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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MED20 |
Basic gene info. | Gene symbol | MED20 |
Gene name | mediator complex subunit 20 | |
Synonyms | PRO0213|TRFP | |
Cytomap | UCSC genome browser: 6p21.1 | |
Genomic location | chr6 :41873091-41888877 | |
Type of gene | protein-coding | |
RefGenes | NM_004275.3, | |
Ensembl id | ENSG00000124641 | |
Description | TRF-proximal protein homologTrf (TATA binding protein-related factor)-proximal homologhTRFPmediator complex subunit 20mediator complex subunit 20mediator complex subunit 20Trf (TATA binding protein-related factor)-proximal homologmediator of RNA polym | |
Modification date | 20141207 | |
dbXrefs | MIM : 612915 | |
HGNC : HGNC | ||
Ensembl : ENSG00000124641 | ||
HPRD : 15638 | ||
Vega : OTTHUMG00000014689 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_MED20 | |
BioGPS: 9477 | ||
Gene Expression Atlas: ENSG00000124641 | ||
The Human Protein Atlas: ENSG00000124641 | ||
Pathway | NCI Pathway Interaction Database: MED20 | |
KEGG: MED20 | ||
REACTOME: MED20 | ||
ConsensusPathDB | ||
Pathway Commons: MED20 | ||
Metabolism | MetaCyc: MED20 | |
HUMANCyc: MED20 | ||
Regulation | Ensembl's Regulation: ENSG00000124641 | |
miRBase: chr6 :41,873,091-41,888,877 | ||
TargetScan: NM_004275 | ||
cisRED: ENSG00000124641 | ||
Context | iHOP: MED20 | |
cancer metabolism search in PubMed: MED20 | ||
UCL Cancer Institute: MED20 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for MED20(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: MED20 |
Familial Cancer Database: MED20 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
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REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: MED20 |
MedGen: MED20 (Human Medical Genetics with Condition) | |
ClinVar: MED20 | |
Phenotype | MGI: MED20 (International Mouse Phenotyping Consortium) |
PhenomicDB: MED20 |
Mutations for MED20 |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
large_intestine | MED20 | chr6 | 41881465 | 41881465 | PKHD1 | chr6 | 51608916 | 51608916 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MED20 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
AI110770 | AKR1A1 | 7 | 518 | 1 | 46033008 | 46033519 | MED20 | 517 | 634 | 6 | 41874553 | 41874670 | |
AF116602 | AKR1A1 | 7 | 518 | 1 | 46033008 | 46033519 | MED20 | 517 | 2095 | 6 | 41873092 | 41874670 | |
AF074677 | AKR1A1 | 7 | 518 | 1 | 46033008 | 46033519 | MED20 | 517 | 634 | 6 | 41874553 | 41874670 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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Stat. for Non-Synonymous SNVs (# total SNVs=16) | (# total SNVs=4) |
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(# total SNVs=0) | (# total SNVs=0) |
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* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr6:41874851-41874851 | p.I200V | 3 |
chr6:41874991-41874991 | p.C153Y | 1 |
chr6:41877201-41877201 | p.A77T | 1 |
chr6:41875024-41875024 | p.V142A | 1 |
chr6:41877202-41877202 | p.F76F | 1 |
chr6:41877006-41877006 | p.? | 1 |
chr6:41877243-41877243 | p.M63V | 1 |
chr6:41877023-41877023 | p.R136Q | 1 |
chr6:41884548-41884548 | p.T48T | 1 |
chr6:41877043-41877043 | p.V129V | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 1 |   | 1 |   |   |   |   | 1 |   |   | 2 |   | 1 |   |   | 2 | 4 |   | 2 |
# mutation |   | 1 |   | 1 |   |   |   |   | 1 |   |   | 2 |   | 1 |   |   | 2 | 4 |   | 2 |
nonsynonymous SNV |   | 1 |   |   |   |   |   |   | 1 |   |   |   |   | 1 |   |   | 1 | 2 |   | 2 |
synonymous SNV |   |   |   | 1 |   |   |   |   |   |   |   | 2 |   |   |   |   | 1 | 2 |   |   |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr6:41877046 | p.V126G | 1 |
chr6:41877053 | p.K97Q | 1 |
chr6:41877141 | p.A77T | 1 |
chr6:41877201 | p.M63V | 1 |
chr6:41877243 | p.T48T | 1 |
chr6:41884548 | p.E22E | 1 |
chr6:41874858 | p.T20S | 1 |
chr6:41884626 | p.A12A | 1 |
chr6:41874865 | p.F197F | 1 |
chr6:41884633 | p.E195V | 1 |
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* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
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cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for MED20 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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BYSL,OARD1,CCND3,CUL7,FLJ41941,HSP90AB1,GLTSCR1L, KLC4,MED20,MRPL2,MRPS10,NFYA,OLIG1,PPP2R5D, RPL7L1,SLC29A1,TBCC,TOMM6,UBR2,USP49,XPO5 | BEND3,RHNO1,VWA9,FAM222B,C2orf15,CASP2,CSTF1, DCAF12,ENOPH1,ESRP1,FANCF,LRRC8D,MED20,PAICS, PEX11B,PRMT6,SHQ1,SUDS3,TRIM59,TUSC3,VSNL1 |
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BYSL,CDC5L,FOXP4,KLHDC3,MAD2L1BP,MAPK14,MEA1, MED20,MRPS10,BLOC1S5,NFYA,POLR1C,PPP2R5D,RPL7L1, SLC35B2,TAF11,TAF8,TBCC,TOMM6,XPO5,ZNF322 | ACTL6A,BTBD10,DHRS4-AS1,CSTF1,DLEU1,DPH5,ESD, LYRM7,MED20,MED28,MRPL30,MSL3P1,PDHB,RAP1GDS1, RNF2,RPS15A,RPS8,SCAF11___GEMIN2___ZEB2,TMEM182,USP39,ZNF627 |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Pharmacological Information for MED20 |
There's no related Drug. |
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Cross referenced IDs for MED20 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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