Gene Page:NKX6-1
Summary?
| GeneID | 4825 |
| Symbol | NKX6-1 |
| Synonyms | NKX6.1|NKX6A |
| Description | NK6 homeobox 1 |
| Reference | MIM: 602563|HGNC:HGNC:7839|Ensembl:ENSG00000163623|HPRD:09092|Vega:OTTHUMG00000130426 |
| Gene type | protein-coding |
| Map location | 4q21.33 |
| Pascal p-value | 0.109 |
| Fetal beta | -0.239 |
| eGene | Caudate basal ganglia 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: 2 |
Section I. Genetics and epigenetics annotation
eQTL annotation
eQTL annotation| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs843350 | chr3 | 183946273 | NKX6-1 | 4825 | 0.18 | trans | ||
| rs10994209 | chr10 | 61877705 | NKX6-1 | 4825 | 0.17 | trans |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 |
| RP4-788L13.1 | 0.75 | 0.80 |
| CRY2 | 0.74 | 0.78 |
| PRICKLE2 | 0.71 | 0.77 |
| SCN3B | 0.69 | 0.80 |
| PCDHA5 | 0.69 | 0.77 |
| GABRA5 | 0.68 | 0.71 |
| SLC8A2 | 0.68 | 0.77 |
| LINGO1 | 0.67 | 0.75 |
| WSB2 | 0.67 | 0.78 |
| DLG2 | 0.67 | 0.74 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson'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 function | 去的术语 | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0003700 | transcription factor activity | IEA | - | |
| GO:0043565 | sequence-specific DNA binding | IEA | - | |
| Biological process | 去的术语 | Evidence | Neuro keywords | PubMed ID |
| GO:0045687 | positive regulation of glial cell differentiation | IEA | Glial (GO term level: 11) | - |
| GO:0045686 | negative regulation of glial cell differentiation | IEA | Glial (GO term level: 11) | - |
| GO:0006355 | regulation of transcription, DNA-dependent | IEA | - | |
| GO:0009887 | organ morphogenesis | TAS | 10567713 | |
| GO:0007275 | multicellular organismal development | IEA | - | |
| GO:0030154 | cell differentiation | IEA | - | |
| GO:0031018 | endocrine pancreas development | IEA | - | |
| Cellular component | 去的术语 | Evidence | Neuro keywords | PubMed ID |
| GO:0005634 | nucleus | IEA | - |
Section V. Pathway annotation
| 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 |
| TAYLOR METHYLATED IN ACUTE LYMPHOBLASTIC LEUKEMIA | 77 | 52 | 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 H3K27ME3 | 269 | 159 | All SZGR 2.0 genes in this pathway |
| MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3 | 349 | 234 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MCV6 HCP WITH H3K27ME3 | 435 | 318 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN NPC HCP WITH H3K27ME3 | 341 | 243 | 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 |
| WANG MLL TARGETS | 289 | 188 | All SZGR 2.0 genes in this pathway |
| ROLEF GLIS3 TARGETS | 37 | 29 | All SZGR 2.0 genes in this pathway |