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 symbolCCT7
Gene namechaperonin containing TCP1, subunit 7 (eta)
SynonymsCCTETA|CCTH|NIP7-1|TCP1ETA
CytomapUCSC genome browser: 2p13.2
Genomic locationchr2 :73461363-73480150
Type of geneprotein-coding
RefGenesNM_001009570.2,
NM_001166284.1,NM_001166285.1,NM_006429.3,NR_029402.1,
NR_029403.1,
Ensembl idENSG00000135624
DescriptionCCT-etaHIV-1 Nef interacting proteinHIV-1 Nef-interacting proteinT-complex protein 1 subunit etaTCP-1-etachaperonin containing t-complex polypeptide 1, eta subunit
Modification date20141207
dbXrefs MIM : 605140
HGNC : HGNC
Ensembl : ENSG00000135624
HPRD : 06896
Vega : OTTHUMG00000152765
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CCT7
BioGPS: 10574
Gene Expression Atlas: ENSG00000135624
The Human Protein Atlas: ENSG00000135624
PathwayNCI Pathway Interaction Database: CCT7
KEGG: CCT7
REACTOME: CCT7
ConsensusPathDB
Pathway Commons: CCT7
MetabolismMetaCyc: CCT7
HUMANCyc: CCT7
RegulationEnsembl's Regulation: ENSG00000135624
miRBase: chr2 :73,461,363-73,480,150
TargetScan: NM_001009570
cisRED: ENSG00000135624
ContextiHOP: CCT7
cancer metabolism search in PubMed: CCT7
UCL Cancer Institute: CCT7
Assigned class in ccmGDBC

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Phenotypic Information for CCT7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CCT7
MedGen: CCT7 (Human Medical Genetics with Condition)
ClinVar: CCT7
PhenotypeMGI: CCT7 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryCCT7chr27347928173479301CCT7chr27347708073477100
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 CCT7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA192763CCT717727347492773475003CCT77417627347502673476192
BE295614RIMS3116314108863441088797CCT716143927347495873476304
BF818027HLA-B18253626285752628815CCT724946127346145673466923
BM423518SMAP2150714088245140887836CCT750877827347986273480133
AW410065RIMS31920214108863441088817CCT720054327347495873477007
AW410067RIMS31920214108863441088817CCT720048327347495873476308
AI183764CCT71520527347994373480133MOSPD32042987100211226100211320
BI113920RIMS318320214108860841088627CCT720265027347497973477515
BM809370SMAP22352914088245140887836CCT753080127347986273480133
BM915408SMAP2150614088245140887835CCT750777827347986273480133
BQ646179ENO139575189210618923343CCT757579027346145073466921
CV324589CCT71822027347701073478390CCT721648627347840673479883

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                
GAIN (# sample)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=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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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
chr2:73478461-73478461p.A233A3
chr2:73476217-73476217p.P90P2
chr2:73479988-73479988p.*340*2
chr2:73461511-73461511p.M2K1
chr2:73477523-73477523p.R183Q1
chr2:73476157-73476157p.L70L1
chr2:73477005-73477005p.R140Q1
chr2:73474911-73474911p.V10I1
chr2:73478400-73478400p.S213Y1
chr2:73476202-73476202p.V85V1

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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
# sample1114  1 1  641  38 7
# mutation1114  1 1  741  38 7
nonsynonymous SNV1  1  1 1  321  14 6
synonymous SNV 113       42   24 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
chr2:73479988p.X340X,CCT72
chr2:73461511p.E11G1
chr2:73477500p.V10I,CCT71
chr2:73470241p.R183Q,CCT71
chr2:73476202p.V23V1
chr2:73466796p.P31S,CCT71
chr2:73477523p.S213Y,CCT71
chr2:73471709p.S27N1
chr2:73476217p.L40L,CCT71
chr2:73466833p.I231T,CCT71

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 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

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

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
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 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



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