO:0009986cell surfaceISS-
GO:0005886plasma membraneIEA-
GO:0045121membrane raftISS-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG HEDGEHOG SIGNALING PATHWAY 5642All SZGR 2.0 genes in this pathway
KEGG PATHWAYS IN CANCER 328259All SZGR 2.0 genes in this pathway
KEGG BASAL CELL CARCINOMA 5544All SZGR 2.0 genes in this pathway
BIOCARTA SHH PATHWAY 1615All SZGR 2.0 genes in this pathway
BIOCARTA PTC1 PATHWAY 116All SZGR 2.0 genes in this pathway
PID HEDGEHOG 2PATHWAY 2217All SZGR 2.0 genes in this pathway
PID HEDGEHOG GLI PATHWAY 4835All SZGR 2.0 genes in this pathway
PID TAP63 PATHWAY 5440All SZGR 2.0 genes in this pathway
PID HNF3A PATHWAY 4429All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY GPCR 920449All SZGR 2.0 genes in this pathway
REACTOME CLASS B 2 SECRETIN FAMILY RECEPTORS 8858All SZGR 2.0 genes in this pathway
REACTOME GPCR LIGAND BINDING 408246All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN 391222All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS DN 459276All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 12HR UP 11679All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR UP 487286All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038678All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062725All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS 652441All SZGR 2.0 genes in this pathway
WEBER METHYLATED IN COLON CANCER 1813All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 18HR DN 178121All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435318All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K4ME3 AND H3K27ME3 210148All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3 590403All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway
NABA SECRETED FACTORS 344197All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED 753411All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028559All SZGR 2.0 genes in this pathway