Gene Page:NKX2-2

Summary?
GeneID 4821
Symbol NKX2-2
Synonyms NKX2.2|NKX2B
Description NK2 homeobox 2
Reference MIM:604612|HGNC:HGNC:7835|Ensembl:ENSG00000125820|HPRD:05213|Vega:OTTHUMG00000170524
Gene type protein-coding
Map location 20p11.22
Pascal p-value 0.001
Sherlock p-value 0.173
Fetal beta -1.914
eGene Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
PMID:cooccur High-throughput literature-search 系统的搜索PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature High-throughput literature-search Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 5

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs6448932 chr4 12595798 NKX2-2 4821 0.16 trans

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
Gene Pearson's Correlation Spearman's Correlation
CORT 0.69 0.71
APITD1 0.68 0.69
EXOC3L 0.65 0.48
LRRC56 0.64 0.69
PLCB2 0.63 0.66
KRTCAP3 0.61 0.33
WFDC2 0.59 0.58
RPP25 0.59 0.59
RXRG 0.59 0.31
CASZ1 0.58 0.44
Top 10 negatively co-expressed genes
Gene Pearson'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 function 去的术语 Evidence Neuro keywords PubMed ID
GO:0003700 transcription factor activity IEA -
GO:0005515 protein binding IEA -
GO:0043565 sequence-specific DNA binding IEA -
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0007420 brain development TAS Brain (GO term level: 7) 1346742
GO:0048665 neuron fate specification IEA neuron (GO term level: 10) -
GO:0014003 少突细胞development IEA axon, oligodendrocyte, Glial (GO term level: 10) -
GO:0021529 spinal cord oligodendrocyte cell differentiation IEA neuron, axon, oligodendrocyte (GO term level: 10) -
GO:0007399 nervous system development IEA neurite (GO term level: 5) -
GO:0006355 regulation of transcription, DNA-dependent IEA -
GO:0048468 cell development IEA -
GO:0007275 multicellular organismal development IEA -
GO:0031018 endocrine pancreas development IEA -
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IEA -
GO:0045597 positive regulation of cell differentiation IEA -
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0005634 nucleus IEA -
GO:0005730 nucleolus IDA 18029348
GO:0005737 cytoplasm IDA 18029348

部分诉通路注释

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG MATURITY ONSET DIABETES OF THE YOUNG 25 19 All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396 292 All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF BETA CELL DEVELOPMENT 30 23 All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF GENE EXPRESSION IN BETA CELLS 20 15 All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038 678 All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062 725 All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118 744 All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS 652 441 All SZGR 2.0 genes in this pathway
ASTON MAJOR DEPRESSIVE DISORDER DN 160 110 All SZGR 2.0 genes in this pathway
LU AGING BRAIN UP 262 186 All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 48HR DN 161 105 All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP 566 371 All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR UP 430 288 All SZGR 2.0 genes in this pathway
ZHOU PANCREATIC ENDOCRINE PROGENITOR 14 11 All SZGR 2.0 genes in this pathway
ZHOU PANCREATIC BETA CELL 11 9 All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069 729 All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3 590 403 All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP 857 456 All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL 177 132 All SZGR 2.0 genes in this pathway
MIYAGAWA TARGETS OF EWSR1 ETS FUSIONS UP 259 159 All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 227 149 All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY 1839 928 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-17-5p/20/93.mr/106/519.d 441 447 1A hsa-miR-17-5p CAAAGUGCUUACAGUGCAGGUAGU
hsa-miR-20abrain UAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106a AAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZ UAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZ CAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519d CAAAGUGCCUCCCUUUAGAGUGU
miR-182 574 581 1A,m8 hsa-miR-182 UUUGGCAAUGGUAGAACUCACA
miR-30-5p 253 260 1A,m8 hsa-miR-30a-5p UGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrain UGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZ UGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZ UGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5p UGUAAACAUCCUUGACUGGA
miR-363 714 720 1A hsa-miR-363 AUUGCACGGUAUCCAUCUGUAA
miR-369-3p 97 103 1A hsa-miR-369-3p AAUAAUACAUGGUUGAUCUUU
miR-374 97 104 1A,m8 hsa-miR-374 UUAUAAUACAACCUGAUAAGUG
miR-377 394 400 m8 hsa-miR-377 AUCACACAAAGGCAACUUUUGU
miR-452 715 722 1A,m8 hsa-miR-452 UGUUUGCAGAGGAAACUGAGAC
miR-543 261 267 m8 hsa-miR-543 AAACAUUCGCGGUGCACUUCU
miR-96 575 581 1A hsa-miR-96brain UUUGGCACUAGCACAUUUUUGC