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 CCT7

Basic gene info.	Gene symbol	CCT7
	Gene name	chaperonin containing TCP1, subunit 7 (eta)
	Synonyms	CCTETA\|CCTH\|NIP7-1\|TCP1ETA
	Cytomap	UCSC genome browser: 2p13.2
	Genomic location	chr2 :73461363-73480150
	Type of gene	protein-coding
	RefGenes	NM_001009570.2, NM_001166284.1,NM_001166285.1,NM_006429.3,NR_029402.1, NR_029403.1,
	Ensembl id	ENSG00000135624
	Description	CCT-etaHIV-1 Nef interacting proteinHIV-1 Nef-interacting proteinT-complex protein 1 subunit etaTCP-1-etachaperonin containing t-complex polypeptide 1, eta subunit
	Modification date	20141207
dbXrefs	MIM : 605140
	HGNC : HGNC
	Ensembl : ENSG00000135624
	HPRD : 06896
	Vega : OTTHUMG00000152765
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CCT7
	BioGPS: 10574
	Gene Expression Atlas: ENSG00000135624
	The Human Protein Atlas: ENSG00000135624
Pathway	NCI Pathway Interaction Database: CCT7
	KEGG: CCT7
	REACTOME: CCT7
	ConsensusPathDB
	Pathway Commons: CCT7
Metabolism	MetaCyc: CCT7
	HUMANCyc: CCT7
Regulation	Ensembl's Regulation: ENSG00000135624
	miRBase: chr2 :73,461,363-73,480,150
	TargetScan: NM_001009570
	cisRED: ENSG00000135624
Context	iHOP: CCT7
	cancer metabolism search in PubMed: CCT7
	UCL Cancer Institute: CCT7
Assigned class in ccmGDB	C

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Phenotypic Information for CCT7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CCT7
	Familial Cancer Database: CCT7

* 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: CCT7
	MedGen: CCT7 (Human Medical Genetics with Condition)
	ClinVar: CCT7
Phenotype	MGI: CCT7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CCT7

Mutations for CCT7

* 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

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	CCT7	chr2	73479281	73479301	CCT7	chr2	73477080	73477100

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 CCT7 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
AA192763	CCT7	1	77	2	73474927	73475003	CCT7	74	176	2	73475026	73476192
BE295614	RIMS3	1	163	1	41088634	41088797	CCT7	161	439	2	73474958	73476304
BF818027	HLA-B	18	253	6	2628575	2628815	CCT7	249	461	2	73461456	73466923
BM423518	SMAP2	1	507	1	40882451	40887836	CCT7	508	778	2	73479862	73480133
AW410065	RIMS3	19	202	1	41088634	41088817	CCT7	200	543	2	73474958	73477007
AW410067	RIMS3	19	202	1	41088634	41088817	CCT7	200	483	2	73474958	73476308
AI183764	CCT7	15	205	2	73479943	73480133	MOSPD3	204	298	7	100211226	100211320
BI113920	RIMS3	183	202	1	41088608	41088627	CCT7	202	650	2	73474979	73477515
BM809370	SMAP2	23	529	1	40882451	40887836	CCT7	530	801	2	73479862	73480133
BM915408	SMAP2	1	506	1	40882451	40887835	CCT7	507	778	2	73479862	73480133
BQ646179	ENO1	39	575	1	8921061	8923343	CCT7	575	790	2	73461450	73466921
CV324589	CCT7	18	220	2	73477010	73478390	CCT7	216	486	2	73478406	73479883

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=20)	Stat. for Synonymous SNVs (# total SNVs=12)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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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
chr2:73478461-73478461	p.A233A	3
chr2:73479988-73479988	p.340	2
chr2:73476217-73476217	p.P90P	2
chr2:73477039-73477039	p.G151G	1
chr2:73478454-73478454	p.I231T	1
chr2:73474974-73474974	p.P31S	1
chr2:73476221-73476221	p.G92W	1
chr2:73477435-73477435	p.Y154H	1
chr2:73474975-73474975	p.P31R	1
chr2:73476273-73476273	p.R109P	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=2

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	1	1	1	4			1		1			6	4	1			3	8		7
# mutation	1	1	1	4			1		1			7	4	1			3	8		7
nonsynonymous SNV	1			1			1		1			3	2	1			1	4		6
synonymous SNV		1	1	3								4	2				2	4		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
chr2:73479988	p.X340X,CCT7	2
chr2:73476280	p.L40L,CCT7	1
chr2:73478454	p.I231T,CCT7	1
chr2:73466844	p.S27N	1
chr2:73471736	p.V56A,CCT7	1
chr2:73476281	p.R243H,CCT7	1
chr2:73478490	p.E34K	1
chr2:73466864	p.L70L,CCT7	1
chr2:73471807	p.A301T,CCT7	1
chr2:73476288	p.D46N,CCT7	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 CCT7 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 CCT7

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


AUP1,BOLA3,CCT4,CCT7,DGUOK,EIF5AL1,FAM136A, MRPL12,MRPS5,PCGF1,PNO1,PPM1G,PTGES2,RTKN, SF3B14,SMYD5,SNRPG,SUCLG1,TSSC1,UBE2S,ZMYND19	HYPK,CCT7,COX4I1,ECSIT,EIF3G,EIF3I,GRHPR, LOC152217,MRPL11,MRPL51,MRPS18A,MRPS34,PHB,POLR2F, POLR2I,PSMB7,STOML2,TUFM,TXN2,WBSCR22,ZNF511

ACP1,BOLA3,CCT4,CCT7,CPSF3,FAM136A,HSPD1, NIFK,MRPL30,MRPS9,OLA1,PDCL3,PNO1,POLR2D, PPM1G,PREB,PSMD14,PTCD3,SF3B14,TSSC1,USP39	ATXN10,CMSS1,CCT3,CCT4,CCT7,CDK4,EBNA1BP2, EIF3I,NHP2L1,NME1,NPM1,NPM3,PA2G4,PARK7, PRMT1,PSMB5,PSMC3,RAN,RANBP1,TUBA1B,XRCC6

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 CCT7

There's no related Drug.

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Cross referenced IDs for CCT7

* 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