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 MED23

Basic gene info.	Gene symbol	MED23
	Gene name	mediator complex subunit 23
	Synonyms	ARC130\|CRSP130\|CRSP133\|CRSP3\|DRIP130\|MRT18\|SUR-2\|SUR2
	Cytomap	UCSC genome browser: 6q22.33-q24.1
	Genomic location	chr6 :131895105-131949363
	Type of gene	protein-coding
	RefGenes	NM_001270521.1, NM_001270522.1,NM_004830.3,NM_015979.3,
	Ensembl id	ENSG00000112282
	Description	130 kDa transcriptional co-activator133 kDa transcriptional co-activatoractivator-recruited cofactor 130 kDa componentcofactor required for Sp1 transcriptional activation subunit 3mediator of RNA polymerase II transcription subunit 23vitamin D3 recep
	Modification date	20141207
dbXrefs	MIM : 605042
	HGNC : HGNC
	Ensembl : ENSG00000112282
	HPRD : 05436
	Vega : OTTHUMG00000015565
Protein	UniProt: Q9ULK4 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MED23
	BioGPS: 9439
	Gene Expression Atlas: ENSG00000112282
	The Human Protein Atlas: ENSG00000112282
Pathway	NCI Pathway Interaction Database: MED23
	KEGG: MED23
	REACTOME: MED23
	ConsensusPathDB
	Pathway Commons: MED23
Metabolism	MetaCyc: MED23
	HUMANCyc: MED23
Regulation	Ensembl's Regulation: ENSG00000112282
	miRBase: chr6 :131,895,105-131,949,363
	TargetScan: NM_001270521
	cisRED: ENSG00000112282
Context	iHOP: MED23
	cancer metabolism search in PubMed: MED23
	UCL Cancer Institute: MED23
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for MED23(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MED23
	Familial Cancer Database: MED23

* 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 BRCA 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/v490/n7418/full/nature11412.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	605042; gene. 605042; gene. 614249; phenotype. 614249; phenotype.
Orphanet	88616; Autosomal recessive non-syndromic intellectual disability. 88616; Autosomal recessive non-syndromic intellectual disability.
Disease	KEGG Disease: MED23
	MedGen: MED23 (Human Medical Genetics with Condition)
	ClinVar: MED23
Phenotype	MGI: MED23 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MED23

Mutations for MED23

* 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

- Statistics for Tissue and Mutation type

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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'.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MED23 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
CN388362	MMP14	13	63	14	23305808	23305858	MED23	55	275	6	131908097	131908317
AA648640	MED23	5	95	6	131932398	131932488	MED23	89	434	6	131932481	131932825
AA721515	MED23	7	97	6	131932398	131932488	MED23	91	469	6	131932481	131932859
AA648178	MED23	6	96	6	131932398	131932488	MED23	90	406	6	131932481	131932798
BQ223279	MED23	43	98	6	131910602	131910657	MED23	97	879	6	131908205	131908986
AW363299	MED23	20	89	6	131930300	131930370	MED23	74	644	6	131931103	131931678

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=75)	Stat. for Synonymous SNVs (# total SNVs=19)

Stat. for Deletions (# total SNVs=12)	Stat. for Insertions (# total SNVs=2)

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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
chr6:131919885-131919885	p.N746fs*11	3
chr6:131921249-131921249	p.Q717*	3
chr6:131912472-131912472	p.Q1223*	3
chr6:131911468-131911468	p.M1267I	2
chr6:131931276-131931276	p.L329L	2
chr6:131917822-131917822	p.R872C	2
chr6:131927661-131927661	p.K442T	2
chr6:131939626-131939626	p.S234L	2
chr6:131944520-131944520	p.R123W	2
chr6:131937037-131937037	p.?	2

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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=2

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	5		13			7		3			8	5				8	13	1	13
# mutation	1	5		16			7		3			8	5				8	16	1	14
nonsynonymous SNV	1	5		12			4		2			4	4				4	10	1	11
synonymous SNV				4			3		1			4	1				4	6		3

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
chr6:131912565	p.D1192Y,MED23	3
chr6:131931276	p.L329L,MED23	2
chr6:131929091	p.D400N,MED23	2
chr6:131915244	p.Y1186F,MED23	1
chr6:131926585	p.M922I,MED23	1
chr6:131946127	p.K549T,MED23	1
chr6:131917827	p.G368G,MED23	1
chr6:131931197	p.K139N,MED23	1
chr6:131912516	p.I1153I,MED23	1
chr6:131924311	p.R872C,MED23	1

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 MED23 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 MED23

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


AIM1,AKAP7,ASCC3,ATG5,BCLAF1,C6orf203,ENPP1, GOLGA1,HBS1L,LATS1,LOC100129034,MED23,NEDD1,PDSS2, PREP,QRSL1,SCAF8,RTN4IP1,SENP6,SHPRH,STX7	ARID2,MMS22L,TBC1D32,CCNT2,CD2AP,CNOT6,DCAF17, MED23,PHF6,PPIP5K2,RBM26,SMARCAD1,TRIM33,USP37, WRN,ZBTB26,ZNF24,ZNF260,ZNF417,ZNF518A,ZNF91

BAZ2B,CDK19,DOPEY1,ERCC6,FAM120B,FBXL4,GOPC, HEATR5B,GLTSCR1L,UFL1,KLHL24,LATS1,MED23,PHC3, PHF3,RASA2,SCAF8,SENP6,SHPRH,TAB2,ZNF292	CEP192,CMTM4,DOPEY2,ERCC6,HEATR5B,HOXA6,JRKL, KIAA1147,LIMD1,MBTD1,MED23,NFYA,PHLPP1,PTCH1, TTC17,ZCCHC8,ZFP62,ZKSCAN1,ZNF141,ZNF41,ZNF81

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 MED23

There's no related Drug.

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Cross referenced IDs for MED23

* 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