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 MED15

Basic gene info.	Gene symbol	MED15
	Gene name	mediator complex subunit 15
	Synonyms	ARC105\|CAG7A\|CTG7A\|PCQAP\|TIG-1\|TIG1\|TNRC7
	Cytomap	UCSC genome browser: 22q11.2
	Genomic location	chr22 :20861885-20941919
	Type of gene	protein-coding
	RefGenes	NM_001003891.2, NM_001293234.1,NM_001293235.1,NM_001293236.1,NM_001293237.1, NM_015889.4,
	Ensembl id	ENSG00000099917
	Description	CTG repeat protein 7aPC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated proteinPC2 glutamine/Q-rich-associated proteinPC2-glutamine-rich-associated proteinTPA inducible gene-1TPA inducible proteinTPA-inducible gene 1 protein
	Modification date	20141207
dbXrefs	MIM : 607372
	HGNC : HGNC
	Ensembl : ENSG00000099917
	HPRD : 12117
	Vega : OTTHUMG00000150810
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MED15
	BioGPS: 51586
	Gene Expression Atlas: ENSG00000099917
	The Human Protein Atlas: ENSG00000099917
Pathway	NCI Pathway Interaction Database: MED15
	KEGG: MED15
	REACTOME: MED15
	ConsensusPathDB
	Pathway Commons: MED15
Metabolism	MetaCyc: MED15
	HUMANCyc: MED15
Regulation	Ensembl's Regulation: ENSG00000099917
	miRBase: chr22 :20,861,885-20,941,919
	TargetScan: NM_001003891
	cisRED: ENSG00000099917
Context	iHOP: MED15
	cancer metabolism search in PubMed: MED15
	UCL Cancer Institute: MED15
Assigned class in ccmGDB	C

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Phenotypic Information for MED15(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MED15
	Familial Cancer Database: MED15

* 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: MED15
	MedGen: MED15 (Human Medical Genetics with Condition)
	ClinVar: MED15
Phenotype	MGI: MED15 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MED15

Mutations for MED15

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
ovary	MED15	chr22	20894360	20894380	KLHL22	chr22	20828830	20828850
ovary	MED15	chr22	20902091	20902111		chr22	19632321	19632341
ovary	MED15	chr22	20920146	20920166	MED15	chr22	20922582	20922602
pancreas	MED15	chr22	20879731	20879751		chr22	21018928	21018948
pancreas	MED15	chr22	20915323	20915343	MED15	chr22	20915804	20915824

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 MED15 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
BI051034	MED15	5	110	22	20939460	20939565	MED15	106	165	22	20939403	20939462
CF125171	RPN2	1	104	20	35835739	35835842	MED15	97	666	22	20861958	20918847
DB259160	FAM46A	1	180	6	82462217	82462396	MED15	175	579	22	20937008	20938693
BG003281	EWSR1	3	64	22	29695685	29695746	MED15	53	210	22	20928982	20929139
DB193761	RPLP2	1	245	11	809968	811645	MED15	240	477	22	20922848	20937156
BF999641	MED15	1	163	22	20923723	20923885	MED15	159	454	22	20928720	20929015
BG003287	EWSR1	8	69	22	29695685	29695746	MED15	58	215	22	20928982	20929139
BG003288	EWSR1	11	72	22	29695685	29695746	MED15	61	217	22	20928982	20929139
BF991563	MED15	15	134	22	20928838	20928959	TRIM40	128	178	6	1445388	1445438

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=30)	Stat. for Synonymous SNVs (# total SNVs=18)

Stat. for Deletions (# total SNVs=5)	Stat. for Insertions (# total SNVs=9)

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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
chr22:20920813-20920814	p.Q250_Q251insQ	8
chr22:20918916-20918918	p.Q211delQ	3
chr22:20918772-20918772	p.Q163*	2
chr22:20905758-20905758	p.I64I	2
chr22:20920813-20920813	p.Q250Q	2
chr22:20937642-20937642	p.M566I	2
chr22:20937674-20937674	p.S577L	2
chr22:20929471-20929471	p.S408S	2
chr22:20918750-20918750	p.L155L	2
chr22:20921089-20921089	p.Q342Q	1

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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	4	1		4	1		1		3			6	2			2	6	7		11
# mutation	4	1		4	1		1		3			6	2			2	6	8		13
nonsynonymous SNV	4	1		2	1		1		1			5	1			2	3	5		9
synonymous SNV				2					2			1	1				3	3		4

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
chr22:20929471	p.S408S	2
chr22:20937674	p.S466L,MED15	2
chr22:20937505	p.V283L,MED15	1
chr22:20907439	p.K467T,MED15	1
chr22:20939481	p.G112E,MED15	1
chr22:20920938	p.Q300H,MED15	1
chr22:20909246	p.A480T,MED15	1
chr22:20940112	p.A142S,MED15	1
chr22:20920999	p.T387A	1
chr22:20929492	p.P509P,MED15	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 MED15 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 MED15

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


ARHGEF1,ARVCF,CDPF1,DGCR14,DGCR2,DGCR6L,GGA1, KLHL22,LZTR1,MED15,MKL1,NOL12,PPIL2,PRR5, TBC1D22A,THAP7,TOP3B,TRIOBP,TRMT2A,YDJC,ZDHHC8	BTBD2,TMEM259,BRAT1,HGS,AP5Z1,LMF2,LZTS2, MAP3K11,MBD3,MED15,NCLN,PLCB3,PNPLA6,RANBP3, SH3GL1,SIPA1,SLC39A13,SLC4A2,STRN4,VAC14,ZDHHC8

AP1B1,BCAR1,BCR,GUCD1,PRR14L,KIAA0930,CYB5R3, DGCR14,DGCR2,GGA1,GTPBP1,LMF2,MED15,MKL1, MYH9,PLEC,PLXNB2,PPIL2,RHOF,TBC1D22A,TOM1	AP2A1,ELMSAN1,FLII,GBF1,ARHGAP35,KDM2A,KSR1, MED15,NDST1,NFE2L1,OTUD7B,PI4KA,PLXNB2,RAPGEF1, SOX13,TAOK2,UBR4,ZFYVE26,ZGPAT,ZMIZ1,ZNF592

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 MED15

There's no related Drug.

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Cross referenced IDs for MED15

* 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