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 MUC4

Basic gene info.	Gene symbol	MUC4
	Gene name	mucin 4, cell surface associated
	Synonyms	ASGP\|HSA276359\|MUC-4
	Cytomap	UCSC genome browser: 3q29
	Genomic location	chr3 :195473637-195538844
	Type of gene	protein-coding
	RefGenes	NM_004532.5, NM_018406.6,NM_138297.4,NM_138298.1,NM_138299.1,
	Ensembl id	ENSG00000145113
	Description	ascites sialoglycoproteinmucin 4, tracheobronchialmucin-4pancreatic adenocarcinoma mucintestis mucintracheobronchial mucin
	Modification date	20141207
dbXrefs	MIM : 158372
	HGNC : HGNC
	Ensembl : ENSG00000145113
	HPRD : 11829
	Vega : OTTHUMG00000151827
Protein	UniProt: Q99102 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MUC4
	BioGPS: 4585
	Gene Expression Atlas: ENSG00000145113
	The Human Protein Atlas: ENSG00000145113
Pathway	NCI Pathway Interaction Database: MUC4
	KEGG: MUC4
	REACTOME: MUC4
	ConsensusPathDB
	Pathway Commons: MUC4
Metabolism	MetaCyc: MUC4
	HUMANCyc: MUC4
Regulation	Ensembl's Regulation: ENSG00000145113
	miRBase: chr3 :195,473,637-195,538,844
	TargetScan: NM_004532
	cisRED: ENSG00000145113
Context	iHOP: MUC4
	cancer metabolism search in PubMed: MUC4
	UCL Cancer Institute: MUC4
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for MUC4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MUC4
	Familial Cancer Database: MUC4

* 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	158372; gene. 158372; gene.
Orphanet
Disease	KEGG Disease: MUC4
	MedGen: MUC4 (Human Medical Genetics with Condition)
	ClinVar: MUC4
Phenotype	MGI: MUC4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MUC4

Mutations for MUC4

* 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
central_nervous_system	MUC4	chr3	195499188	195499188	MUC4	chr3	195499969	195499969
central_nervous_system	MUC4	chr3	195502833	195502833	MUC4	chr3	195504730	195504730
NS	MUC4	chr3	195502794	195502794	MUC4	chr3	195503226	195503226
ovary	MUC4	chr3	195486769	195486789		chr3	196324135	196324155
ovary	MUC4	chr3	195498236	195498436	MUC4	chr3	195497741	195497941
ovary	MUC4	chr3	195506927	195507127	MUC4	chr3	195510642	195510842
ovary	MUC4	chr3	195506979	195507179	MUC4	chr3	195510638	195510838
pancreas	MUC4	chr3	195512087	195512287	MUC4	chr3	195506660	195506860
pancreas	MUC4	chr3	195512104	195512304	MUC4	chr3	195507016	195507216
pancreas	MUC4	chr3	195513095	195513295	MUC4	chr3	195514906	195515106
pancreas	MUC4	chr3	195515227	195515427	MUC4	chr3	195506649	195506849

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 MUC4 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
BG015132	VPS72	15	203	1	151149313	151149497	MUC4	194	273	3	195515498	195515577
BG984966	CLDN4	1	123	7	73245858	73245980	MUC4	117	423	3	195516287	195516593
DA435621	MUC4	1	134	3	195477236	195477374	MUC4	130	567	3	195487821	195489124
BQ689257	MUC4	333	443	3	195515054	195515492	MAGEF1	440	786	3	184428153	184428499
AW391858	LMO7	1	189	13	76430648	76432149	MUC4	182	520	3	195530516	195530853
BQ689139	MUC4	333	443	3	195515054	195515492	MAGEF1	440	787	3	184428156	184428499
AW391853	LMO7	1	189	13	76430648	76432151	MUC4	182	517	3	195530516	195530852

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=85)	Stat. for Synonymous SNVs (# total SNVs=31)

Stat. for Deletions (# total SNVs=5)	Stat. for Insertions (# total SNVs=0)
	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
chr3:195487765-195487765	p.N710N	3
chr3:195493607-195493607	p.F279F	3
chr3:195492231-195492231	p.R334W	3
chr3:195487898-195487898	p.N666fs*8	3
chr3:195481161-195481161	p.P848L	2
chr3:195492266-195492266	p.R322H	2
chr3:195492211-195492211	p.W340*	2
chr3:195489009-195489009	p.A585S	2
chr3:195481223-195481223	p.D827D	2
chr3:195475775-195475775	p.C1108C	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=6

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	64	3	41	16		13		76	3		16	20	6	1	6	35	40		42
# mutation	5	70	3	49	13		13		104	3		24	26	6	1	6	48	55		68
nonsynonymous SNV	3	51	2	29	10		8		81	3		19	16	5		4	38	35		46
synonymous SNV	2	19	1	20	3		5		23			5	10	1	1	2	10	20		22

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
chr3:195505867	p.V4195D	6
chr3:195505836	p.H4205Q	6
chr3:195506940	p.P3952S	5
chr3:195506597	p.H3837Q	5
chr3:195505811	p.T4214A	4
chr3:195505772	p.V4227L	4
chr3:195505855	p.S4199Y	4
chr3:195516064	p.R796Q	3
chr3:195516435	p.A2310P	3
chr3:195493607	p.D2309G	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 MUC4 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 MUC4

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


ADAMTSL4,BTN1A1,TMEM51-AS1,LINC00518,CACNA1E,HILS1,IGFL2, KCNA10,KLK7,KRT9,MUC12,MUC4,MYBPHL,NEFL, NMU,OR10Q1,RS1,SLC6A7,SPATA19,EPPIN,VGLL3	CXCL13,DEFB125,DIO2,FAM83A,HDGFL1,HELT,HS6ST2, LHX9,LOC100130274,LOC100130933,LPAR3,MEPE,MUC4,OLAH, OR10J5,OR2M3,PLA2G3,PSG8,PTHLH,SLC6A19,SLC9A4

ALDH1L1,CAPN5,CASP7,CES3,CREB3L1,ERN2,GNAQ, HK2,ITM2C,KIAA0513,KLF4,MRAP2,MUC4,NR3C2, PIGR,SLC22A23,SLC44A4,SPTLC2,ST3GAL4,VSIG2,ZBTB7C	ABL2,ATR,FAM208B,CDK12,E2F3,FASN,JPH1, KIAA1244,KIF14,LARP1,LMNB2,MDN1,MKI67,MUC4, MUC5B,MYBBP1A,PDCD11,SLC7A1,SRRT,UGGT1,WHSC1

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 MUC4

There's no related Drug.

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Cross referenced IDs for MUC4

* 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