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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MED25 |
Basic gene info. | Gene symbol | MED25 |
Gene name | mediator complex subunit 25 | |
Synonyms | ACID1|ARC92|CMT2B2|P78|PTOV2 | |
Cytomap | UCSC genome browser: 19q13.3 | |
Genomic location | chr19 :50321535-50340237 | |
Type of gene | protein-coding | |
RefGenes | NM_030973.3, | |
Ensembl id | ENSG00000104973 | |
Description | ARC/mediator transcriptional coactivator subunitactivator interaction domain-containing protein 1activator-recruited cofactor 92 kDa componentmediator of RNA polymerase II transcription subunit 25mediator of RNA polymerase II transcription, subunit 25 | |
Modification date | 20141219 | |
dbXrefs | MIM : 610197 | |
HGNC : HGNC | ||
Ensembl : ENSG00000104973 | ||
HPRD : 14380 | ||
Vega : OTTHUMG00000183161 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_MED25 | |
BioGPS: 81857 | ||
Gene Expression Atlas: ENSG00000104973 | ||
The Human Protein Atlas: ENSG00000104973 | ||
Pathway | NCI Pathway Interaction Database: MED25 | |
KEGG: MED25 | ||
REACTOME: MED25 | ||
ConsensusPathDB | ||
Pathway Commons: MED25 | ||
Metabolism | MetaCyc: MED25 | |
HUMANCyc: MED25 | ||
Regulation | Ensembl's Regulation: ENSG00000104973 | |
miRBase: chr19 :50,321,535-50,340,237 | ||
TargetScan: NM_030973 | ||
cisRED: ENSG00000104973 | ||
Context | iHOP: MED25 | |
cancer metabolism search in PubMed: MED25 | ||
UCL Cancer Institute: MED25 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for MED25(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: MED25 |
Familial Cancer Database: MED25 |
* 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: MED25 |
MedGen: MED25 (Human Medical Genetics with Condition) | |
ClinVar: MED25 | |
Phenotype | MGI: MED25 (International Mouse Phenotyping Consortium) |
PhenomicDB: MED25 |
Mutations for MED25 |
* 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 |
ovary | MED25 | chr19 | 50334110 | 50334130 | MED25 | chr19 | 50336090 | 50336110 |
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 MED25 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 |
BF934224 | SIRT3 | 7 | 173 | 11 | 234864 | 235031 | MED25 | 166 | 292 | 19 | 50334666 | 50335266 | |
BI036185 | SIRT3 | 1 | 84 | 11 | 234864 | 234946 | MED25 | 77 | 263 | 19 | 50334666 | 50335404 |
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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 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 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=26) | (# total SNVs=18) |
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(# total SNVs=4) | (# total SNVs=1) |
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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 |
chr19:50333113-50333113 | p.P201fs*13 | 3 |
chr19:50332310-50332310 | p.G163E | 2 |
chr19:50334697-50334697 | p.S403S | 2 |
chr19:50333403-50333403 | p.P249P | 2 |
chr19:50339043-50339043 | p.T602T | 1 |
chr19:50322430-50322430 | p.Y61C | 1 |
chr19:50333449-50333449 | p.L265M | 1 |
chr19:50332242-50332242 | p.R140R | 1 |
chr19:50334046-50334046 | p.A335T | 1 |
chr19:50333146-50333146 | p.P210L | 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 | 4 |   | 5 |   |   | 1 |   | 4 |   |   | 5 | 3 | 1 |   |   | 12 | 4 |   | 3 |
# mutation | 1 | 4 |   | 6 |   |   | 1 |   | 4 |   |   | 5 | 3 | 1 |   |   | 12 | 4 |   | 7 |
nonsynonymous SNV | 1 | 3 |   | 3 |   |   | 1 |   | 2 |   |   | 3 | 3 | 1 |   |   | 9 | 3 |   | 5 |
synonymous SNV |   | 1 |   | 3 |   |   |   |   | 2 |   |   | 2 |   |   |   |   | 3 | 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 |
chr19:50331769 | p.S531S | 1 |
chr19:50338244 | p.T138T | 1 |
chr19:50333347 | p.E290G | 1 |
chr19:50334032 | p.R586C | 1 |
chr19:50331794 | p.R140W | 1 |
chr19:50338288 | p.P308P | 1 |
chr19:50333362 | p.T602T | 1 |
chr19:50334046 | p.R140R | 1 |
chr19:50332235 | p.G315R | 1 |
chr19:50338308 | p.P605A | 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 MED25 |
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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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AKT1S1,ALDH16A1,AP2A1,EPN1,FUZ,HSPBP1,MED25, NOSIP,NR1H2,PNKP,PTOV1,SCAF1,SUV420H2,TBC1D17, ZBTB45,ZNF205,ZNF444,ZNF446,ZNF579,ZNF628,ZNF787 | ACTR1B,ALKBH7,APBA3,ARMC5,CHMP6,UBALD1,HSPBP1, LRWD1,MAP2K2,MED16,MED25,NUBP2,POLRMT,RNF126, SGTA,STK11,TBL3,THOP1,TIMM17B,TMUB1,ZNF414 |
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AKAP8L,AKT1S1,DHX34,EPN1,FBXO46,FIZ1,GLTSCR1, CAMSAP3,MED25,PPDPF,PRR12,RAVER1,RBM42,SCAF1, CLASRP,STK11,STRN4,XAB2,ZNF574,ZNF628,ZNF787 | CABIN1,CAMTA2,CARM1,DCTN1,EHMT1,FLII,GYS1, HDGFRP2,INPPL1,MAP1S,MED12,MED25,MOB3A,NCOR2, PIAS4,PIGQ,PRR12,SCAF1,ZBTB17,ZC3H3,ZNF710 |
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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 MED25 |
There's no related Drug. |
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Cross referenced IDs for MED25 |
* 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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