Gene Page: KDM4A
Summary ?
| GeneID | 9682 |
| Symbol | KDM4A |
| Synonyms | JHDM3A|JMJD2|JMJD2A|TDRD14A |
| Description | lysine demethylase 4A |
| Reference | MIM:609764|HGNC:HGNC:22978|Ensembl:ENSG00000066135|HPRD:17168|Vega:OTTHUMG00000007560 |
| Gene type | protein-coding |
| Map location | 1p34.1 |
| Pascal p-value | 4.947E-7 |
| Fetal beta | 1.128 |
| Support | Ascano FMRP targets Chromatin Remodeling Genes |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:GWAScat | Genome-wide Association Studies | This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb. | |
| CV:PGC128 | Genome-wide Association Study | A multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci | |
| CV:PGCnp | Genome-wide Association Study | GWAS |
Section I. Genetics and epigenetics annotation
CV:PGC128
| SNP ID | Chromosome | Position | Allele | P | Function | Gene | Up/Down Distance |
|---|---|---|---|---|---|---|---|
| rs11210892 | chr1 | 44100084 | AG | 4.97E-10 | intergenic | PTPRF,KDM4A | dist=10741;dist=15713 |
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 |
| UBE2O | 0.92 | 0.94 |
| GGA3 | 0.92 | 0.93 |
| DEPDC5 | 0.91 | 0.92 |
| GBF1 | 0.91 | 0.91 |
| FAM168B | 0.90 | 0.91 |
| ZDHHC5 | 0.90 | 0.91 |
| VPS53 | 0.89 | 0.91 |
| RPTOR | 0.89 | 0.91 |
| CLCN6 | 0.88 | 0.90 |
| MYBBP1A | 0.88 | 0.90 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.21 | -0.72 | -0.77 |
| AF347015.31 | -0.69 | -0.69 |
| GNG11 | -0.68 | -0.73 |
| C1orf54 | -0.67 | -0.78 |
| MT-CO2 | -0.67 | -0.67 |
| HIGD1B | -0.65 | -0.66 |
| AF347015.8 | -0.65 | -0.65 |
| VAMP5 | -0.64 | -0.68 |
| MT-CYB | -0.64 | -0.62 |
| AF347015.27 | -0.63 | -0.65 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN | 335 | 193 | All SZGR 2.0 genes in this pathway |
| GINESTIER BREAST CANCER 20Q13 AMPLIFICATION DN | 180 | 101 | All SZGR 2.0 genes in this pathway |
| LASTOWSKA NEUROBLASTOMA COPY NUMBER DN | 800 | 473 | All SZGR 2.0 genes in this pathway |
| SCHLOSSER SERUM RESPONSE DN | 712 | 443 | All SZGR 2.0 genes in this pathway |
| PUJANA ATM PCC NETWORK | 1442 | 892 | All SZGR 2.0 genes in this pathway |
| PUJANA CHEK2 PCC NETWORK | 779 | 480 | All SZGR 2.0 genes in this pathway |
| BUYTAERT PHOTODYNAMIC THERAPY STRESS UP | 811 | 508 | All SZGR 2.0 genes in this pathway |
| BENPORATH CYCLING GENES | 648 | 385 | All SZGR 2.0 genes in this pathway |
| WHITFIELD CELL CYCLE G2 | 182 | 102 | All SZGR 2.0 genes in this pathway |
| WANG RESPONSE TO GSK3 INHIBITOR SB216763 UP | 397 | 206 | All SZGR 2.0 genes in this pathway |