Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 MED12
Basic gene info.Gene symbolMED12
Gene namemediator complex subunit 12
SynonymsARC240|CAGH45|FGS1|HOPA|MED12S|OHDOX|OKS|OPA1|TNRC11|TRAP230
CytomapUCSC genome browser: Xq13
Genomic locationchrX :70338405-70362304
Type of geneprotein-coding
RefGenesNM_005120.2,
Ensembl idENSG00000184634
DescriptionCAG repeat protein 45OPA-containing proteinactivator-recruited cofactor 240 kDa componenthuman opposite pairedmediator of RNA polymerase II transcription subunit 12mediator of RNA polymerase II transcription, subunit 12 homologputative mediator subu
Modification date20141219
dbXrefs MIM : 300188
HGNC : HGNC
Ensembl : ENSG00000184634
HPRD : 02176
Vega : OTTHUMG00000021788
ProteinUniProt: Q93074
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED12
BioGPS: 9968
Gene Expression Atlas: ENSG00000184634
The Human Protein Atlas: ENSG00000184634
PathwayNCI Pathway Interaction Database: MED12
KEGG: MED12
REACTOME: MED12
ConsensusPathDB
Pathway Commons: MED12
MetabolismMetaCyc: MED12
HUMANCyc: MED12
RegulationEnsembl's Regulation: ENSG00000184634
miRBase: chrX :70,338,405-70,362,304
TargetScan: NM_005120
cisRED: ENSG00000184634
ContextiHOP: MED12
cancer metabolism search in PubMed: MED12
UCL Cancer Institute: MED12
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MED12 in cancer cell metabolism1. Grants JM, Goh GY, Taubert S (2015) The Mediator complex of Caenorhabditis elegans: insights into the developmental and physiological roles of a conserved transcriptional coregulator. Nucleic Acids Res 43: 2442-2453. doi: 10.1093/nar/gkv037. pmid: 4344494. go to article

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Phenotypic Information for MED12(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED12
Familial Cancer Database: MED12
* 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 PRAD 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 300188; gene.
300895; phenotype.
305450; phenotype.
309520; phenotype.
Orphanet 293707; Blepharophimosis-intellectual disability syndrome, MKB type.
776; X-linked intellectual disability with marfanoid habitus.
777; X-linked non-syndromic intellectual disability.
93932; FG syndrome type 1.
DiseaseKEGG Disease: MED12
MedGen: MED12 (Human Medical Genetics with Condition)
ClinVar: MED12
PhenotypeMGI: MED12 (International Mouse Phenotyping Consortium)
PhenomicDB: MED12

Mutations for MED12
* 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 MED12 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG519661RPL1427634050356740503641MED1271399X7036176170362299
AF117755RPRD211061150407357150407462MED121076757X7033857370362147
BF361917ANKS1B8570129978369399784255MED12562641X7034301970343465
BE005998AKAP12252516151670841151671064MED12252645X7034611170347191
BE005999AKAP1282236151670841151671056MED12224663X7034611170347238

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=398

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=242)
Stat. for Synonymous SNVs
(# total SNVs=55)
Stat. for Deletions
(# total SNVs=11)
Stat. for Insertions
(# total SNVs=10)

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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
chr23:70339254-70339254p.G44D240
chr23:70339253-70339253p.G44R158
chr23:70339230-70339230p.L36R25
chr23:70339215-70339215p.E33_D34insPQ21
chr23:70339251-70339251p.Q43P16
chr23:70349258-70349258p.L1224F8
chr23:70339241-70339267p.N40_Q48del5
chr23:70339249-70339263p.K42_N46del4
chr23:70338701-70338701p.E33*4
chr23:70339245-70339271p.V41_P49del4

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13142274 13 81 2761151411 36
# mutation13142264 15 81 3361141411 53
nonsynonymous SNV10112204 12 71 255113118 36
synonymous SNV33 6  3 1  81  133 18
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
chrX:70349258p.L1224V4
chrX:70356862p.N1845T3
chrX:70346843p.R817H2
chrX:70343021p.F684L2
chrX:70344691p.R1138G2
chrX:70354597p.V1588M2
chrX:70354958p.R1627H2
chrX:70345913p.E904Q2
chrX:70343476p.Q2065Q2
chrX:70360635p.R521H2

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 MED12 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 MED12

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

ATF7IP,ATRX,BRWD3,EP400,EPC1,FOXO4,HUWE1,
LMTK2,MED12,KMT2B___KMT2D,NONO,RAD54L2,RBM41,SNX12,
TAF1,TRRAP,ZMYM3,ZNF142,ZNF41,ZNF81,ZXDA
ARID1B,PRRC2B,BAZ2A,HECTD4,CREBBP,EP300,EP400,
EVC,HERC2,LMTK2,MDN1,MECP2,MED12,KMT2B___KMT2D,
NUP214,PRPF8,RAD54L2,RGP1,SPEN,TRRAP,ZNF142

ATRX,BCORL1,BRWD3,SOGA1,CHD6,CUL4B,AMER1,
FOXO4,HDAC6,HUWE1,MECP2,MED12,MTMR1,PHF8,
SHROOM4,TAF1,TAF1L,ZBTB33,ZMYM3,ZNF275,ZNF81
ARID1A,BRD1,CHD8,CREBBP,EP300,FAM193A,GTF3C1,
KDM2A,EPG5,MAML1,MED12,MEGF8,PHF8,PRPF8,
PRR12,SMARCC2,SMG6,SNRNP200,SRCAP,TRRAP,USP22
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 MED12


There's no related Drug.
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Cross referenced IDs for MED12
* 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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