Gene Page: NKX6-1

Summary ?
GeneID4825
SymbolNKX6-1
SynonymsNKX6.1|NKX6A
DescriptionNK6 homeobox 1
ReferenceMIM:602563|HGNC:HGNC:7839|Ensembl:ENSG00000163623|HPRD:09092|Vega:OTTHUMG00000130426
Gene typeprotein-coding
Map location4q21.33
Pascal p-value0.109
Fetal beta-0.239
eGeneCaudate basal ganglia
Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
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,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 2 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs843350chr3183946273NKX6-148250.18trans
rs10994209chr1061877705NKX6-148250.17trans

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
RP4-788L13.10.750.80
CRY20.740.78
PRICKLE20.710.77
SCN3B0.690.80
PCDHA50.690.77
GABRA50.680.71
SLC8A20.680.77
LINGO10.670.75
WSB20.670.78
DLG20.670.74
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AL139819.3-0.43-0.52
AF347015.26-0.42-0.47
AP002478.3-0.42-0.55
AF347015.33-0.41-0.48
AF347015.21-0.41-0.47
C11orf67-0.41-0.55
MT-CO2-0.41-0.50
AF347015.18-0.40-0.53
AF347015.8-0.40-0.49
S100A1-0.40-0.39

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityIEA-
GO:0043565sequence-specific DNA bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0045687positive regulation of glial cell differentiationIEAGlial (GO term level: 11)-
GO:0045686negative regulation of glial cell differentiationIEAGlial (GO term level: 11)-
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0009887organ morphogenesisTAS10567713 
GO:0007275multicellular organismal developmentIEA-
GO:0030154cell differentiationIEA-
GO:0031018endocrine pancreas developmentIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG MATURITY ONSET DIABETES OF THE YOUNG 2519All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396292All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF BETA CELL DEVELOPMENT 3023All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF GENE EXPRESSION IN BETA CELLS 2015All 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
TAYLOR METHYLATED IN ACUTE LYMPHOBLASTIC LEUKEMIA 7752All SZGR 2.0 genes in this pathway
ZHOU PANCREATIC ENDOCRINE PROGENITOR 1411All SZGR 2.0 genes in this pathway
ZHOU PANCREATIC BETA CELL 119All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K27ME3 269159All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3 349234All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435318All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K27ME3 341243All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3 590403All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP 857456All SZGR 2.0 genes in this pathway
WANG MLL TARGETS 289188All SZGR 2.0 genes in this pathway
ROLEF GLIS3 TARGETS 3729All SZGR 2.0 genes in this pathway