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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MED10 |
Basic gene info. | Gene symbol | MED10 |
Gene name | mediator complex subunit 10 | |
Synonyms | NUT2|TRG20 | |
Cytomap | UCSC genome browser: 5p15.31 | |
Genomic location | chr5 :6372038-6378639 | |
Type of gene | protein-coding | |
RefGenes | NM_032286.2, | |
Ensembl id | ENSG00000133398 | |
Description | TRG-17TRG-20mediator of RNA polymerase II transcription subunit 10mediator of RNA polymerase II transcription, subunit 10transformation-related gene 17 proteintransformation-related gene 20 protein | |
Modification date | 20141207 | |
dbXrefs | MIM : 612382 | |
HGNC : HGNC | ||
Ensembl : ENSG00000133398 | ||
HPRD : 14680 | ||
Vega : OTTHUMG00000161682 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_MED10 | |
BioGPS: 84246 | ||
Gene Expression Atlas: ENSG00000133398 | ||
The Human Protein Atlas: ENSG00000133398 | ||
Pathway | NCI Pathway Interaction Database: MED10 | |
KEGG: MED10 | ||
REACTOME: MED10 | ||
ConsensusPathDB | ||
Pathway Commons: MED10 | ||
Metabolism | MetaCyc: MED10 | |
HUMANCyc: MED10 | ||
Regulation | Ensembl's Regulation: ENSG00000133398 | |
miRBase: chr5 :6,372,038-6,378,639 | ||
TargetScan: NM_032286 | ||
cisRED: ENSG00000133398 | ||
Context | iHOP: MED10 | |
cancer metabolism search in PubMed: MED10 | ||
UCL Cancer Institute: MED10 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for MED10(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: MED10 |
Familial Cancer Database: MED10 |
* 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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: MED10 |
MedGen: MED10 (Human Medical Genetics with Condition) | |
ClinVar: MED10 | |
Phenotype | MGI: MED10 (International Mouse Phenotyping Consortium) |
PhenomicDB: MED10 |
Mutations for MED10 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MED10 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 |
AY453399 | SUN2 | 1 | 349 | 22 | 39175441 | 39178755 | MED10 | 350 | 446 | 5 | 6372616 | 6372712 | |
BU686640 | CC2D1A | 18 | 513 | 19 | 14041197 | 14041692 | MED10 | 512 | 604 | 5 | 6372242 | 6372334 | |
CA433841 | MED10 | 11 | 257 | 5 | 6377063 | 6377309 | SPARCL1 | 250 | 403 | 4 | 88415592 | 88415745 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=7) | (# total SNVs=2) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr5:6374509-6374509 | p.L79L | 2 |
chr5:6377297-6377297 | p.V63A | 1 |
chr5:6378532-6378532 | p.L22H | 1 |
chr5:6378552-6378552 | p.F15F | 1 |
chr5:6372619-6372619 | p.S135S | 1 |
chr5:6378580-6378580 | p.D6V | 1 |
chr5:6372624-6372624 | p.P134S | 1 |
chr5:6378594-6378594 | p.M1I | 1 |
chr5:6372670-6372670 | p.P118P | 1 |
chr5:6372697-6372697 | p.L109L | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   | 1 |   | 1 |   |   |   |   |   |   |
# mutation | 1 |   |   | 1 |   |   |   |   | 1 |   |   | 1 |   | 1 |   |   |   |   |   |   |
nonsynonymous SNV |   |   |   |   |   |   |   |   | 1 |   |   | 1 |   | 1 |   |   |   |   |   |   |
synonymous SNV | 1 |   |   | 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]) |
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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 |
chr5:6372624 | p.P134S | 1 |
chr5:6372670 | p.P118P | 1 |
chr5:6372701 | p.L108Q | 1 |
chr5:6374488 | p.E86D | 1 |
chr5:6378552 | p.F15F | 1 |
Other DBs for Point Mutations |
Copy Number for MED10 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] |
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Gene Expression for MED10 |
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)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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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 |
BRD9,BUD31,CCT5,CLPTM1L,CTU2,DGUOK,DNTTIP1, FAM96B,LOC388796,MED10,MRPL36,MRPS5,NDUFA11,NDUFS6, NUDT1,PDCD6,PSMC3,TMED9,TMEM208,UBE2C,ZNF622 | ATP5E,BLOC1S1,BRI3,C1orf123,CCDC23,ENY2,LGALS3, MED10,CMC4,NEDD8,PPP1R7,PSMB4,RNASEK,RNF181, RPS20,S100A13,SAT2,SLC25A28,STX8,TNFSF12,TRNAU1AP |
BANF1,BRIX1,BUD31,C5orf28,CCDC127,CCDC59,CCT5, DDX47,DGUOK,FASTKD3,MED10,MRPL36,PAIP1,PDCD6, PFDN5,RNF181,RPL37,SUB1,TARS,TXNL4B,ZNF622 | ANAPC16,ATG12,AZI2,LYRM9,SMIM11,FBXL5,FIS1, FNTA,HMGN4,LYRM5,MANBAL,MED10,METTL5,NEK7, PCNP,RHEB,S100A13,SNX3,STARD3NL,TMEM14A,YPEL5 |
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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for MED10 |
There's no related Drug. |
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Cross referenced IDs for MED10 |
* 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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