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 MUC2

Basic gene info.	Gene symbol	MUC2
	Gene name	mucin 2, oligomeric mucus/gel-forming
	Synonyms	MLP\|MUC-2\|SMUC
	Cytomap	UCSC genome browser: 11p15.5
	Genomic location	chr11 :1074874-1104417
	Type of gene	protein-coding
	RefGenes	NM_002457.3,
	Ensembl id	ENSG00000198788
	Description	intestinal mucin-2mucin 2, intestinal/trachealmucin-2mucin-like protein
	Modification date	20141207
dbXrefs	MIM : 158370
	HGNC : HGNC
	HPRD : 11828
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MUC2
	BioGPS: 4583
	Gene Expression Atlas: ENSG00000198788
	The Human Protein Atlas: ENSG00000198788
Pathway	NCI Pathway Interaction Database: MUC2
	KEGG: MUC2
	REACTOME: MUC2
	ConsensusPathDB
	Pathway Commons: MUC2
Metabolism	MetaCyc: MUC2
	HUMANCyc: MUC2
Regulation	Ensembl's Regulation: ENSG00000198788
	miRBase: chr11 :1,074,874-1,104,417
	TargetScan: NM_002457
	cisRED: ENSG00000198788
Context	iHOP: MUC2
	cancer metabolism search in PubMed: MUC2
	UCL Cancer Institute: MUC2
Assigned class in ccmGDB	C

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Phenotypic Information for MUC2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MUC2
	Familial Cancer Database: MUC2

* 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
Orphanet
Disease	KEGG Disease: MUC2
	MedGen: MUC2 (Human Medical Genetics with Condition)
	ClinVar: MUC2
Phenotype	MGI: MUC2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MUC2

Mutations for MUC2

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MUC2 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
BG982813	MUC2	12	242	11	1097853	1098806	LSR	229	306	19	35739940	35740016
AW842723	TPM2	15	149	9	35689761	35689893	MUC2	150	235	11	1092956	1093041
DV080414	MUC2	1	414	11	1075879	1078510	CKM	415	623	19	45818743	45821178

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

There's no copy number variation information in COSMIC data for this gene.

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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=9

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=169)	Stat. for Synonymous SNVs (# total SNVs=77)

Stat. for Deletions (# total SNVs=54)	Stat. for Insertions (# total SNVs=4)

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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
chr11:1092802-1092802	p.T1542fs*6	46
chr11:1093452-1093452	p.P1724P	6
chr11:1093354-1093354	p.S1692T	6
chr11:1093072-1093072	p.A1598P	6
chr11:1093286-1093286	p.T1669S	6
chr11:1092554-1092554	p.I1459T	6
chr11:1092910-1092910	p.G1578S	5
chr11:1093204-1093204	p.P1642T	5
chr11:1092647-1092647	p.T1490I	5
chr11:1093412-1093412	p.T1711M	5

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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	3	22	2	21	7		7	2	15	4		29	12			5	39	20	1	19
# mutation	3	21	2	24	7		7	2	14	4		29	12			4	51	25	1	25
nonsynonymous SNV	2	16		17	6		5	1	11	3		23	8				31	15		19
synonymous SNV	1	5	2	7	1		2	1	3	1		6	4			4	20	10	1	6

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
chr11:1101611	p.T1777T	3
chr11:1093448	p.E2538K	3
chr11:1093512	p.T1756N	3
chr11:1092540	p.R1171M	2
chr11:1093286	p.S2361S	2
chr11:1088727	p.T1453T	2
chr11:1097313	p.I1540S	2
chr11:1098725	p.T1270T	2
chr11:1092800	p.D2120N	2
chr11:1097728	p.F2239L	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 MUC2 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 MUC2

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


ASTL,ATP10B,BMP7,CA12,CCRN4L,DDHD2,DOC2B, IL5,LOC285401,LOC285593,MAMLD1,MUC21,MYF6,PDE5A, PEG3,PEG3-AS1,SALL1,TAS2R7,THSD7A,ZIM2,ZNF385B	CTSE,GKN2,HNF1B,KRTAP13-1,MSLN,MUC21,NAPSA, NKX2-1,PAEP,BPIFA1,PSAPL1,SCGB3A2,SFTA2,SFTA3, SFTPB,SFTPC,SLC26A9,SPINK1,TM4SF20,TM4SF5,XAGE1D

CNBD2,GPX6,IL22,KRT75,KRTAP1-3,KRTAP1-5,KRTAP2-1, KRTAP2-2,KRTAP2-4,KRTAP4-11,KRTAP4-12,KRTAP4-4,KRTAP4-7,KRTAP4-9, KRTAP9-4,KRTAP9-8,LMO3,MT4,MUC21,PSORS1C2,TMEM30C	NA,NA,NA,NA,NA,NA,NA, NA,NA,NA,NA,NA,NA,NA, NA,NA,NA,NA,NA,NA,NA

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 MUC2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01411	mucin 2, oligomeric mucus/gel-forming	approved	Pranlukast
DB01234	mucin 2, oligomeric mucus/gel-forming	approved; investigational	Dexamethasone

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Cross referenced IDs for MUC2

* 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