Gene Page: VAX2

Summary ?
GeneID25806
SymbolVAX2
SynonymsDRES93
Descriptionventral anterior homeobox 2
ReferenceMIM:604295|HGNC:HGNC:12661|Ensembl:ENSG00000116035|HPRD:05051|Vega:OTTHUMG00000129714
Gene typeprotein-coding
Map location2p13
Pascal p-value0.963
Fetal beta-0.297
DMG2 (# studies)

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: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
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg20267441271127363VAX29.8E-5-0.2650.028DMG:Wockner_2014
cg01719210271128191VAX24.91E-4-0.2630.047DMG:Wockner_2014
cg15423212271115225VAX23.54E-8-0.0161.03E-5DMG: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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
UBE4B0.960.96
DYRK1A0.960.96
HERC10.950.95
HUWE10.950.96
CKAP50.950.96
GON4L0.950.96
KIAA09470.950.96
KIAA14090.950.95
RPRD20.950.96
TP53BP10.940.94
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.31-0.81-0.85
HIGD1B-0.79-0.86
FXYD1-0.79-0.83
MT-CO2-0.79-0.84
IFI27-0.78-0.84
AF347015.21-0.76-0.87
AF347015.33-0.76-0.78
AF347015.27-0.75-0.79
AF347015.8-0.75-0.81
S100A16-0.74-0.79

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityNAS10485894 
GO:0031490chromatin DNA bindingIEA-
GO:0043565sequence-specific DNA bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007409axonogenesisIEAneuron, axon, neurite (GO term level: 12)-
GO:0000122negative regulation of transcription from RNA polymerase II promoterIEA-
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0009950dorsal/ventral axis specificationIEA-
GO:0007398ectoderm developmentTAS10485894 
GO:0048048embryonic eye morphogenesisIEA-
GO:0007601visual perceptionTAS10485894 
GO:0007275multicellular organismal developmentIEA-
GO:0043010camera-type eye developmentIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP 1142669All 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
MEISSNER BRAIN HCP WITH H3K27ME3 269159All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL 177132All SZGR 2.0 genes in this pathway
WANG MLL TARGETS 289188All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway