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 CCT4
Basic gene info.Gene symbolCCT4
Gene namechaperonin containing TCP1, subunit 4 (delta)
SynonymsCCT-DELTA|Cctd|SRB
CytomapUCSC genome browser: 2p15
Genomic locationchr2 :62095261-62115806
Type of geneprotein-coding
RefGenesNM_001256721.1,
NM_006430.3,
Ensembl idENSG00000115484
DescriptionT-complex protein 1 subunit deltaTCP-1-deltachaperonin containing t-complex polypeptide 1, delta subunitstimulator of TAR RNA-binding
Modification date20141207
dbXrefs MIM : 605142
HGNC : HGNC
Ensembl : ENSG00000115484
HPRD : 05506
Vega : OTTHUMG00000152166
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CCT4
BioGPS: 10575
Gene Expression Atlas: ENSG00000115484
The Human Protein Atlas: ENSG00000115484
PathwayNCI Pathway Interaction Database: CCT4
KEGG: CCT4
REACTOME: CCT4
ConsensusPathDB
Pathway Commons: CCT4
MetabolismMetaCyc: CCT4
HUMANCyc: CCT4
RegulationEnsembl's Regulation: ENSG00000115484
miRBase: chr2 :62,095,261-62,115,806
TargetScan: NM_001256721
cisRED: ENSG00000115484
ContextiHOP: CCT4
cancer metabolism search in PubMed: CCT4
UCL Cancer Institute: CCT4
Assigned class in ccmGDBC

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Phenotypic Information for CCT4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CCT4
Familial Cancer Database: CCT4
* 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: CCT4
MedGen: CCT4 (Human Medical Genetics with Condition)
ClinVar: CCT4
PhenotypeMGI: CCT4 (International Mouse Phenotyping Consortium)
PhenomicDB: CCT4

Mutations for CCT4
* 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
pancreasCCT4chr26209548962095509chr26189872261898742
pancreasCCT4chr26210263762102657NRXN1chr25037480950374829
skinCCT4chr26210207862102078chr26246561662465616
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 CCT4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI814482CCT4110926211215562115571ATG51095456106634116106634552
BE698729CLNK13215641060207110602096CCT415321826209571662095781
X55330CCT4110826209558062095687AGA10921504178351924178363591
CB243441CCT41416326209556062095709CCT415838126209570762096663
BM918916CCT43116026210016962100383CCT415923926209940962099630

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        
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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr2:62099331-62099331p.E459D4
chr2:62099332-62099332p.E459G3
chr2:62099658-62099658p.V397V2
chr2:62100176-62100176p.A362A2
chr2:62104536-62104536p.K212K2
chr2:62115590-62115590p.G18D1
chr2:62099450-62099450p.A420P1
chr2:62103241-62103241p.K302N1
chr2:62106140-62106140p.H129R1
chr2:62096668-62096668p.L504F1

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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
# sample 2 14  1  1 513   4 2
# mutation 3 12  1  1 613   4 2
nonsynonymous SNV 1 8  1  1 5 2   3 1
synonymous SNV 2 4       111   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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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
chr2:62099332p.E429G,CCT43
chr2:62099658p.V367V,CCT42
chr2:62096595p.R497W,CCT41
chr2:62099624p.T357A,CCT41
chr2:62106067p.E494K,CCT41
chr2:62096601p.G264E,CCT41
chr2:62099626p.R466Q,CCT41
chr2:62106082p.P226P,CCT41
chr2:62096610p.R453R,CCT41
chr2:62099641p.K215K,CCT41

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 CCT4 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 CCT4

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

CCT4,CCT7,CEBPZ,CENPA,CHAC2,CPSF3,FAM136A,
GMPS,GPN1,HDAC2,KCMF1,MDH1,MSH6,MTIF2,
PNO1,PPP3R1,SERBP1,SF3B14,SUV39H2,TCP1,WDR43
BTF3,CCT4,DPH5,EEF1B2,NPM1,RPL10A,RPL15,
RPL22,RPL23A,RPL24,RPL32,RPL35A,RPL41,RPL5,
RPL6,RPS15A,RPS24,RPS3A,RPS4X,RPS6,RPS7

ASNSD1,C12orf29,C2orf49,CCT4,CCT7,COX7A2L,EEF1B2,
GPN1,MEMO1,MRPL30,NIF3L1,OLA1,ORC4,PNO1,
PSMD14,RPS7,SF3B14,SNRPG,USP39,WDR12,YWHAQ
ACTL6A,ADSL,CACYBP,CCT4,CDK4,COPS3,DAP3,
DDX47,DRG1,EIF2B3,LOC441089,MRPL24,NPM1,NUP35,
NUP54,OLA1,POLE3,TIMM9,TMEM126A,UBA2,VDAC3
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 CCT4


There's no related Drug.
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Cross referenced IDs for CCT4
* 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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