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 MED24

Basic gene info.	Gene symbol	MED24
	Gene name	mediator complex subunit 24
	Synonyms	ARC100\|CRSP100\|CRSP4\|DRIP100\|THRAP4\|TRAP100
	Cytomap	UCSC genome browser: 17q21.1
	Genomic location	chr17 :38175349-38210889
	Type of gene	protein-coding
	RefGenes	NM_001079518.1, NM_001267797.1,NM_014815.3,NR_052017.1,
	Ensembl id	ENSG00000008838
	Description	CRSP complex subunit 4activator-recruited cofactor 100 kDa componentcofactor required for Sp1 transcriptional activation subunit 4cofactor required for Sp1 transcriptional activation, subunit 4, 100kDamediator of RNA polymerase II transcription subuni
	Modification date	20141207
dbXrefs	MIM : 607000
	HGNC : HGNC
	Ensembl : ENSG00000008838
	HPRD : 06107
	Vega : OTTHUMG00000133329
Protein	UniProt: O75448 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MED24
	BioGPS: 9862
	Gene Expression Atlas: ENSG00000008838
	The Human Protein Atlas: ENSG00000008838
Pathway	NCI Pathway Interaction Database: MED24
	KEGG: MED24
	REACTOME: MED24
	ConsensusPathDB
	Pathway Commons: MED24
Metabolism	MetaCyc: MED24
	HUMANCyc: MED24
Regulation	Ensembl's Regulation: ENSG00000008838
	miRBase: chr17 :38,175,349-38,210,889
	TargetScan: NM_001079518
	cisRED: ENSG00000008838
Context	iHOP: MED24
	cancer metabolism search in PubMed: MED24
	UCL Cancer Institute: MED24
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for MED24(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MED24
	Familial Cancer Database: MED24

* 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	607000; gene.
Orphanet
Disease	KEGG Disease: MED24
	MedGen: MED24 (Human Medical Genetics with Condition)
	ClinVar: MED24
Phenotype	MGI: MED24 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MED24

Mutations for MED24

* 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
pancreas	MED24	chr17	38210334	38210354	TNS4	chr17	38649300	38649320

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 MED24 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
CV410516	MED24	1	186	17	38189708	38189891	MED24	180	383	17	38189951	38190154
BG957436	EIF3CL	10	78	16	28412550	28412620	MED24	70	462	17	38176138	38178965
BG108372	SETD5	1	492	3	9509998	9510489	MED24	475	566	17	38175355	38175446
BE465519	UFD1L	1	233	22	19438170	19438402	MED24	232	506	17	38176561	38178935
BE465526	UFD1L	1	233	22	19438170	19438402	MED24	232	515	17	38176561	38178944

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=59)	Stat. for Synonymous SNVs (# total SNVs=38)

Stat. for Deletions (# total SNVs=8)	Stat. for Insertions (# total SNVs=1)

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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
chr17:38178256-38178256	p.R859*	4
chr17:38176550-38176550	p.R894W	3
chr17:38191512-38191512	p.A139A	3
chr17:38178659-38178659	p.R837R	3
chr17:38186004-38186004	p.L421L	2
chr17:38209768-38209768	p.K28N	2
chr17:38179499-38179499	p.T712M	2
chr17:38178916-38178916	p.P805L	2
chr17:38189431-38189431	p.E234*	2
chr17:38179414-38179414	p.G740G	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=3

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	5	4		8			4		2	1	1	5	6	3			6	7		17
# mutation	5	6		9			4		2	1	1	5	6	3			6	7		19
nonsynonymous SNV	3	4		6			4		2			2	4	2			3	4		11
synonymous SNV	2	2		3						1	1	3	2	1			3	3		8

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
chr17:38209742	p.W37L,MED24	3
chr17:38178659	p.R824R,MED24	2
chr17:38179414	p.G727G,MED24	2
chr17:38209762	p.R372R,MED24	1
chr17:38178227	p.G141R,MED24	1
chr17:38184193	p.E825K,MED24	1
chr17:38189317	p.V605E,MED24	1
chr17:38179470	p.D345Y,MED24	1
chr17:38191547	p.A140T,MED24	1
chr17:38183162	p.S588F,MED24	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 MED24 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 MED24

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


MIEN1,C2orf54,CASC3,CDC6,CDK12,ERBB2,FBXL20, GRB7,GSDMB,MED1,MED24,MSL1,ORMDL3,PGAP3, PPP1R1B,PSMD3,RARA,SMARCE1,STARD3,THRA,WIPF2	AHDC1,ATXN7L2,CNKSR1,DPH2,FOXK2,HEATR2,HMGA1, MED24,MYBBP1A,PPP2R4,PRMT1,RNF31,RRP12,SBK1, SLC37A4,SMARCD3,MIEF2,TBRG4,TMEM201,UBQLN4,WNK2

AATF,MIEN1,CASC3,ERBB2,FXYD2,GRB7,KCNA10, MED24,MSL1,ORMDL3,PGAP3,PPP1R1B,PSMD3,RAPGEFL1, RGSL1,RPL19,SNAR-A2,STARD3,TCAP,THRA,UGT1A6	CHAF1A,CHTF18,DAZAP1,DDX54,DIS3L2,EFTUD2,HNRNPM, CLUH,LMNB2,LRRC45,MED24,NBEAL2,NCLN,TONSL, PAXIP1,PTBP1,RECQL4,SRRT,SYMPK,TTLL4,VARS

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 MED24

There's no related Drug.

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Cross referenced IDs for MED24

* 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