Gene Page: KDM2B
Summary ?
| GeneID | 84678 |
| Symbol | KDM2B |
| Synonyms | CXXC2|FBXL10|Fbl10|JHDM1B|PCCX2 |
| Description | lysine demethylase 2B |
| Reference | MIM:609078|HGNC:HGNC:13610|Ensembl:ENSG00000089094|HPRD:12362|Vega:OTTHUMG00000169071 |
| Gene type | protein-coding |
| Map location | 12q24.31 |
| Pascal p-value | 0.191 |
| Fetal beta | 1.471 |
| DMG | 1 (# studies) |
| Support | CompositeSet Chromatin Remodeling Genes |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| 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). | 2 |
| DNM:Girard_2011 | Whole Exome Sequencing analysis | The data set included 15 DNMs found from the exomes of 14 schizophrenia probands and their parents. |
Section I. Genetics and epigenetics annotation
DNM table
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| KDM2B | chr12 | 121882033 | C | T | NM_001005366 NM_032590 | p.714G>S p.745G>S | missense missense | Schizophrenia | DNM:Girard_2011 |
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg21249371 | 12 | 122019117 | KDM2B | 1.19E-4 | 0.412 | 0.029 | DMG:Wockner_2014 |
| cg25482146 | 12 | 122016415 | KDM2B | 3.571E-4 | 0.425 | 0.042 | DMG:Wockner_2014 |
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 V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| PEREZ TP53 TARGETS | 1174 | 695 | All SZGR 2.0 genes in this pathway |
| JIANG HYPOXIA NORMAL | 311 | 205 | All SZGR 2.0 genes in this pathway |
| BILD E2F3 ONCOGENIC SIGNATURE | 246 | 153 | All SZGR 2.0 genes in this pathway |
| MARSON BOUND BY FOXP3 STIMULATED | 1022 | 619 | All SZGR 2.0 genes in this pathway |
| MARSON BOUND BY FOXP3 UNSTIMULATED | 1229 | 713 | All SZGR 2.0 genes in this pathway |
| MARSON FOXP3 TARGETS STIMULATED UP | 29 | 19 | All SZGR 2.0 genes in this pathway |
| VANTVEER BREAST CANCER BRCA1 UP | 36 | 18 | All SZGR 2.0 genes in this pathway |
| PILON KLF1 TARGETS DN | 1972 | 1213 | All SZGR 2.0 genes in this pathway |
| SERVITJA ISLET HNF1A TARGETS DN | 109 | 71 | All SZGR 2.0 genes in this pathway |
| KRIEG HYPOXIA NOT VIA KDM3A | 770 | 480 | All SZGR 2.0 genes in this pathway |
| RAO BOUND BY SALL4 | 227 | 149 | All SZGR 2.0 genes in this pathway |