Gene Page: MED4
Summary ?
| GeneID | 29079 |
| Symbol | MED4 |
| Synonyms | ARC36|DRIP36|HSPC126|TRAP36|VDRIP |
| Description | mediator complex subunit 4 |
| Reference | MIM:605718|HGNC:HGNC:17903|Ensembl:ENSG00000136146|HPRD:16145|Vega:OTTHUMG00000016891 |
| Gene type | protein-coding |
| Map location | 13q14.2 |
| Pascal p-value | 0.336 |
| Sherlock p-value | 0.971 |
| Fetal beta | 0.114 |
| DMG | 1 (# studies) |
| eGene | Cerebellar Hemisphere Cerebellum Cortex Myers' cis & trans Meta |
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. | 1 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg24429159 | 13 | 48669391 | MED4 | 5.21E-9 | -0.011 | 2.92E-6 | DMG:Jaffe_2016 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs4941618 | chr13 | 48517288 | MED4 | 29079 | 0 | cis | ||
| rs7996581 | chr13 | 48636963 | MED4 | 29079 | 6.294E-4 | cis | ||
| rs7332363 | chr13 | 48666760 | MED4 | 29079 | 0.01 | cis | ||
| rs7332994 | chr13 | 48674134 | MED4 | 29079 | 1.316E-4 | cis | ||
| rs1410116 | chr13 | 48685915 | MED4 | 29079 | 5.356E-4 | cis | ||
| rs7326381 | chr13 | 48696213 | MED4 | 29079 | 6.016E-4 | cis | ||
| rs7317685 | chr13 | 48715752 | MED4 | 29079 | 0.02 | cis | ||
| rs4941618 | chr13 | 48517288 | MED4 | 29079 | 0.19 | trans | ||
| rs7996581 | chr13 | 48636963 | MED4 | 29079 | 0.05 | trans | ||
| rs7332994 | chr13 | 48674134 | MED4 | 29079 | 0.01 | trans | ||
| rs1410116 | chr13 | 48685915 | MED4 | 29079 | 0.04 | trans | ||
| rs7326381 | chr13 | 48696213 | MED4 | 29079 | 0.05 | 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:0004872 | receptor activity | IDA | 12218053 | |
| GO:0003712 | transcription cofactor activity | IDA | 12218053 | |
| GO:0005515 | protein binding | IPI | 17438371 | |
| GO:0016455 | RNA polymerase II transcription mediator activity | IDA | 10882111 | |
| GO:0016563 | transcription activator activity | IDA | 10198638 | |
| GO:0030374 | ligand-dependent nuclear receptor transcription coactivator activity | NAS | 10235266 | |
| GO:0042809 | vitamin D receptor binding | NAS | 10235266 | |
| GO:0046966 | thyroid hormone receptor binding | IDA | 10198638 | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0006355 | regulation of transcription, DNA-dependent | IEA | - | |
| GO:0006367 | transcription initiation from RNA polymerase II promoter | IDA | 12218053 | |
| GO:0006350 | transcription | IEA | - | |
| GO:0030521 | androgen receptor signaling pathway | IDA | 12218053 | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0000119 | mediator complex | IDA | 10882111 | |
| GO:0005634 | nucleus | IDA | 10235267 | |
| GO:0005730 | nucleolus | IDA | 18029348 | |
| GO:0005737 | cytoplasm | IDA | 18029348 |
Section IV. Protein-protein interaction annotation
| Interactors | Aliases B | Official full name B | Experimental | Source | PubMed ID |
|---|---|---|---|---|---|
| AP2M1 | AP50 | CLAPM1 | mu2 | adaptor-related protein complex 2, mu 1 subunit | Two-hybrid | BioGRID | 16189514 |
| MCRS1 | ICP22BP | INO80Q | MCRS2 | MSP58 | P78 | microspherule protein 1 | Two-hybrid | BioGRID | 16189514 |
| MED10 | L6 | MGC5309 | NUT2 | TRG20 | mediator complex subunit 10 | Affinity Capture-MS Affinity Capture-Western | BioGRID | 14638676 |15175163 |
| MED19 | DT2P1G7 | LCMR1 | mediator complex subunit 19 | Affinity Capture-MS Affinity Capture-Western | BioGRID | 14638676 |15175163 |
| MED25 | ACID1 | ARC92 | DKFZp434K0512 | MGC70671 | P78 | PTOV2 | TCBAP0758 | mediator complex subunit 25 | Affinity Capture-Western Reconstituted Complex | BioGRID | 14638676 |
| MED26 | CRSP7 | CRSP70 | mediator complex subunit 26 | Affinity Capture-MS | BioGRID | 15175163 |
| MED28 | 1500003D12Rik | DKFZp434N185 | EG1 | magicin | mediator complex subunit 28 | Affinity Capture-MS | BioGRID | 15175163 |
| MED29 | DKFZp434H247 | IXL | mediator complex subunit 29 | - | HPRD | 14576168 |
| MED29 | DKFZp434H247 | IXL | mediator complex subunit 29 | Affinity Capture-MS Affinity Capture-Western | BioGRID | 14638676 |15175163 |
| MED30 | MGC9890 | THRAP6 | TRAP25 | mediator complex subunit 30 | TRAP36 interacts with TRAP25. This interaction was modelled on a demonstrated interaction between human TRAP36 and mouse TRAP25. | BIND | 12584197 |
| MED30 | MGC9890 | THRAP6 | TRAP25 | mediator complex subunit 30 | Reconstituted Complex | BioGRID | 12584197 |
| MED9 | FLJ10193 | MED25 | MGC138234 | mediator complex subunit 9 | Affinity Capture-MS | BioGRID | 15175163 |
| MED9 | FLJ10193 | MED25 | MGC138234 | mediator complex subunit 9 | - | HPRD | 14638676 |
| TNFAIP8 | GG2-1 | MDC-3.13 | SCC-S2 | SCCS2 | tumor necrosis factor, alpha-induced protein 8 | Two-hybrid | BioGRID | 16189514 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| REACTOME DEVELOPMENTAL BIOLOGY | 396 | 292 | All SZGR 2.0 genes in this pathway |
| REACTOME PPARA ACTIVATES GENE EXPRESSION | 104 | 72 | 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 TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION | 72 | 53 | All SZGR 2.0 genes in this pathway |
| DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP | 1382 | 904 | All SZGR 2.0 genes in this pathway |
| LIU CMYB TARGETS UP | 165 | 106 | All SZGR 2.0 genes in this pathway |
| LIU VMYB TARGETS UP | 127 | 78 | All SZGR 2.0 genes in this pathway |
| TIEN INTESTINE PROBIOTICS 24HR UP | 557 | 331 | All SZGR 2.0 genes in this pathway |
| ENK UV RESPONSE EPIDERMIS DN | 508 | 354 | All SZGR 2.0 genes in this pathway |
| NUYTTEN NIPP1 TARGETS UP | 769 | 437 | All SZGR 2.0 genes in this pathway |
| SCHAEFFER PROSTATE DEVELOPMENT AND CANCER BOX5 DN | 8 | 5 | All SZGR 2.0 genes in this pathway |
| SHEN SMARCA2 TARGETS UP | 424 | 268 | All SZGR 2.0 genes in this pathway |
| KRIGE RESPONSE TO TOSEDOSTAT 6HR DN | 911 | 527 | All SZGR 2.0 genes in this pathway |
| KRIGE RESPONSE TO TOSEDOSTAT 24HR DN | 1011 | 592 | All SZGR 2.0 genes in this pathway |
| LIN MELANOMA COPY NUMBER DN | 41 | 34 | All SZGR 2.0 genes in this pathway |
| JOHNSTONE PARVB TARGETS 2 DN | 336 | 211 | All SZGR 2.0 genes in this pathway |
| JOHNSTONE PARVB TARGETS 3 DN | 918 | 550 | All SZGR 2.0 genes in this pathway |