Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolCTNNB1
Gene namecatenin (cadherin-associated protein), beta 1, 88kDa
SynonymsCTNNB|MRD19|armadillo
CytomapUCSC genome browser: 3p21
Genomic locationchr3 :41240941-41281939
Type of geneprotein-coding
RefGenesNM_001098209.1,
NM_001098210.1,NM_001904.3,
Ensembl idENSG00000168036
Descriptioncatenin beta-1
Modification date20141222
dbXrefs MIM : 116806
HGNC : HGNC
Ensembl : ENSG00000168036
HPRD : 00286
Vega : OTTHUMG00000131393
ProteinUniProt: P35222
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CTNNB1
BioGPS: 1499
Gene Expression Atlas: ENSG00000168036
The Human Protein Atlas: ENSG00000168036
PathwayNCI Pathway Interaction Database: CTNNB1
KEGG: CTNNB1
REACTOME: CTNNB1
ConsensusPathDB
Pathway Commons: CTNNB1
MetabolismMetaCyc: CTNNB1
HUMANCyc: CTNNB1
RegulationEnsembl's Regulation: ENSG00000168036
miRBase: chr3 :41,240,941-41,281,939
TargetScan: NM_001098209
cisRED: ENSG00000168036
ContextiHOP: CTNNB1
cancer metabolism search in PubMed: CTNNB1
UCL Cancer Institute: CTNNB1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CTNNB1 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
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.
DiseaseKEGG Disease: CTNNB1
MedGen: CTNNB1 (Human Medical Genetics with Condition)
ClinVar: CTNNB1
PhenotypeMGI: CTNNB1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CTNNB1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE177332CTNNB13530034128115841281426SREK129258556545206465452357
AK098472CTNNB122133534127483141281339BOLA213292265162945455129465668
DA715882RHOA115034944925249449401CTNNB114855234126551041266558
AW361450CTNNB1141234128035541280764AKAP11412539134286935642869483
BI003062TG112818133907316133907588CTNNB127751334127954241280835
BE835337CTNNB1122634128101041281235MRPS332163857140706014140706183
DB360697TTLL91263203046942630469688CTNNB126454334128067141281414
DA215427CTNNB1317334124099241241162FAR1171538111374327513750266
BP232398CTNNB1142034124098141266194OLFML2B4215821161993499161993659
DB330856GNB2L111895180663937180664690CTNNB118547934127484141275219
AF130085SCAF1111064124632422546325288CTNNB11055234534127716341278958

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample112   1 2 1    1 
GAIN (# sample)11      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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr3:41266124-41266124p.T41S837
chr3:41266137-41266137p.S45F573
chr3:41266113-41266113p.S37F395
chr3:41266101-41266101p.S33F374
chr3:41266097-41266097p.D32Y283
chr3:41266136-41266136p.S45A244
chr3:41266104-41266104p.G34V177
chr3:41266098-41266098p.D32V132
chr3:41266103-41266103p.G34R108
chr3:41266125-41266125p.T41I104

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample 311034 2 11 116213712278
# mutation 31885 2 11 117213714234
nonsynonymous SNV 11602   1  114113713226
synonymous SNV 2 293 2  1  31   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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr3:41266113p.S37F,CTNNB120
chr3:41266101p.S33C,CTNNB116
chr3:41266097p.D32H,CTNNB112
chr3:41266103p.G34R,CTNNB17
chr3:41267062p.G245C,CTNNB16
chr3:41266181p.S60P,CTNNB16
chr3:41266142p.S37P,CTNNB15
chr3:41266112p.S45F,CTNNB15
chr3:41266100p.S47G,CTNNB15
chr3:41267063p.G245V,CTNNB15

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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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check002.gifProtein 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P35222; -.
ChemistryChEMBL CHEMBL3038464; -.
Organism-specific databasesPharmGKB PA27013; -.
Organism-specific databasesCTD 1499; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB03904catenin (cadherin-associated protein), beta 1, 88kDaexperimentalUrea
DB00125catenin (cadherin-associated protein), beta 1, 88kDaapproved; nutraceuticalL-Arginine
DB00435catenin (cadherin-associated protein), beta 1, 88kDaapprovedNitric Oxide
DB00122catenin (cadherin-associated protein), beta 1, 88kDaapproved; nutraceuticalCholine
DB00482catenin (cadherin-associated protein), beta 1, 88kDaapproved; investigationalCelecoxib


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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



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