Gene Page: KDM5C
Summary ?
| GeneID | 8242 |
| Symbol | KDM5C |
| Synonyms | DXS1272E|JARID1C|MRX13|MRXJ|MRXSCJ|MRXSJ|SMCX|XE169 |
| Description | lysine demethylase 5C |
| Reference | MIM:314690|HGNC:HGNC:11114|Ensembl:ENSG00000126012|HPRD:02442|Vega:OTTHUMG00000021606 |
| Gene type | protein-coding |
| Map location | Xp11.22-p11.21 |
| Sherlock p-value | 0.505 |
| TADA p-value | 0.004 |
| Fetal beta | 0.423 |
| eGene | Myers' cis & trans |
| Support | CompositeSet Darnell FMRP targets Ascano FMRP targets Chromatin Remodeling Genes Potential synaptic genes |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DNM:Xu_2012 | Whole Exome Sequencing analysis | De novo mutations of 4 genes were identified by exome sequencing of 795 samples in this study | |
| 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 |
Section I. Genetics and epigenetics annotation
DNM table
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| KDM5C | chrX | 53245325..53245326 | TC | T | NM_001146702 NM_004187 | . . | frameshift frameshift | Schizophrenia | DNM:Xu_2012 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs4862188 | chr4 | 184355369 | KDM5C | 8242 | 6.381E-4 | trans | ||
| rs2880301 | chr13 | 20100533 | KDM5C | 8242 | 0.01 | 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 |
| CREBBP | 0.98 | 0.98 |
| EP300 | 0.98 | 0.98 |
| EP400 | 0.97 | 0.97 |
| SPEN | 0.97 | 0.97 |
| ARID1A | 0.97 | 0.98 |
| DIDO1 | 0.96 | 0.98 |
| ZZEF1 | 0.96 | 0.97 |
| C11orf30 | 0.96 | 0.97 |
| ZMIZ1 | 0.96 | 0.96 |
| GCN1L1 | 0.96 | 0.97 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.31 | -0.71 | -0.87 |
| MT-CO2 | -0.69 | -0.87 |
| C5orf53 | -0.69 | -0.75 |
| FXYD1 | -0.69 | -0.84 |
| AF347015.27 | -0.68 | -0.83 |
| S100B | -0.68 | -0.81 |
| IFI27 | -0.68 | -0.83 |
| AF347015.33 | -0.67 | -0.82 |
| HIGD1B | -0.67 | -0.86 |
| MT-CYB | -0.66 | -0.81 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| LAIHO COLORECTAL CANCER SERRATED DN | 86 | 47 | All SZGR 2.0 genes in this pathway |
| GAUSSMANN MLL AF4 FUSION TARGETS A UP | 191 | 128 | All SZGR 2.0 genes in this pathway |
| MCBRYAN PUBERTAL BREAST 4 5WK DN | 196 | 131 | All SZGR 2.0 genes in this pathway |
| MCBRYAN PUBERTAL BREAST 6 7WK UP | 197 | 135 | All SZGR 2.0 genes in this pathway |
| SCHLOSSER SERUM RESPONSE AUGMENTED BY MYC | 108 | 74 | All SZGR 2.0 genes in this pathway |
| SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP | 479 | 299 | All SZGR 2.0 genes in this pathway |
| SCHAEFFER PROSTATE DEVELOPMENT 48HR DN | 428 | 306 | All SZGR 2.0 genes in this pathway |
| BENPORATH MYC MAX TARGETS | 775 | 494 | All SZGR 2.0 genes in this pathway |
| SMITH TERT TARGETS UP | 145 | 91 | All SZGR 2.0 genes in this pathway |
| CROMER METASTASIS UP | 79 | 46 | All SZGR 2.0 genes in this pathway |
| FAELT B CLL WITH VH3 21 UP | 44 | 30 | All SZGR 2.0 genes in this pathway |
| KAYO CALORIE RESTRICTION MUSCLE DN | 87 | 59 | All SZGR 2.0 genes in this pathway |
| ZHU CMV ALL UP | 120 | 89 | All SZGR 2.0 genes in this pathway |
| DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN | 287 | 208 | All SZGR 2.0 genes in this pathway |
| ZHU CMV 24 HR UP | 93 | 65 | All SZGR 2.0 genes in this pathway |
| WELCSH BRCA1 TARGETS DN | 141 | 92 | 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 |
| DANG BOUND BY MYC | 1103 | 714 | All SZGR 2.0 genes in this pathway |