Gene Page: NR2E1
Summary ?
| GeneID | 7101 |
| Symbol | NR2E1 |
| Synonyms | TLL|TLX|XTLL |
| Description | nuclear receptor subfamily 2 group E member 1 |
| Reference | MIM:603849|HGNC:HGNC:7973|Ensembl:ENSG00000112333|HPRD:07230|Vega:OTTHUMG00000015319 |
| Gene type | protein-coding |
| Map location | 6q21 |
| Pascal p-value | 0.359 |
| Sherlock p-value | 0.116 |
| Fetal beta | 0.874 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Jaffe_2016 | Genome-wide DNA methylation analysis | This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. | 1 |
| PMID:cooccur | High-throughput literature-search | Systematic search in 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: 6 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg20652607 | 6 | 108485837 | NR2E1 | 5.65E-8 | -0.016 | 1.45E-5 | DMG:Jaffe_2016 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs11582961 | chr1 | 184023058 | NR2E1 | 7101 | 0.17 | trans | ||
| rs11003013 | chr10 | 81230988 | NR2E1 | 7101 | 0.13 | trans | ||
| rs2068673 | chr12 | 60333402 | NR2E1 | 7101 | 0.06 | trans | ||
| rs2655880 | chr12 | 60797980 | NR2E1 | 7101 | 0.06 | 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.
No co-expressed genes in brain regions
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0003700 | transcription factor activity | IEA | - | |
| GO:0003707 | steroid hormone receptor activity | IEA | - | |
| GO:0003707 | steroid hormone receptor activity | TAS | 9628820 | |
| GO:0005496 | steroid binding | IEA | - | |
| GO:0005515 | protein binding | IEA | - | |
| GO:0008270 | zinc ion binding | IEA | - | |
| GO:0016564 | transcription repressor activity | IEA | - | |
| GO:0046872 | metal ion binding | IEA | - | |
| GO:0043565 | sequence-specific DNA binding | IEA | - | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0007420 | brain development | IEA | Brain (GO term level: 7) | - |
| GO:0008347 | glial cell migration | IEA | neuron, Glial (GO term level: 8) | - |
| GO:0021960 | anterior commissure morphogenesis | IEA | neuron, axon (GO term level: 15) | - |
| GO:0045665 | negative regulation of neuron differentiation | IEA | neuron (GO term level: 10) | - |
| GO:0021772 | olfactory bulb development | IEA | neuron (GO term level: 11) | - |
| GO:0007399 | nervous system development | TAS | neurite (GO term level: 5) | 9628820 |
| GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | IEA | - | |
| GO:0006355 | regulation of transcription, DNA-dependent | IEA | - | |
| GO:0006350 | transcription | IEA | - | |
| GO:0008284 | positive regulation of cell proliferation | IEA | - | |
| GO:0007610 | behavior | IEA | - | |
| GO:0007601 | visual perception | IEA | - | |
| GO:0007275 | multicellular organismal development | IEA | - | |
| GO:0043066 | negative regulation of apoptosis | IEA | - | |
| GO:0021987 | cerebral cortex development | IEA | - | |
| GO:0035176 | social behavior | IEA | - | |
| GO:0045165 | cell fate commitment | IEA | - | |
| GO:0060041 | retina development in camera-type eye | IEA | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005634 | nucleus | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| REACTOME GENERIC TRANSCRIPTION PATHWAY | 352 | 181 | All SZGR 2.0 genes in this pathway |
| REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY | 49 | 36 | 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 |
| SHEPARD BMYB MORPHOLINO DN | 200 | 112 | All SZGR 2.0 genes in this pathway |
| SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 | 419 | 273 | All SZGR 2.0 genes in this pathway |
| SHARMA PILOCYTIC ASTROCYTOMA LOCATION UP | 25 | 12 | 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 IPS WITH HCP H3K27ME3 | 102 | 76 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MEF HCP WITH H3K27ME3 | 590 | 403 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 4HR DN | 254 | 158 | All SZGR 2.0 genes in this pathway |
| VERHAAK GLIOBLASTOMA CLASSICAL | 162 | 122 | All SZGR 2.0 genes in this pathway |