Gene Page:SMARCD3
Summary?
| GeneID | 6604 |
| Symbol | SMARCD3 |
| Synonyms | BAF60C|CRACD3|Rsc6p |
| Description | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 |
| Reference | MIM:601737|HGNC:HGNC:11108|Ensembl:ENSG00000082014|HPRD:03440|Vega:OTTHUMG00000157431 |
| Gene type | protein-coding |
| Map location | 7q35-q36 |
| Pascal p-value | 0.08 |
| Sherlock p-value | 0.375 |
| Fetal beta | 0.268 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
| Support | Chromatin Remodeling Genes |
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. | 2 |
| 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: 1 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
Differentially methylated gene| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg00092967 | 7 | 151000789 | SMARCD3 | 2.45E-10 | -0.018 | 6.18E-7 | DMG:Jaffe_2016 |
| cg08487696 | 7 | 150945928 | SMARCD3 | 2.86E-8 | -0.013 | 8.87E-6 | DMG:Jaffe_2016 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs7158406 | chr14 | 40156482 | SMARCD3 | 6604 | 0.16 | trans | ||
| rs2781346 | chr14 | 40163474 | SMARCD3 | 6604 | 0.14 | 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:0005102 | receptor binding | IPI | Neurotransmitter (GO term level: 4) | 14701856 |
| GO:0003713 | transcription coactivator activity | TAS | 8804307 | |
| GO:0008134 | transcription factor binding | IPI | 14701856 | |
| GO:0030528 | transcription regulator activity | IDA | 14701856 | |
| GO:0035257 | nuclear hormone receptor binding | IPI | 14701856 | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0003007 | heart morphogenesis | IEA | - | |
| GO:0006357 | regulation of transcription from RNA polymerase II promoter | TAS | 8804307 | |
| GO:0016568 | chromatin modification | IEA | - | |
| GO:0042692 | muscle cell differentiation | IEA | - | |
| GO:0043393 | regulation of protein binding | IEA | - | |
| GO:0045893 | positive regulation of transcription, DNA-dependent | IDA | 14701856 | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005634 | nucleus | IDA | 14701856 | |
| GO:0005654 | nucleoplasm | TAS | 8804307 | |
| GO:0016514 | SWI/SNF complex | NAS | 14701856 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| PID LKB1 PATHWAY | 47 | 37 | All SZGR 2.0 genes in this pathway |
| PID TAP63 PATHWAY | 54 | 40 | All SZGR 2.0 genes in this pathway |
| REACTOME DEVELOPMENTAL BIOLOGY | 396 | 292 | All SZGR 2.0 genes in this pathway |
| REACTOME BMAL1时钟NPAS2激活生理实验RESSION | 36 | 27 | All SZGR 2.0 genes in this pathway |
| REACTOME PPARA ACTIVATES GENE EXPRESSION | 104 | 72 | All SZGR 2.0 genes in this pathway |
| REACTOME RORA ACTIVATES CIRCADIAN EXPRESSION | 24 | 17 | All SZGR 2.0 genes in this pathway |
| REACTOME YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION | 24 | 16 | All SZGR 2.0 genes in this pathway |
| REACTOME CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA | 23 | 16 | All SZGR 2.0 genes in this pathway |
| REACTOME GENERIC TRANSCRIPTION PATHWAY | 352 | 181 | All SZGR 2.0 genes in this pathway |
| REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS | 478 | 302 | All SZGR 2.0 genes in this pathway |
| REACTOME FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM | 168 | 115 | All SZGR 2.0 genes in this pathway |
| REACTOME生物钟 | 53 | 40 | All SZGR 2.0 genes in this pathway |
| REACTOME TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION | 72 | 53 | All SZGR 2.0 genes in this pathway |
| LIU SOX4 TARGETS DN | 309 | 191 | All SZGR 2.0 genes in this pathway |
| TIMOFEEVA GROWTH STRESS VIA STAT1 DN | 16 | 12 | All SZGR 2.0 genes in this pathway |
| SMIRNOV CIRCULATING ENDOTHELIOCYTES IN CANCER UP | 158 | 103 | All SZGR 2.0 genes in this pathway |
| MULLIGHAN NPM1 SIGNATURE 3 UP | 341 | 197 | All SZGR 2.0 genes in this pathway |
| ROVERSI GLIOMA COPY NUMBER UP | 100 | 75 | All SZGR 2.0 genes in this pathway |
| FARMER BREAST CANCER APOCRINE VS LUMINAL | 326 | 213 | All SZGR 2.0 genes in this pathway |
| KOMMAGANI TP63 GAMMA TARGETS | 9 | 7 | All SZGR 2.0 genes in this pathway |
| DACOSTA UV RESPONSE VIA ERCC3 UP | 309 | 199 | All SZGR 2.0 genes in this pathway |
| LOPEZ MBD TARGETS | 957 | 597 | All SZGR 2.0 genes in this pathway |
| KOYAMA SEMA3B TARGETS DN | 411 | 249 | All SZGR 2.0 genes in this pathway |
| ROSS AML WITH PML RARA FUSION | 77 | 62 | All SZGR 2.0 genes in this pathway |
| MARIADASON REGULATED BY HISTONE ACETYLATION UP | 83 | 49 | All SZGR 2.0 genes in this pathway |
| HELLER HDAC TARGETS UP | 317 | 208 | All SZGR 2.0 genes in this pathway |
| 海勒HDAC目标SILENCED BY METHYLATION UP | 461 | 298 | All SZGR 2.0 genes in this pathway |
| SHEDDEN LUNG CANCER GOOD SURVIVAL A4 | 196 | 124 | All SZGR 2.0 genes in this pathway |
| CROONQUIST STROMAL STIMULATION UP | 60 | 42 | All SZGR 2.0 genes in this pathway |
| CROONQUIST NRAS VS STROMAL STIMULATION DN | 99 | 65 | All SZGR 2.0 genes in this pathway |
| CAIRO LIVER DEVELOPMENT UP | 166 | 105 | All SZGR 2.0 genes in this pathway |
| KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP | 756 | 494 | All SZGR 2.0 genes in this pathway |
| KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP | 682 | 440 | All SZGR 2.0 genes in this pathway |
| BRUINS UVC RESPONSE VIA TP53 GROUP A | 898 | 516 | All SZGR 2.0 genes in this pathway |
| ACEVEDO FGFR1 TARGETS IN PROSTATE CANCER MODEL DN | 308 | 187 | All SZGR 2.0 genes in this pathway |
| ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY | 1839 | 928 | All SZGR 2.0 genes in this pathway |