Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 MUC17

Basic gene info.	Gene symbol	MUC17
	Gene name	mucin 17, cell surface associated
	Synonyms	MUC3
	Cytomap	UCSC genome browser: 7q22.1
	Genomic location	chr7 :100663363-100702140
	Type of gene	protein-coding
	RefGenes	NM_001040105.1, NM_001004430.1,
	Ensembl id	ENSG00000169876
	Description	MUC-17MUC-3membrane mucin MUC17mucin-17secreted mucin MUC17small intestinal mucin MUC3small intestinal mucin-3
	Modification date	20141207
dbXrefs	MIM : 608424
	HGNC : HGNC
	Ensembl : ENSG00000169876
	HPRD : 16335
	Vega : OTTHUMG00000157030
Protein	UniProt: Q685J3 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MUC17
	BioGPS: 140453
	Gene Expression Atlas: ENSG00000169876
	The Human Protein Atlas: ENSG00000169876
Pathway	NCI Pathway Interaction Database: MUC17
	KEGG: MUC17
	REACTOME: MUC17
	ConsensusPathDB
	Pathway Commons: MUC17
Metabolism	MetaCyc: MUC17
	HUMANCyc: MUC17
Regulation	Ensembl's Regulation: ENSG00000169876
	miRBase: chr7 :100,663,363-100,702,140
	TargetScan: NM_001040105
	cisRED: ENSG00000169876
Context	iHOP: MUC17
	cancer metabolism search in PubMed: MUC17
	UCL Cancer Institute: MUC17
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

Top

Phenotypic Information for MUC17(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MUC17
	Familial Cancer Database: MUC17

* 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 GBM ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.sciencedirect.com/science/article/pii/S0092867413012087,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	608424; gene.
Orphanet
Disease	KEGG Disease: MUC17
	MedGen: MUC17 (Human Medical Genetics with Condition)
	ClinVar: MUC17
Phenotype	MGI: MUC17 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MUC17

Mutations for MUC17

* 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

Top

- 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
ovary	MUC17	chr7	100699692	100699712	PIK3CG	chr7	106544439	106544459
pancreas	MUC17	chr7	100665367	100665567	MUC17	chr7	100672510	100672710
pancreas	MUC17	chr7	100671956	100671976	MUC17	chr7	100673162	100673182
pancreas	MUC17	chr7	100682570	100682590	DYNC1I1	chr7	95699401	95699421

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 MUC17 related fusion information.

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

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=11

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=689)	Stat. for Synonymous SNVs (# total SNVs=213)

Stat. for Deletions (# total SNVs=4)	Stat. for Insertions (# total SNVs=1)

Top

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
chr7:100677279-100677279	p.S861T	8
chr7:100680242-100680242	p.P1849A	4
chr7:100683647-100683647	p.E2984K	4
chr7:100678887-100678887	p.P1397L	4
chr7:100686777-100686777	p.T4027K	4
chr7:100680060-100680060	p.S1788L	4
chr7:100683048-100683048	p.T2784I	3
chr7:100683157-100683157	p.T2820T	3
chr7:100680821-100680821	p.R2042W	3
chr7:100679543-100679543	p.A1616T	3

Top

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	22	27	7	60	29		40		28	4	1	101	39	31	2	8	100	47	9	42
# mutation	24	27	8	71	28		52		26	4	1	155	53	31	2	8	193	67	9	97
nonsynonymous SNV	19	22	6	54	21		33		22	1	1	119	35	18	2	6	148	51	6	78
synonymous SNV	5	5	2	17	7		19		4	3		36	18	13		2	45	16	3	19

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])

Top

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
chr7:100680242	p.P1849S	4
chr7:100680525	p.S131S	3
chr7:100680060	p.S1788L	3
chr7:100685938	p.P2880P	3
chr7:100676844	p.I1943T	3
chr7:100675090	p.M3747I	3
chr7:100683337	p.S716N	3
chr7:100682579	p.T2937T	2
chr7:100682001	p.E2453K	2
chr7:100663431	p.G5G	2

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 MUC17 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]

Top

Gene Expression for MUC17

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


ACTR3BP2,GK2,KRTAP19-2,KRTAP25-1,KRTAP6-1,MUC17,OR10H3, OR4C16,OR4L1,OR51A4,OR51G1,OR52A5,OR52J3,OR5D18, OR5I1,OR5L1,OR5L2,OR6C75,OR8H3,POM121L12,REG1P	CA1,CCL14-CCL15,CES1,COL8A1,DGKK,FAM92A1P2,LOC100287718, LOC643923,MGC27382,MUC17,NLRP3,NNAT,OR10K1,OR2B11, OR3A4P,OR5AS1,POU6F2,PRAMEF6,PROK1,SLC6A18,TAAR1

ABCG2,ALPI,BTNL8,C11orf86,LINC00520,C1orf94,CAPN11, CIDEC,CTSE,FAM25BP,GCNT3,MALL,MUC17,MYPN, PTPRH,SDCBP2,TMEM92,UGT1A1,UGT1A4,UGT1A5,VSIG1	ABCC2,ACE,ALDOB,CYP2D6,CYP3A4,DPP4,FABP6, FGF19,GSTA1,GSTA2,HAPLN4,MGAM,MME,MUC17, NTS,RBP2,SLC10A2,SLC34A3,SLC5A12,SULT1E1,UGT1A4

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for MUC17

There's no related Drug.

Top

Cross referenced IDs for MUC17

* 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