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 CCT3

Basic gene info.	Gene symbol	CCT3
	Gene name	chaperonin containing TCP1, subunit 3 (gamma)
	Synonyms	CCT-gamma\|CCTG\|PIG48\|TCP-1-gamma\|TRIC5
	Cytomap	UCSC genome browser: 1q23
	Genomic location	chr1 :156278751-156308206
	Type of gene	protein-coding
	RefGenes	NM_001008800.2, NM_005998.4,NR_036564.1,NR_036565.1,NM_001008883.1,
	Ensembl id	ENSG00000163468
	Description	T-complex protein 1 subunit gammaT-complex protein 1, gamma subunitTCP1 (t-complex-1) ring complex, polypeptide 5hTRiC5
	Modification date	20141207
dbXrefs	MIM : 600114
	HGNC : HGNC
	Ensembl : ENSG00000163468
	HPRD : 08969
	Vega : OTTHUMG00000024061
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CCT3
	BioGPS: 7203
	Gene Expression Atlas: ENSG00000163468
	The Human Protein Atlas: ENSG00000163468
Pathway	NCI Pathway Interaction Database: CCT3
	KEGG: CCT3
	REACTOME: CCT3
	ConsensusPathDB
	Pathway Commons: CCT3
Metabolism	MetaCyc: CCT3
	HUMANCyc: CCT3
Regulation	Ensembl's Regulation: ENSG00000163468
	miRBase: chr1 :156,278,751-156,308,206
	TargetScan: NM_001008800
	cisRED: ENSG00000163468
Context	iHOP: CCT3
	cancer metabolism search in PubMed: CCT3
	UCL Cancer Institute: CCT3
Assigned class in ccmGDB	C

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Phenotypic Information for CCT3(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: CCT3
	MedGen: CCT3 (Human Medical Genetics with Condition)
	ClinVar: CCT3
Phenotype	MGI: CCT3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	CCT3	chr1	156306971	156306991	PTPN1	chr20	49197356	49197376

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 CCT3 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
AA748732	CCT3	10	379	1	156278759	156280436	HVCN1	374	489	12	111091636	111091751
CB114948	CCT3	1	87	1	156287279	156288685	RAC1	79	167	7	6442050	6442138
AA010637	CCT3	1	265	1	156306743	156307005	TRAF3IP1	259	359	2	239309092	239309191
BE783136	CCT3	20	99	1	156303346	156303425	CCT3	90	140	1	156290660	156290710
BQ353904	MDM2	1	235	12	69237587	69237822	CCT3	234	463	1	156280758	156280987
DB040324	LOC100507412	1	107	?	112074	112180	CCT3	108	572	1	156290766	156308030

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=3

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Somatic 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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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
chr1:156280399-156280399	p.I495V	2
chr1:156290648-156290648	p.K197fs*23	2
chr1:156290753-156290753	p.T162T	2
chr1:156280744-156280744	p.L466L	2
chr1:156288685-156288685	p.L245V	2
chr1:156281939-156281939	p.L350M	2
chr1:156287030-156287030	p.Q301E	2
chr1:156288708-156288708	p.R237H	2
chr1:156280936-156280936	p.L402L	2
chr1:156287296-156287296	p.L268I	1

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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=1

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	4	4		4			1					7	4	2			4	4		10
# mutation	4	4		4			1					8	4	2			4	4		11
nonsynonymous SNV	2	4		3			1					5	1	2			2	3		10
synonymous SNV	2			1								3	3				2	1		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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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
chr1:156288685	p.L207M,CCT3	2
chr1:156280760	p.T335A,CCT3	1
chr1:156303398	p.M2V,CCT3	1
chr1:156286994	p.T326T,CCT3	1
chr1:156288708	p.R199H,CCT3	1
chr1:156280783	p.A309T,CCT3	1
chr1:156303399	p.R193H,CCT3	1
chr1:156287012	p.G500W,CCT3	1
chr1:156288726	p.L300L,CCT3	1
chr1:156280816	p.R190C,CCT3	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 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

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


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

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 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