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 CCT3
Basic gene info.Gene symbolCCT3
Gene namechaperonin containing TCP1, subunit 3 (gamma)
SynonymsCCT-gamma|CCTG|PIG48|TCP-1-gamma|TRIC5
CytomapUCSC genome browser: 1q23
Genomic locationchr1 :156278751-156308206
Type of geneprotein-coding
RefGenesNM_001008800.2,
NM_005998.4,NR_036564.1,NR_036565.1,NM_001008883.1,
Ensembl idENSG00000163468
DescriptionT-complex protein 1 subunit gammaT-complex protein 1, gamma subunitTCP1 (t-complex-1) ring complex, polypeptide 5hTRiC5
Modification date20141207
dbXrefs MIM : 600114
HGNC : HGNC
Ensembl : ENSG00000163468
HPRD : 08969
Vega : OTTHUMG00000024061
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CCT3
BioGPS: 7203
Gene Expression Atlas: ENSG00000163468
The Human Protein Atlas: ENSG00000163468
PathwayNCI Pathway Interaction Database: CCT3
KEGG: CCT3
REACTOME: CCT3
ConsensusPathDB
Pathway Commons: CCT3
MetabolismMetaCyc: CCT3
HUMANCyc: CCT3
RegulationEnsembl's Regulation: ENSG00000163468
miRBase: chr1 :156,278,751-156,308,206
TargetScan: NM_001008800
cisRED: ENSG00000163468
ContextiHOP: CCT3
cancer metabolism search in PubMed: CCT3
UCL Cancer Institute: CCT3
Assigned class in ccmGDBC

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Phenotypic Information for CCT3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CCT3
Familial Cancer Database: CCT3
* 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: CCT3
MedGen: CCT3 (Human Medical Genetics with Condition)
ClinVar: CCT3
PhenotypeMGI: CCT3 (International Mouse Phenotyping Consortium)
PhenomicDB: CCT3

Mutations for CCT3
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasCCT3chr1156306971156306991PTPN1chr204919735649197376
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CCT3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA748732CCT3103791156278759156280436HVCN137448912111091636111091751
CB114948CCT31871156287279156288685RAC179167764420506442138
AA010637CCT312651156306743156307005TRAF3IP12593592239309092239309191
BE783136CCT320991156303346156303425CCT3901401156290660156290710
BQ353904MDM21235126923758769237822CCT32344631156280758156280987
DB040324LOC1005074121107?112074112180CCT31085721156290766156308030

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 # sample1         1      
GAIN (# sample)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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=2)

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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
chr1:156290753-156290753p.T162T2
chr1:156280744-156280744p.L466L2
chr1:156288685-156288685p.L245V2
chr1:156281939-156281939p.L350M2
chr1:156287030-156287030p.Q301E2
chr1:156288708-156288708p.R237H2
chr1:156280936-156280936p.L402L2
chr1:156280399-156280399p.I495V2
chr1:156290648-156290648p.K197fs*232
chr1:156307949-156307949p.V9V1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample44 4  1    742  44 10
# mutation44 4  1    842  44 11
nonsynonymous SNV24 3  1    512  23 10
synonymous SNV2  1       33   21 1
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
chr1:156288685p.L207M,CCT32
chr1:156280816p.R199H,CCT31
chr1:156304662p.T326T,CCT31
chr1:156287236p.R193H,CCT31
chr1:156279016p.A309T,CCT31
chr1:156288736p.R190C,CCT31
chr1:156280936p.G500W,CCT31
chr1:156305652p.L300L,CCT31
chr1:156287288p.V176V,CCT31
chr1:156279018p.G499V,CCT31

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 CCT3 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 CCT3

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

CACYBP,CCT3,CKS1B,DAP3,FAM189B,FLAD1,GPATCH4,
HAX1,HDGF,ILF2,MRPL9,PRCC,PSMB4,PSMD4,
RUVBL1,SMG5,SSR2,UBE2Q1,UBQLN4,UCK2,VPS72
AHCY,ALKBH2,C1QBP,CCT3,EBNA1BP2,ECE2,EIF3B,
H2AFY2,IPO4,LAD1,NIPSNAP1,NPM3,PIK3R2,PRPF19,
RPL3,RPS3,RUVBL1,RUVBL2,SHMT2,SMARCA4,SMPDL3B

ACBD6,C1orf43,CACYBP,CCT3,DAP3,FLAD1,HAX1,
HDGF,ILF2,MRPL9,MRPS14,PRCC,PSMB4,PSMD4,
SNRPE,TADA1,TBCE,TFB2M,TSEN15,UCK2,VPS72
AHSA1,ATXN10,CCT3,CCT4,CCT6A,CCT7,CDK4,
CSE1L,DDX47,EIF3I,FTSJ2,HNRNPC,IPO11,IPO5,
NOP56,NPM1,PA2G4,SF3A3,STIP1,XRCC6,YBX1
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 CCT3


There's no related Drug.
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Cross referenced IDs for CCT3
* 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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