Gene Page: NKX2-2

Summary ?
GeneID4821
SymbolNKX2-2
SynonymsNKX2.2|NKX2B
DescriptionNK2 homeobox 2
ReferenceMIM:604612|HGNC:HGNC:7835|Ensembl:ENSG00000125820|HPRD:05213|Vega:OTTHUMG00000170524
Gene typeprotein-coding
Map location20p11.22
Pascal p-value0.001
Sherlock p-value0.173
Fetal beta-1.914
eGeneMyers' 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: 5 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6448932chr412595798NKX2-248210.16trans

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
CORT0.690.71
APITD10.680.69
EXOC3L0.650.48
LRRC560.640.69
PLCB20.630.66
KRTCAP30.610.33
WFDC20.590.58
RPP250.590.59
RXRG0.590.31
CASZ10.580.44
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
NET1-0.31-0.33
AF347015.2-0.30-0.25
AF347015.26-0.29-0.29
AF347015.15-0.28-0.25
MT-CYB-0.28-0.25
PREX2-0.27-0.30
AF347015.8-0.27-0.23
PITPNC1-0.27-0.26
PTRF-0.27-0.23
EGLN3-0.26-0.23

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityIEA-
GO:0005515protein bindingIEA-
GO:0043565sequence-specific DNA bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007420brain developmentTASBrain (GO term level: 7)1346742 
GO:0048665neuron fate specificationIEAneuron (GO term level: 10)-
GO:0014003oligodendrocyte developmentIEAaxon, oligodendrocyte, Glial (GO term level: 10)-
GO:0021529spinal cord oligodendrocyte cell differentiationIEAneuron, axon, oligodendrocyte (GO term level: 10)-
GO:0007399nervous system developmentIEAneurite (GO term level: 5)-
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0048468cell developmentIEA-
GO:0007275multicellular organismal developmentIEA-
GO:0031018endocrine pancreas developmentIEA-
GO:0045944positive regulation of transcription from RNA polymerase II promoterIEA-
GO:0045597positive regulation of cell differentiationIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-
GO:0005730nucleolusIDA18029348 
GO:0005737cytoplasmIDA18029348 

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
ASTON MAJOR DEPRESSIVE DISORDER DN 160110All SZGR 2.0 genes in this pathway
LU AGING BRAIN UP 262186All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 48HR DN 161105All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP 566371All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR UP 430288All 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 H3K4ME3 AND H3K27ME3 1069729All 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
VERHAAK GLIOBLASTOMA PRONEURAL 177132All SZGR 2.0 genes in this pathway
MIYAGAWA TARGETS OF EWSR1 ETS FUSIONS UP 259159All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 227149All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY 1839928All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-17-5p/20/93.mr/106/519.d4414471Ahsa-miR-17-5pCAAAGUGCUUACAGUGCAGGUAGU
hsa-miR-20abrainUAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106aAAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZUAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZCAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519dCAAAGUGCCUCCCUUUAGAGUGU
miR-1825745811A,m8hsa-miR-182UUUGGCAAUGGUAGAACUCACA
miR-30-5p2532601A,m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-3637147201Ahsa-miR-363AUUGCACGGUAUCCAUCUGUAA
miR-369-3p971031Ahsa-miR-369-3pAAUAAUACAUGGUUGAUCUUU
miR-374971041A,m8hsa-miR-374UUAUAAUACAACCUGAUAAGUG
miR-377394400m8hsa-miR-377AUCACACAAAGGCAACUUUUGU
miR-4527157221A,m8hsa-miR-452UGUUUGCAGAGGAAACUGAGAC
miR-543261267m8hsa-miR-543AAACAUUCGCGGUGCACUUCU
miR-965755811Ahsa-miR-96brainUUUGGCACUAGCACAUUUUUGC