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 CCT2
Basic gene info.Gene symbolCCT2
Gene namechaperonin containing TCP1, subunit 2 (beta)
Synonyms99D8.1|CCT-beta|CCTB|HEL-S-100n|PRO1633|TCP-1-beta
CytomapUCSC genome browser: 12q15
Genomic locationchr12 :69979207-69995357
Type of geneprotein-coding
RefGenesNM_001198842.1,
NM_006431.2,
Ensembl idENSG00000166226
DescriptionT-complex protein 1 subunit betaT-complex protein 1, beta subunitchaperonin containing t-complex polypeptide 1, beta subunitchaperonin containing t-complex polypeptide 1, subunit 2epididymis secretory sperm binding protein Li 100n
Modification date20141207
dbXrefs MIM : 605139
HGNC : HGNC
Ensembl : ENSG00000166226
HPRD : 06895
Vega : OTTHUMG00000169383
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CCT2
BioGPS: 10576
Gene Expression Atlas: ENSG00000166226
The Human Protein Atlas: ENSG00000166226
PathwayNCI Pathway Interaction Database: CCT2
KEGG: CCT2
REACTOME: CCT2
ConsensusPathDB
Pathway Commons: CCT2
MetabolismMetaCyc: CCT2
HUMANCyc: CCT2
RegulationEnsembl's Regulation: ENSG00000166226
miRBase: chr12 :69,979,207-69,995,357
TargetScan: NM_001198842
cisRED: ENSG00000166226
ContextiHOP: CCT2
cancer metabolism search in PubMed: CCT2
UCL Cancer Institute: CCT2
Assigned class in ccmGDBC

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Phenotypic Information for CCT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CCT2
Familial Cancer Database: CCT2
* 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CCT2
MedGen: CCT2 (Human Medical Genetics with Condition)
ClinVar: CCT2
PhenotypeMGI: CCT2 (International Mouse Phenotyping Consortium)
PhenomicDB: CCT2

Mutations for CCT2
* 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 CCT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN431150HMGA23107126635857266358676CCT2108748126997925169991838
BG180662ELF11375134151713841524088CCT2370723126999364969995292
AW518263CCT2189126999526269995350PAN378484132879346428793870

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 # sample 1      1    1   
GAIN (# sample) 1      1    1   
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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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=34)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr12:69981312-69981312p.D58Y2
chr12:69981336-69981336p.D66H2
chr12:69981396-69981396p.D86N2
chr12:69981763-69981763p.V104I2
chr12:69987309-69987309p.P300S2
chr12:69987312-69987312p.E301*2
chr12:69981998-69981998p.T134T2
chr12:69992196-69992196p.G477V2
chr12:69983267-69983267p.S150F2
chr12:69991509-69991509p.A398A2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12123 2 1  51   42112
# mutation12123 2 1  51   42113
nonsynonymous SNV12112 2    41   3217
synonymous SNV   11   1  1    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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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
chr12:69987309p.P253S,CCT22
chr12:69990984p.E219Q,CCT21
chr12:69993722p.L458L,CCT21
chr12:69980567p.L38S1
chr12:69985849p.R234H,CCT21
chr12:69991012p.A476V,CCT21
chr12:69993775p.D19H,CCT21
chr12:69981336p.R481G,CCT21
chr12:69985881p.V29A,CCT21
chr12:69991024p.H267L,CCT21

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 CCT2 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 CCT2

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.

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

BEST3,LINC00320,CAND1,CCT2,CNOT2,CPSF6,FRS2,
LEMD3,MDM1,MDM2,NUP107,RAB21,RAB3IP,RAP1B,
SLC35E3,TBC1D15,TBK1,TMEM19,TSG1,YEATS4,YTHDF1
CAND1,CCT2,CDK7,CNOT2,DCAF13,GMPS,GOLM1,
GRIP1,HDAC2,ILF2,LRRC42,NME5,PAICS,PRPF4,
RAB3IP,RFC4,SFXN2,SLC35E3,SPATS2,TMEM5,YEATS4

C12orf29,PARPBP,CCDC59,CCT2,CDK4,GPN3,METAP2,
MRPL42,NDUFA12,NUP37,PA2G4,PTGES3,PWP1,RAN,
RFC5,SRSF3,SRSF7,SRSF9,UBE2N,VPS29,YEATS4
ABCE1,BCCIP,BRIX1,CCT2,CHAC2,DCAF13,EEF1E1,
ENOPH1,HSPE1,METTL1,MRPL3,MRTO4,PAK1IP1,PINX1,
PNO1,RAN,RPP40,SNRPD1,SRPRB,UTP6,WDR77
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 CCT2


There's no related Drug.
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Cross referenced IDs for CCT2
* 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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