|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MED1 |
Basic gene info. | Gene symbol | MED1 |
Gene name | mediator complex subunit 1 | |
Synonyms | CRSP1|CRSP200|DRIP205|DRIP230|PBP|PPARBP|PPARGBP|RB18A|TRAP220|TRIP2 | |
Cytomap | UCSC genome browser: 17q12 | |
Genomic location | chr17 :37560537-37607527 | |
Type of gene | protein-coding | |
RefGenes | NM_004774.3, | |
Ensembl id | ENSG00000125686 | |
Description | ARC205PPAR binding proteinPPAR-binding proteinPPARG binding proteinTR-interacting protein 2TRIP-2activator-recruited cofactor 205 kDa componentmediator of RNA polymerase II transcription subunit 1p53 regulatory protein RB18Aperoxisome proliferato | |
Modification date | 20141207 | |
dbXrefs | MIM : 604311 | |
HGNC : HGNC | ||
Ensembl : ENSG00000125686 | ||
HPRD : 05055 | ||
Vega : OTTHUMG00000133216 | ||
Protein | UniProt: Q15648 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_MED1 | |
BioGPS: 5469 | ||
Gene Expression Atlas: ENSG00000125686 | ||
The Human Protein Atlas: ENSG00000125686 | ||
Pathway | NCI Pathway Interaction Database: MED1 | |
KEGG: MED1 | ||
REACTOME: MED1 | ||
ConsensusPathDB | ||
Pathway Commons: MED1 | ||
Metabolism | MetaCyc: MED1 | |
HUMANCyc: MED1 | ||
Regulation | Ensembl's Regulation: ENSG00000125686 | |
miRBase: chr17 :37,560,537-37,607,527 | ||
TargetScan: NM_004774 | ||
cisRED: ENSG00000125686 | ||
Context | iHOP: MED1 | |
cancer metabolism search in PubMed: MED1 | ||
UCL Cancer Institute: MED1 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
Top |
Phenotypic Information for MED1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: MED1 |
Familial Cancer Database: MED1 |
* This gene is included in those cancer gene databases. |
. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | 604311; gene. |
Orphanet | |
Disease | KEGG Disease: MED1 |
MedGen: MED1 (Human Medical Genetics with Condition) | |
ClinVar: MED1 | |
Phenotype | MGI: MED1 (International Mouse Phenotyping Consortium) |
PhenomicDB: MED1 |
Mutations for MED1 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
breast | MED1 | chr17 | 37594061 | 37594061 | chr17 | 38075641 | 38075641 | |
breast | MED1 | chr17 | 37604775 | 37604775 | chr17 | 41099312 | 41099312 | |
breast | MED1 | chr17 | 37606863 | 37607263 | WIPF2 | chr17 | 38398667 | 38399067 |
pancreas | MED1 | chr17 | 37596461 | 37596481 | chr17 | 46550428 | 46550448 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MED1 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 |
BE818200 | DNAJC5 | 25 | 194 | 20 | 62565964 | 62566133 | MED1 | 185 | 539 | 17 | 37563597 | 37563951 | |
H19757 | MED1 | 14 | 80 | 17 | 37565572 | 37565638 | HPCAL4 | 68 | 304 | 1 | 40144653 | 40144881 | |
H21133 | MED1 | 2 | 68 | 17 | 37565572 | 37565638 | HPCAL4 | 56 | 291 | 1 | 40144655 | 40144881 |
Other DBs for Structural Variants |
Top |
Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 10 |   |   |   |   |   | 1 |   | 2 |   |   |   |   |   | 2 |   |   | |||
GAIN (# sample) | 10 |   |   |   |   |   | 1 |   | 2 |   |   |   |   |   | 2 |   |   | |||
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) |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=88) | (# total SNVs=22) |
(# total SNVs=4) | (# total SNVs=0) |
Top |
Top 10 SNVs Having the Most Samples in COSMIC data |
* 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 |
chr17:37566456-37566456 | p.S673F | 3 |
chr17:37565611-37565611 | p.G955S | 2 |
chr17:37566882-37566882 | p.T531I | 2 |
chr17:37565455-37565455 | p.D1007H | 2 |
chr17:37566511-37566511 | p.Q655E | 2 |
chr17:37587411-37587411 | p.K202N | 2 |
chr17:37563791-37563791 | p.S1561R | 2 |
chr17:37566444-37566444 | p.R677H | 2 |
chr17:37563898-37563898 | p.H1526D | 2 |
chr17:37564239-37564239 | p.K1412R | 2 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 | 6 | 1 | 3 | 16 |   |   | 7 |   | 3 | 2 |   | 13 | 9 | 1 | 1 | 1 | 10 | 12 |   | 8 |
# mutation | 7 | 1 | 3 | 17 |   |   | 9 |   | 3 | 2 |   | 13 | 11 | 1 | 1 | 1 | 10 | 13 |   | 12 |
nonsynonymous SNV | 6 | 1 | 3 | 13 |   |   | 8 |   | 2 | 1 |   | 10 | 8 | 1 | 1 | 1 | 8 | 7 |   | 11 |
synonymous SNV | 1 |   |   | 4 |   |   | 1 |   | 1 | 1 |   | 3 | 3 |   |   |   | 2 | 6 |   | 1 |
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]) |
Top |
Top 10 SNVs Having the Most Samples in TCGA data |
* 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 |
chr17:37564132 | p.P1448S | 2 |
chr17:37587411 | p.G955G | 2 |
chr17:37565966 | p.K202N | 2 |
chr17:37565609 | p.R677H | 2 |
chr17:37566444 | p.T836T | 2 |
chr17:37565297 | p.S1239L | 1 |
chr17:37566692 | p.H1024Y | 1 |
chr17:37563981 | p.P834P | 1 |
chr17:37564497 | p.S588L | 1 |
chr17:37565808 | p.S314S | 1 |
Other DBs for Point Mutations |
Copy Number for MED1 in TCGA |
* 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. |
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] |
Top |
Gene Expression for MED1 |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* 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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* 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 |
ATP1A1,C11orf31,ATP1A1-AS1,CD58,CDH19,CLP1,CTNND1, GDAP2,KCTD14,LCN2,MED19,OR6C70,OR6Q1,PLSCR5, PRG2,SLC43A3,TIMM10,TMX2,VTCN1,WDR3,ZDHHC5 | APOA1BP,ARF5,BUD31,C12orf57,C17orf49,CUTA,DPCD, MED19,MED27,OVCA2,PDCD6,PHF5A,PRELID1,RAB34, SDF2,SF3B5,SNRPF,TMEM208,UFC1,VPS25,ZNRD1 | ||||
ASNA1,ATP5L,BANF1,C11orf31,LAMTOR1,COA4,FAU, MED19,MRPL11,MRPL21,MRPL49,MRPL54,NDUFS3,POLR2G, PPP1CA,SDHAF2,TIMM8B,TMEM223,TRMT112,TTC9C,YIF1A | ASNA1,ATP6V0B,BID,BUD31,C1orf174,TIMMDC1,TMEM261, CHCHD2,DCTPP1,DPM3,FAM58A,FAM96B,LSM7,LYRM2, MED19,MRPL54,NDUFA7,RPSAP58,SERF2,SSR2,STOML2 |
Co-Expressed gene's Protein-protein interaction Network Plot |
* 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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for MED1 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA33556; -. |
Organism-specific databases | CTD | 5469; -. |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB08696 | mediator complex subunit 1 | experimental | 5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL | ||
DB00755 | mediator complex subunit 1 | approved; nutraceutical; investigational | Tretinoin |
Top |
Cross referenced IDs for MED1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |