Gene Page: CBFA2T2
Summary ?
| GeneID | 9139 |
| Symbol | CBFA2T2 |
| Synonyms | EHT|MTGR1|ZMYND3|p85 |
| Description | core-binding factor, runt domain, alpha subunit 2; translocated to, 2 |
| Reference | MIM:603672|HGNC:HGNC:1536|Ensembl:ENSG00000078699|HPRD:04721|Vega:OTTHUMG00000032261 |
| Gene type | protein-coding |
| Map location | 20q11 |
| Pascal p-value | 0.478 |
| Sherlock p-value | 0.394 |
| DEG p-value | DEG:Zhao_2015:p=3.21e-04:q=0.0924 |
| Fetal beta | 0.522 |
| DMG | 1 (# studies) |
| eGene | Cerebellar Hemisphere Cerebellum Myers' cis & trans |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DEG:Zhao_2015 | RNA Sequencing analysis | Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder. | |
| DMG:Wockner_2014 | Genome-wide DNA methylation analysis | This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). | 1 |
Section I. Genetics and epigenetics annotation
DNM table
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CBFA2T2 | chr20 | 32228199 | C | T | NM_001032999 NM_001039709 NM_005093 | . . . | silent silent silent | Schizophrenia | DNM:Fromer_2014 |
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg05002800 | 20 | 32231392 | CBFA2T2 | 3.18E-4 | -0.734 | 0.04 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs4864466 | chr4 | 54403975 | CBFA2T2 | 9139 | 0.18 | 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 |
| KIAA0562 | 0.85 | 0.88 |
| ARHGAP21 | 0.85 | 0.88 |
| MAP3K4 | 0.84 | 0.85 |
| TSC1 | 0.84 | 0.88 |
| SLC11A2 | 0.83 | 0.84 |
| MUM1 | 0.83 | 0.84 |
| INO80 | 0.83 | 0.87 |
| CLIP1 | 0.83 | 0.84 |
| FAM171A1 | 0.82 | 0.85 |
| DOCK9 | 0.82 | 0.85 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.21 | -0.67 | -0.69 |
| C1orf54 | -0.67 | -0.73 |
| AF347015.31 | -0.67 | -0.65 |
| ENHO | -0.65 | -0.69 |
| MT-CO2 | -0.64 | -0.63 |
| VAMP5 | -0.63 | -0.65 |
| IFI27 | -0.63 | -0.60 |
| HIGD1B | -0.63 | -0.64 |
| GNG11 | -0.62 | -0.64 |
| FXYD1 | -0.61 | -0.59 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| LIU SOX4 TARGETS DN | 309 | 191 | All SZGR 2.0 genes in this pathway |
| OSMAN BLADDER CANCER DN | 406 | 230 | All SZGR 2.0 genes in this pathway |
| PEREZ TP53 TARGETS | 1174 | 695 | All SZGR 2.0 genes in this pathway |
| KLEIN TARGETS OF BCR ABL1 FUSION | 45 | 34 | All SZGR 2.0 genes in this pathway |
| PUJANA ATM PCC NETWORK | 1442 | 892 | All SZGR 2.0 genes in this pathway |
| BUYTAERT PHOTODYNAMIC THERAPY STRESS UP | 811 | 508 | All SZGR 2.0 genes in this pathway |
| LIAO METASTASIS | 539 | 324 | All SZGR 2.0 genes in this pathway |
| RICKMAN TUMOR DIFFERENTIATED WELL VS POORLY UP | 236 | 139 | All SZGR 2.0 genes in this pathway |
| SCHAEFFER PROSTATE DEVELOPMENT 48HR DN | 428 | 306 | All SZGR 2.0 genes in this pathway |
| BYSTRYKH HEMATOPOIESIS STEM CELL QTL CIS | 128 | 77 | All SZGR 2.0 genes in this pathway |
| TENEDINI MEGAKARYOCYTE MARKERS | 66 | 48 | All SZGR 2.0 genes in this pathway |
| CHANG IMMORTALIZED BY HPV31 DN | 65 | 45 | All SZGR 2.0 genes in this pathway |
| DAZARD RESPONSE TO UV NHEK DN | 318 | 220 | All SZGR 2.0 genes in this pathway |
| IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR | 681 | 420 | All SZGR 2.0 genes in this pathway |
| MCCABE BOUND BY HOXC6 | 469 | 239 | All SZGR 2.0 genes in this pathway |
| MCCABE HOXC6 TARGETS CANCER UP | 31 | 23 | All SZGR 2.0 genes in this pathway |
| MOLENAAR TARGETS OF CCND1 AND CDK4 UP | 67 | 48 | All SZGR 2.0 genes in this pathway |
| RATTENBACHER BOUND BY CELF1 | 467 | 251 | All SZGR 2.0 genes in this pathway |