Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for MED8
Basic gene info.Gene symbolMED8
Gene namemediator complex subunit 8
SynonymsARC32
CytomapUCSC genome browser: 1p34.2
Genomic locationchr1 :43849587-43855483
Type of geneprotein-coding
RefGenesNM_001001653.2,
NM_052877.4,NM_201542.4,
Ensembl idENSG00000159479
Descriptionactivator-recruited cofactor 32 kDa componentmediator of RNA polymerase II transcription subunit 8mediator of RNA polymerase II transcription subunit MED8
Modification date20141207
dbXrefs MIM : 607956
HGNC : HGNC
Ensembl : ENSG00000159479
HPRD : 06991
Vega : OTTHUMG00000007421
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED8
BioGPS: 112950
Gene Expression Atlas: ENSG00000159479
The Human Protein Atlas: ENSG00000159479
PathwayNCI Pathway Interaction Database: MED8
KEGG: MED8
REACTOME: MED8
ConsensusPathDB
Pathway Commons: MED8
MetabolismMetaCyc: MED8
HUMANCyc: MED8
RegulationEnsembl's Regulation: ENSG00000159479
miRBase: chr1 :43,849,587-43,855,483
TargetScan: NM_001001653
cisRED: ENSG00000159479
ContextiHOP: MED8
cancer metabolism search in PubMed: MED8
UCL Cancer Institute: MED8
Assigned class in ccmGDBC

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Phenotypic Information for MED8(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED8
Familial Cancer Database: MED8
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MED8
MedGen: MED8 (Human Medical Genetics with Condition)
ClinVar: MED8
PhenotypeMGI: MED8 (International Mouse Phenotyping Consortium)
PhenomicDB: MED8

Mutations for MED8
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MED8 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr1:43850143-43850143p.N206fs*>73
chr1:43852668-43852668p.R2Q2
chr1:43852669-43852669p.R2W2
chr1:43852577-43852577p.E32E2
chr1:43852603-43852603p.P24S1
chr1:43851797-43851797p.G109G1
chr1:43852618-43852618p.H19Y1
chr1:43850137-43850137p.H208P1
chr1:43851824-43851824p.K100K1
chr1:43852634-43852634p.H13H1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   5  1    2   133 5
# mutation   5  1    2   133 6
nonsynonymous SNV   4       2   112 5
synonymous SNV   1  1         21 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr1:43852653p.R7L,MED82
chr1:43852603p.R2W,MED81
chr1:43850172p.V80V,MED81
chr1:43852634p.F71F,MED81
chr1:43850733p.K285K1
chr1:43851662p.F71L,MED81
chr1:43852669p.M174V,MED81
chr1:43851674p.L63F,MED81
chr1:43853204p.Q154H,MED81
chr1:43851779p.V62V,MED81

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for MED8 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 MED8

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

ADPRHL2,B4GALT2,C1orf50,CDC20,DPH2,EBNA1BP2,EIF2B3,
ELOVL1,ERI3,GNL2,IPO13,KTI12,MAGOH,MED8,
MUTYH,PPIH,PSMB2,TRAPPC3,UQCRH,UQCRHL,YBX1
AP1M1,AVPI1,BCAP31,CD81,CPNE2,ELOVL1,FADS3,
GPX4,GTF2E2,INPP5K,LGALS1,MED8,MGC72080,NADK,
NME4,POLR2L,RPS2P32,RRAS,SURF4,TESK1,TUBB6

ADPRHL2,AK2,ATP6V0B,SMIM12,CDC20,EBNA1BP2,EIF3I,
ELOVL1,LRRC42,LSM10,MED8,MRPL20,PEF1,PRDX1,
PSMA5,RER1,SEC13,TRAPPC3,UROD,UTP11L,ZBTB8OS
ARF1,C19orf10,CHCHD1,FAM96B,GALE,GTF2E2,MED8,
MTX1,NUDT5,PGK1,PSMB3,PSMC4,PSMD13,RPS6KB2,
S100A6,SEC61B,SRA1,STRA13,TMED9,TMEM199,TMEM208
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for MED8


There's no related Drug.
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Cross referenced IDs for MED8
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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