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 MED26

Basic gene info.	Gene symbol	MED26
	Gene name	mediator complex subunit 26
	Synonyms	CRSP7\|CRSP70
	Cytomap	UCSC genome browser: 19p13.11
	Genomic location	chr19 :16685717-16739015
	Type of gene	protein-coding
	RefGenes	NM_004831.3,
	Ensembl id	ENSG00000105085
	Description	ARC70CRSP complex subunit 7activator-recruited cofactor 70 kDa componentcofactor required for Sp1 transcriptional activation subunit 7cofactor required for Sp1 transcriptional activation, subunit 7 (70kD)cofactor required for Sp1 transcriptional acti
	Modification date	20141207
dbXrefs	MIM : 605043
	HGNC : HGNC
	Ensembl : ENSG00000105085
	HPRD : 05437
	Vega : OTTHUMG00000182433
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MED26
	BioGPS: 9441
	Gene Expression Atlas: ENSG00000105085
	The Human Protein Atlas: ENSG00000105085
Pathway	NCI Pathway Interaction Database: MED26
	KEGG: MED26
	REACTOME: MED26
	ConsensusPathDB
	Pathway Commons: MED26
Metabolism	MetaCyc: MED26
	HUMANCyc: MED26
Regulation	Ensembl's Regulation: ENSG00000105085
	miRBase: chr19 :16,685,717-16,739,015
	TargetScan: NM_004831
	cisRED: ENSG00000105085
Context	iHOP: MED26
	cancer metabolism search in PubMed: MED26
	UCL Cancer Institute: MED26
Assigned class in ccmGDB	C

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Phenotypic Information for MED26(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MED26
	Familial Cancer Database: MED26

* 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: MED26
	MedGen: MED26 (Human Medical Genetics with Condition)
	ClinVar: MED26
Phenotype	MGI: MED26 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MED26

Mutations for MED26

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
central_nervous_system	MED26	chr19	16707988	16707988	MED26	chr19	16709424	16709424
ovary	MED26	chr19	16688463	16688483	NAPSB	chr19	50845046	50845066
ovary	MED26	chr19	16697219	16697239	MED26	chr19	16701807	16701827
ovary	MED26	chr19	16712638	16712658		chr19	24588434	24588454
pancreas	MED26	chr19	16707890	16707910	MED26	chr19	16710065	16710085

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 MED26 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
BQ009863	CARM1	18	164	19	11033302	11033448	MED26	158	724	19	16629046	16629612
AL516980	MED26	1	459	19	16636283	16640538	MED26	455	546	19	16646281	16646372
BI019721	PTPRJ	1	283	11	48018145	48018427	MED26	277	424	19	16706253	16706400
BG953012	MED26	11	70	19	16695951	16696010	MED26	65	316	19	16695675	16695926
BF885437	MED26	27	116	19	16664537	16664626	CEP164	112	317	11	117261985	117262190
BC032658	MED26	24	1872	19	16663449	16682389	KIF18B	1867	2361	17	43002079	43002577
DA456356	MED26	1	402	19	16683435	16683835	USP36	401	565	17	76834669	76834833

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=19)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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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
chr19:16689204-16689204	p.A30V	3
chr19:16687139-16687139	p.G501D	1
chr19:16687644-16687644	p.P333S	1
chr19:16688032-16688032	p.G203G	1
chr19:16689216-16689216	p.R26Q	1
chr19:16687167-16687167	p.R492W	1
chr19:16687659-16687659	p.R328W	1
chr19:16688149-16688149	p.K164N	1
chr19:16689217-16689217	p.R26W	1
chr19:16687285-16687285	p.E452E	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	2	1		4			3		1				1	2		1	2	9		7
# mutation	2	1		4			3		1				1	2		1	2	9		8
nonsynonymous SNV	1	1		2			2		1				1	1			2	8		5
synonymous SNV	1			2			1							1		1		1		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
chr19:16687291	p.P354P	1
chr19:16687880	p.R130H	1
chr19:16688320	p.A335E	1
chr19:16687311	p.G107G	1
chr19:16687957	p.P333S	1
chr19:16688338	p.T101T	1
chr19:16687312	p.R328Q	1
chr19:16687968	p.P86P	1
chr19:16688383	p.R590H	1
chr19:16686872	p.R328W	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 MED26 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 MED26

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


AKAP8,ARMC6,KXD1,CHERP,DCAF15,DDA1,DDX39A, DDX49,FAM32A,GATAD2A,GTPBP3,HAUS8,KRI1,MED26, MPV17L2,MRPL34,RAVER1,SIN3B,TIMM44,TRMT1,WIZ	CCDC9,DUS3L,FBXO46,FZR1,GTPBP3,MED26,NOXA1, PPAN,RAB40C,REXO1,RRP9,CLASRP,AKAP17A,SNAPC4, STX1A,TRMT1,NELFA,ZBTB48,ZNF446,ZNF653,ZNF777

AKAP8,AKAP8L,CACTIN,CDC37,CHERP,DOHH,EPS15L1, GTPBP3,KRI1,MED26,MLLT1,PPAN,RAVER1,REXO1, SUGP1,STK11,TNPO2,WIZ,XAB2,ZNF296,ZNF574	ARID3B,BAG6,CLEC16A,CORO7,CYTH1,ELL,ERCC5, GMEB2,LEMD2,MCM3AP,MED26,MICAL1,PHRF1,PRKD2, REPS1,REXO1,RFX1,SKIV2L,SMARCD1,TATDN2,TRIM11

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 MED26

There's no related Drug.

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Cross referenced IDs for MED26

* 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