Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	MED12
	Gene name	mediator complex subunit 12
	Synonyms	ARC240\|CAGH45\|FGS1\|HOPA\|MED12S\|OHDOX\|OKS\|OPA1\|TNRC11\|TRAP230
	Cytomap	UCSC genome browser: Xq13
	Genomic location	chrX :70338405-70362304
	Type of gene	protein-coding
	RefGenes	NM_005120.2,
	Ensembl id	ENSG00000184634
	Description	CAG 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 date	20141219
dbXrefs	MIM : 300188
	HGNC : HGNC
	Ensembl : ENSG00000184634
	HPRD : 02176
	Vega : OTTHUMG00000021788
Protein	UniProt: Q93074 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MED12
	BioGPS: 9968
	Gene Expression Atlas: ENSG00000184634
	The Human Protein Atlas: ENSG00000184634
Pathway	NCI Pathway Interaction Database: MED12
	KEGG: MED12
	REACTOME: MED12
	ConsensusPathDB
	Pathway Commons: MED12
Metabolism	MetaCyc: MED12
	HUMANCyc: MED12
Regulation	Ensembl's Regulation: ENSG00000184634
	miRBase: chrX :70,338,405-70,362,304
	TargetScan: NM_005120
	cisRED: ENSG00000184634
Context	iHOP: MED12
	cancer metabolism search in PubMed: MED12
	UCL Cancer Institute: MED12
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MED12 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
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.
Disease	KEGG Disease: MED12
	MedGen: MED12 (Human Medical Genetics with Condition)
	ClinVar: MED12
Phenotype	MGI: MED12 (International Mouse Phenotyping Consortium)
Phenotype	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.

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 MED12 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
BG519661	RPL14	2	76	3	40503567	40503641	MED12	71	399	X	70361761	70362299
AF117755	RPRD2	1	106	1	150407357	150407462	MED12	107	6757	X	70338573	70362147
BF361917	ANKS1B	8	570	12	99783693	99784255	MED12	562	641	X	70343019	70343465
BE005998	AKAP12	25	251	6	151670841	151671064	MED12	252	645	X	70346111	70347191
BE005999	AKAP12	8	223	6	151670841	151671056	MED12	224	663	X	70346111	70347238

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=398

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Somatic 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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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
chr23:70339254-70339254	p.G44D	240
chr23:70339253-70339253	p.G44R	158
chr23:70339230-70339230	p.L36R	25
chr23:70339215-70339215	p.E33_D34insPQ	21
chr23:70339251-70339251	p.Q43P	16
chr23:70349258-70349258	p.L1224F	8
chr23:70339241-70339267	p.N40_Q48del	5
chr23:70339245-70339271	p.V41_P49del	4
chr23:70339249-70339263	p.K42_N46del	4
chr23:70338701-70338701	p.E33*	4

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	13	14	2	27	4		13		8	1		27	6	1	1	5	14	11		36
# mutation	13	14	2	26	4		15		8	1		33	6	1	1	4	14	11		53
nonsynonymous SNV	10	11	2	20	4		12		7	1		25	5	1	1	3	11	8		36
synonymous SNV	3	3		6			3		1			8	1			1	3	3		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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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
chrX:70349258	p.L1224V	4
chrX:70356862	p.N1845T	3
chrX:70360635	p.E79D	2
chrX:70338703	p.K550N	2
chrX:70348505	p.A240V	2
chrX:70340986	p.R817H	2
chrX:70339568	p.F684L	2
chrX:70346843	p.R1138G	2
chrX:70343021	p.V1588M	2
chrX:70344691	p.R1627H	2

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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