Gene Page: GLI2

Summary ?
GeneID2736
SymbolGLI2
SynonymsCJS|HPE9|PHS2|THP1|THP2
DescriptionGLI family zinc finger 2
ReferenceMIM:165230|HGNC:HGNC:4318|Ensembl:ENSG00000074047|HPRD:01312|Vega:OTTHUMG00000153741
Gene typeprotein-coding
Map location2q14
Pascal p-value0.314
Fetal beta1.634
DMG2 (# studies)
SupportCompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
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: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
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_IGenome scan meta-analysisPsr: 0.023 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.00755 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 7 

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
GLI2chr2121554927GANM_005270p.11E>KmissenseSchizophreniaDNM:Fromer_2014

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
ch.2.121457425R2121740955GLI23.12E-5-0.6850.019DMG:Wockner_2014
cg217599532121748257GLI25.31E-40.3660.048DMG:Wockner_2014
cg035757642121493832GLI22.92E-8-0.019E-6DMG:Jaffe_2016


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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityIDA15994174 
GO:0008270zinc ion bindingIDA8378770 
GO:0016563transcription activator activityIDA15175043 
GO:0046872metal ion bindingIEA-
GO:0043565sequence-specific DNA bindingIDA9557682 |15175043 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007411axon guidanceISSaxon (GO term level: 13)-
GO:0048666neuron developmentISSneuron (GO term level: 9)-
GO:0021965spinal cord ventral commissure morphogenesisISSneuron, axon (GO term level: 15)-
GO:0030902hindbrain developmentISSBrain (GO term level: 8)-
GO:0021517ventral spinal cord developmentISSneuron (GO term level: 8)-
GO:0021508floor plate formationISSneuron, Glial (GO term level: 10)-
GO:0021775smoothened signaling pathway involved in ventral spinal cord interneuron specificationISSneuron (GO term level: 12)-
GO:0000122negative regulation of transcription from RNA polymerase II promoterIMP15994174 
GO:0001501skeletal system developmentISS-
GO:0001822kidney developmentISS-
GO:0002076osteoblast developmentISS-
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0006350transcriptionIEA-
GO:0009954proximal/distal pattern formationISS-
GO:0007224smoothened signaling pathwayIDA15994174 
GO:0008283cell proliferationIDA15994174 
GO:0007507heart developmentISS-
GO:0007442hindgut morphogenesisISS-
GO:0007389pattern specification processISS-
GO:0042475odontogenesis of dentine-containing toothISS-
GO:0021983pituitary gland developmentISS-
GO:0048754branching morphogenesis of a tubeISS-
GO:0030879mammary gland developmentISS-
GO:0030324lung developmentISS-
GO:0035295tube developmentISS-
GO:0030903notochord developmentISS-
GO:0021513spinal cord dorsal/ventral patterningISS-
GO:0021696cerebellar cortex morphogenesisISS-
GO:0045740positive regulation of DNA replicationIDA12165851 
GO:0045944positive regulation of transcription from RNA polymerase II promoterIDA12165851 |15994174 
GO:0048566embryonic gut developmentISS-
GO:0048589developmental growthISS-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005622intracellularIEA-
GO:0005634nucleusIEA-

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
PID HEDGEHOG 2PATHWAY 2217All SZGR 2.0 genes in this pathway
PID HEDGEHOG GLI PATHWAY 4835All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS UP 290177All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS DN 260143All SZGR 2.0 genes in this pathway
SENESE HDAC1 AND HDAC2 TARGETS DN 232139All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR UP 162116All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
SNIJDERS AMPLIFIED IN HEAD AND NECK TUMORS 3727All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 7 2722All SZGR 2.0 genes in this pathway
LEE TARGETS OF PTCH1 AND SUFU UP 5337All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP 390242All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 6HR DN 160101All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN 940425All SZGR 2.0 genes in this pathway
PODAR RESPONSE TO ADAPHOSTIN DN 1816All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE UP 14985All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069729All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 2 2914All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA CLASSICAL 162122All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS DN 211119All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-182141014171A,m8hsa-miR-182UUUGGCAAUGGUAGAACUCACA
miR-30-5p953959m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA