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 CTNNB1

Basic gene info.	Gene symbol	CTNNB1
	Gene name	catenin (cadherin-associated protein), beta 1, 88kDa
	Synonyms	CTNNB\|MRD19\|armadillo
	Cytomap	UCSC genome browser: 3p21
	Genomic location	chr3 :41240941-41281939
	Type of gene	protein-coding
	RefGenes	NM_001098209.1, NM_001098210.1,NM_001904.3,
	Ensembl id	ENSG00000168036
	Description	catenin beta-1
	Modification date	20141222
dbXrefs	MIM : 116806
	HGNC : HGNC
	Ensembl : ENSG00000168036
	HPRD : 00286
	Vega : OTTHUMG00000131393
Protein	UniProt: P35222 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CTNNB1
	BioGPS: 1499
	Gene Expression Atlas: ENSG00000168036
	The Human Protein Atlas: ENSG00000168036
Pathway	NCI Pathway Interaction Database: CTNNB1
	KEGG: CTNNB1
	REACTOME: CTNNB1
	ConsensusPathDB
	Pathway Commons: CTNNB1
Metabolism	MetaCyc: CTNNB1
	HUMANCyc: CTNNB1
Regulation	Ensembl's Regulation: ENSG00000168036
	miRBase: chr3 :41,240,941-41,281,939
	TargetScan: NM_001098209
	cisRED: ENSG00000168036
Context	iHOP: CTNNB1
	cancer metabolism search in PubMed: CTNNB1
	UCL Cancer Institute: CTNNB1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CTNNB1 in cancer cell metabolism	1. Tu HC, Schwitalla S, Qian Z, LaPier GS, Yermalovich A, et al. (2015) LIN28 cooperates with WNT signaling to drive invasive intestinal and colorectal adenocarcinoma in mice and humans. Genes Dev 29: 1074-1086. doi: 10.1101/gad.256693.114. pmid: 4441054. go to article 2. Kabatkova M, Zapletal O, Tylichova Z, Neca J, Machala M, et al. (2015) Inhibition of beta-catenin signalling promotes DNA damage elicited by benzo[a]pyrene in a model of human colon cancer cells via CYP1 deregulation. Mutagenesis 30: 565-576. doi: 10.1093/mutage/gev019. go to article 3. Wang T, Wang G, Hao D, Liu X, Wang D, et al. (2015) Aberrant regulation of the LIN28A/LIN28B and let-7 loop in human malignant tumors and its effects on the hallmarks of cancer. Mol Cancer 14: 125. doi: 10.1186/s12943-015-0402-5 go to article 4. Benham-Pyle BW, Pruitt BL, Nelson WJ (2015) Cell adhesion. Mechanical strain induces E-cadherin-dependent Yap1 and beta-catenin activation to drive cell cycle entry. Science 348: 1024-1027. doi: 10.1126/science.aaa4559. go to article

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Phenotypic Information for CTNNB1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CTNNB1
	Familial Cancer Database: CTNNB1

* 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 COAD ⁶, UCEC ⁷, SKCM ⁸,	Therapeutic Vulnerabilities in Cancer⁹

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.nature.com/nature/journal/v487/n7407/full/nature11252.html,
7 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
8 http://www.sciencedirect.com/science/article/pii/S0092867415006340,
9Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM	114500; phenotype. 116806; gene. 132600; phenotype. 155255; phenotype. 156240; phenotype. 167000; phenotype. 181030; phenotype. 615075; phenotype.
Orphanet	404473; Severe intellectual disability-progressive spastic diplegia syndrome. 54595; Craniopharyngioma. 85142; Aldosterone-producing adenoma. 873; Desmoid tumor. 88673; Hepatocellular carcinoma. 91414; Pilomatrixoma.
Disease	KEGG Disease: CTNNB1
	MedGen: CTNNB1 (Human Medical Genetics with Condition)
	ClinVar: CTNNB1
Phenotype	MGI: CTNNB1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CTNNB1

Mutations for CTNNB1

* 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 CTNNB1 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
BE177332	CTNNB1	35	300	3	41281158	41281426	SREK1	292	585	5	65452064	65452357
AK098472	CTNNB1	22	1335	3	41274831	41281339	BOLA2	1329	2265	16	29454551	29465668
DA715882	RHOA	1	150	3	49449252	49449401	CTNNB1	148	552	3	41265510	41266558
AW361450	CTNNB1	1	412	3	41280355	41280764	AKAP11	412	539	13	42869356	42869483
BI003062	TG	11	281	8	133907316	133907588	CTNNB1	277	513	3	41279542	41280835
BE835337	CTNNB1	1	226	3	41281010	41281235	MRPS33	216	385	7	140706014	140706183
DB360697	TTLL9	1	263	20	30469426	30469688	CTNNB1	264	543	3	41280671	41281414
DA215427	CTNNB1	3	173	3	41240992	41241162	FAR1	171	538	11	13743275	13750266
BP232398	CTNNB1	1	420	3	41240981	41266194	OLFML2B	421	582	1	161993499	161993659
DB330856	GNB2L1	1	189	5	180663937	180664690	CTNNB1	185	479	3	41274841	41275219
AF130085	SCAF11	1	1064	12	46324225	46325288	CTNNB1	1055	2345	3	41277163	41278958

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	1	1	2				1		2		1					1
GAIN (# sample)	1	1							1							1
LOSS (# sample)			2				1		1		1

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=1143

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=2584)	Stat. for Synonymous SNVs (# total SNVs=96)

Stat. for Deletions (# total SNVs=348)	Stat. for Insertions (# total SNVs=9)

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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
chr3:41266124-41266124	p.T41S	837
chr3:41266137-41266137	p.S45F	573
chr3:41266113-41266113	p.S37F	395
chr3:41266101-41266101	p.S33F	374
chr3:41266097-41266097	p.D32Y	283
chr3:41266136-41266136	p.S45A	244
chr3:41266104-41266104	p.G34V	177
chr3:41266098-41266098	p.D32V	132
chr3:41266103-41266103	p.G34R	108
chr3:41266125-41266125	p.T41I	104

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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=11

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	1	103	4		2		1	1		11	6	2	1	3	7	12	2	78
# mutation		3	1	88	5		2		1	1		11	7	2	1	3	7	14	2	34
nonsynonymous SNV		1	1	60	2				1			11	4	1	1	3	7	13	2	26
synonymous SNV		2		29	3		2			1			3	1				1		8

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
chr3:41266113	p.S37F,CTNNB1	20
chr3:41266101	p.S33C,CTNNB1	16
chr3:41266097	p.D32H,CTNNB1	12
chr3:41266103	p.G34R,CTNNB1	7
chr3:41266181	p.G245C,CTNNB1	6
chr3:41267062	p.S60P,CTNNB1	6
chr3:41266137	p.S47G,CTNNB1	5
chr3:41266125	p.G245V,CTNNB1	5
chr3:41266142	p.S33P,CTNNB1	5
chr3:41266112	p.T41I,CTNNB1	5

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 CTNNB1 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 CTNNB1

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.

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Protein Expression Plot (RPPA)

*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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


BTBD17,PPP1R17,CTNNB1,DHX36,EPHA7,ITGA6,ITGA9, KANK4,MAML2,OXSR1,PRKD3,SMARCC1,SOCS5,STAG1, TBR1,TOP2B,WDR48,YAP1,ZNF445,ZNF619,ZNF660	ANO1,DIEXF,CTNNB1,DDX31,EHF,ESYT3,ETV5, ETV6,FAT2,GRHL1,LY75,METAP1,NALCN,PIK3C2G, QTRTD1,RFC5,SFRP1,SHANK2,SMARCC1,SUDS3,ZNF667

ACTR8,FAM217B,CACHD1,CAPN7,CD46,CLASP2,CTNNB1, GLB1,GLCE,GLS,KLHL23,MAPK14,MGAT5,NAALADL2, PPP4R2,PRKAR2A,PROX1,STT3B,WDR48,XRCC5,ZAK	ADIPOR2,BACH1,CAB39,CTNNB1,DYRK2,ERBB2IP,EZR, KIF16B,LMO7,LUZP1,MALL,MYO1E,PELI2,PICALM, PTPRH,RAB22A,RAB5A,RHOF,RIPK1,SOCS6,URGCP

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 CTNNB1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P35222; -.
Chemistry	ChEMBL	CHEMBL3038464; -.
Organism-specific databases	PharmGKB	PA27013; -.
Organism-specific databases	CTD	1499; -.

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
DB03904	catenin (cadherin-associated protein), beta 1, 88kDa	experimental	Urea
DB00125	catenin (cadherin-associated protein), beta 1, 88kDa	approved; nutraceutical	L-Arginine
DB00435	catenin (cadherin-associated protein), beta 1, 88kDa	approved	Nitric Oxide
DB00122	catenin (cadherin-associated protein), beta 1, 88kDa	approved; nutraceutical	Choline
DB00482	catenin (cadherin-associated protein), beta 1, 88kDa	approved; investigational	Celecoxib

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Cross referenced IDs for CTNNB1

* 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