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 MUC16

Basic gene info.	Gene symbol	MUC16
	Gene name	mucin 16, cell surface associated
	Synonyms	CA125
	Cytomap	UCSC genome browser: 19p13.2
	Genomic location	chr19 :8959519-9092018
	Type of gene	protein-coding
	RefGenes	NM_024690.2,
	Ensembl id	ENSG00000181143
	Description	CA-125CA125 ovarian cancer antigenMUC-16mucin-16ovarian cancer-related tumor marker CA125ovarian carcinoma antigen CA125
	Modification date	20141222
dbXrefs	MIM : 606154
	HGNC : HGNC
	Ensembl : ENSG00000181143
	Vega : OTTHUMG00000169191
Protein	UniProt: Q8WXI7 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MUC16
	BioGPS: 94025
	Gene Expression Atlas: ENSG00000181143
	The Human Protein Atlas: ENSG00000181143
Pathway	NCI Pathway Interaction Database: MUC16
	KEGG: MUC16
	REACTOME: MUC16
	ConsensusPathDB
	Pathway Commons: MUC16
Metabolism	MetaCyc: MUC16
	HUMANCyc: MUC16
Regulation	Ensembl's Regulation: ENSG00000181143
	miRBase: chr19 :8,959,519-9,092,018
	TargetScan: NM_024690
	cisRED: ENSG00000181143
Context	iHOP: MUC16
	cancer metabolism search in PubMed: MUC16
	UCL Cancer Institute: MUC16
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MUC16 in cancer cell metabolism	1. Haridas D, Ponnusamy MP, Chugh S, Lakshmanan I, Seshacharyulu P, et al. (2014) MUC16: molecular analysis and its functional implications in benign and malignant conditions. The FASEB Journal 28: 4183-4199. go to article 2. Shukla SK, Gunda V, Abrego J, Haridas D, Mishra A, et al. (2015) MUC16-mediated activation of mTOR and c-Myc reprograms pancreatic cancer metabolism. Oncotarget. go to article

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Phenotypic Information for MUC16(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MUC16
	Familial Cancer Database: MUC16

* 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_PROTEINS

Others
OMIM	606154; gene.
Orphanet
Disease	KEGG Disease: MUC16
	MedGen: MUC16 (Human Medical Genetics with Condition)
	ClinVar: MUC16
Phenotype	MGI: MUC16 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MUC16

Mutations for MUC16

* 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	MUC16	chr19	8971622	8971642	MUC16	chr19	8978386	8978406
ovary	MUC16	chr19	8977219	8977239	FLJ30838	chr2	58947727	58947747
ovary	MUC16	chr19	9035145	9035165	MUC16	chr19	9035574	9035594
ovary	MUC16	chr19	9050563	9050583		chr19	9292048	9292068
ovary	MUC16	chr19	9055871	9055891	ZNF317	chr19	9268420	9268440
ovary	MUC16	chr19	9080898	9080918		chr19	9093726	9093746
ovary	MUC16	chr19	9084550	9084570		chr19	9101765	9101785
ovary	MUC16	chr19	9088983	9089003		chr19	9233686	9233706
pancreas	MUC16	chr19	9027982	9028002	ARHGAP35	chr19	47441021	47441041

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 MUC16 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
AK023298	MUC16	1	433	19	9049994	9056241	DNAJC22	428	1559	12	49742766	49745683
AU133673	MUC16	1	434	19	9049994	9056241	DNAJC22	429	680	12	49742766	49743198
AA640762	MUC16	4	137	19	9000482	9001879	MUC16	131	355	19	8999456	9000489
BI013178	MUC16	8	234	19	8966686	8969304	SCUBE3	218	519	6	35197380	35197681

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	2	3	1	4	2	1	3		5		8		6	2	1	1	5
GAIN (# sample)	2	2	1	4			2		3		6		6		1		3
LOSS (# sample)		1			2	1	1		2		2			2		1	2

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=8

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=1125)	Stat. for Synonymous SNVs (# total SNVs=357)

Stat. for Deletions (# total SNVs=17)	Stat. for Insertions (# total SNVs=6)

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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
chr19:9090831-9090831	p.P328P	8
chr19:9080501-9080501	p.G3177E	6
chr19:9072091-9072091	p.P5119S	6
chr19:9067623-9067623	p.S6608*	5
chr19:9075173-9075173	p.M4091I	4
chr19:9073638-9073638	p.R4603Q	4
chr19:9063678-9063678	p.D7923A	4
chr19:9089508-9089508	p.V769V	4
chr19:9066259-9066259	p.T7063A	4
chr19:9060904-9060904	p.E8848K	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=9

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	53	76	10	144	62		75	2	59	11	5	180	97	26	2	15	194	102	20	73
# mutation	74	87	17	300	65		113	2	66	11	5	355	195	27	3	17	976	203	18	210
nonsynonymous SNV	56	59	13	218	46		81	1	51	9	3	265	134	17	2	11	689	142	11	153
synonymous SNV	18	28	4	83	19		32	1	15	2	2	90	61	10	1	6	287	61	7	57

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
chr19:9072091	p.P5119S	9
chr19:9048764	p.P328P	8
chr19:9090831	p.L10956P	8
chr19:9048771	p.F10954L	5
chr19:9089508	p.G3177E	4
chr19:9080501	p.V769V	4
chr19:9014654	p.R12774H	4
chr19:9054252	p.M4091I	3
chr19:9063963	p.Q6158R	3
chr19:9065721	p.R4603Q	3

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 MUC16 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 MUC16

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


ACSL6,APOBEC3B,ARHGEF9,CAPN14,CDC42EP1,CTSV,CXCL16, KCNG1,KRT9,MFGE8,MUC16,PADI2,PGBD5,PLEKHG1, PRKX,RAET1L,RASGEF1C,ROPN1,SLC15A1,TP53BP2,VGLL1	C12orf77,CD3G,COL22A1,CTLA4,DAPP1,GPR114,GRIN2A, HLA-DOB,HORMAD1,ICOS,IKZF3,MIR155HG,MUC16,NLRC3, OR7G1,P2RY10,RASSF5,TEX11,TLR10,TOX,ZNF80

ACTBL2,ANXA8,ANXA8L1,BPI,C8orf86,CGB1,CPA4, CST6,FAM3C,IL20RB,KRT7,LIPK,LRAT,MUC16, MYH16,PEX5L,PSG6,PSG9,SIGLEC15,THEG,WNT7A	C20orf141,NCOR1P1,CCDC129,CHAT,GNG13,GPX5,KLK13, KPRP,LCE2C,LPA,MEPE,MUC16,CHODL-AS1,OR2D2, PGLYRP3,SEBOX,SNORA79,TAS1R3,TRPM5,VTCN1,ZSWIM2

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 MUC16

There's no related Drug.

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Cross referenced IDs for MUC16

* 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