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 MUC12

Basic gene info.	Gene symbol	MUC12
	Gene name	mucin 12, cell surface associated
	Synonyms	MUC-11\|MUC-12\|MUC11
	Cytomap	UCSC genome browser: 7q22
	Genomic location	chr7 :100612903-100662230
	Type of gene	protein-coding
	RefGenes	NM_001164462.1,
	Ensembl id	ENSG00000205277
	Description	mucin 11mucin-11mucin-12
	Modification date	20141207
dbXrefs	MIM : 604609
	HGNC : HGNC
	Ensembl : ENSG00000205277
	Vega : OTTHUMG00000157042
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MUC12
	BioGPS: 10071
	Gene Expression Atlas: ENSG00000205277
	The Human Protein Atlas: ENSG00000205277
Pathway	NCI Pathway Interaction Database: MUC12
	KEGG: MUC12
	REACTOME: MUC12
	ConsensusPathDB
	Pathway Commons: MUC12
Metabolism	MetaCyc: MUC12
	HUMANCyc: MUC12
Regulation	Ensembl's Regulation: ENSG00000205277
	miRBase: chr7 :100,612,903-100,662,230
	TargetScan: NM_001164462
	cisRED: ENSG00000205277
Context	iHOP: MUC12
	cancer metabolism search in PubMed: MUC12
	UCL Cancer Institute: MUC12
Assigned class in ccmGDB	C

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Phenotypic Information for MUC12(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MUC12
	Familial Cancer Database: MUC12

* 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: MUC12
	MedGen: MUC12 (Human Medical Genetics with Condition)
	ClinVar: MUC12
Phenotype	MGI: MUC12 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MUC12

Mutations for MUC12

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	MUC12	chr7	100619868	100619888	MUC12	chr7	100624110	100624130
pancreas	MUC12	chr7	100636305	100636505	MUC12	chr7	100646425	100646625

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 MUC12 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
BG955820	FLNB	1	168	3	58112376	58116524	MUC12	163	364	7	100634934	100635135
AW603439	SYNE2	279	301	14	64613669	64613691	MUC12	284	554	7	100657290	100661914

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=7

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=391)	Stat. for Synonymous SNVs (# total SNVs=115)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=7)

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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
chr7:100647548-100647548	p.L4568F	7
chr7:100647539-100647539	p.S4565S	6
chr7:100643088-100643088	p.I3082V	5
chr7:100647276-100647276	p.P4478T	5
chr7:100612955-100612956	p.T18_T19insA	5
chr7:100634964-100634964	p.P374T	4
chr7:100647565-100647565	p.S4574L	4
chr7:100644227-100644227	p.E3461E	4
chr7:100643155-100643155	p.K3104I	4
chr7:100637074-100637074	p.R1077H	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=2

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		13										2						1		20
# mutation		14										3						1		40
nonsynonymous SNV		12										3						1		27
synonymous SNV		2																		13

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
chr7:100634368	p.P4251S	2
chr7:100646595	p.T175M	2
chr7:100634091	p.T1226R	1
chr7:100645678	p.S4649F	1
chr7:100635134	p.X5336X	1
chr7:100648354	p.S288L	1
chr7:100637521	p.S358Y	1
chr7:100661916	p.S1604Y	1
chr7:100634127	p.R4679H	1
chr7:100646022	p.E385K	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 MUC12 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 MUC12

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


TMEM51-AS1,GNG3,IGFL2,KCNA10,KLK7,LY6H,MUC12, MUC4,MYBPHL,NACAD,NEFL,NMU,OR10Q1,RS1, SLC6A7,SPATA19,EPPIN,TPPP3,TTC9B,UPK2,WBSCR28	BASP1,BATF3,MEDAG,CCDC109B,CCIN,CD70,CLEC3B, CMTM3,CRIP1,DBN1,EMP3,GLIPR2,LOXL1,METRNL, MFRP,MUC12,NCF4,SH3BGRL3,THBS3,TMSB4XP8,TPPP3

BTNL3,CEACAM5,CLDN23,CLDN3,DHRS11,TMEM236,NXPE4, FOXD2,LRRFIP2,MCOLN2,MUC12,MYO15B,PDE6A,PPP1R14C, RPL10L,SEPP1,TFCP2L1,TM9SF4,TMEM82,ZBTB7A,ZSWIM1	ATP13A3,C2CD3,C3orf52,CLCN3,EPB41L4A,GALNT5,HIPK1, IWS1,JPH1,LMNA,LOC100129637,KMT2B___KMT2D,MUC12,MUC4, MYOF,PKD1L1,PVR,QSOX1,SETD8,TPD52L3,ZSCAN12P1

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 MUC12

There's no related Drug.

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Cross referenced IDs for MUC12

* 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