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 CCT4

Basic gene info.	Gene symbol	CCT4
	Gene name	chaperonin containing TCP1, subunit 4 (delta)
	Synonyms	CCT-DELTA\|Cctd\|SRB
	Cytomap	UCSC genome browser: 2p15
	Genomic location	chr2 :62095261-62115806
	Type of gene	protein-coding
	RefGenes	NM_001256721.1, NM_006430.3,
	Ensembl id	ENSG00000115484
	Description	T-complex protein 1 subunit deltaTCP-1-deltachaperonin containing t-complex polypeptide 1, delta subunitstimulator of TAR RNA-binding
	Modification date	20141207
dbXrefs	MIM : 605142
	HGNC : HGNC
	Ensembl : ENSG00000115484
	HPRD : 05506
	Vega : OTTHUMG00000152166
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CCT4
	BioGPS: 10575
	Gene Expression Atlas: ENSG00000115484
	The Human Protein Atlas: ENSG00000115484
Pathway	NCI Pathway Interaction Database: CCT4
	KEGG: CCT4
	REACTOME: CCT4
	ConsensusPathDB
	Pathway Commons: CCT4
Metabolism	MetaCyc: CCT4
	HUMANCyc: CCT4
Regulation	Ensembl's Regulation: ENSG00000115484
	miRBase: chr2 :62,095,261-62,115,806
	TargetScan: NM_001256721
	cisRED: ENSG00000115484
Context	iHOP: CCT4
	cancer metabolism search in PubMed: CCT4
	UCL Cancer Institute: CCT4
Assigned class in ccmGDB	C

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Phenotypic Information for CCT4(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: CCT4
	MedGen: CCT4 (Human Medical Genetics with Condition)
	ClinVar: CCT4
Phenotype	MGI: CCT4 (International Mouse Phenotyping Consortium)
Phenotype	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.

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
pancreas	CCT4	chr2	62095489	62095509		chr2	61898722	61898742
pancreas	CCT4	chr2	62102637	62102657	NRXN1	chr2	50374809	50374829
skin	CCT4	chr2	62102078	62102078		chr2	62465616	62465616

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 CCT4 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
AI814482	CCT4	1	109	2	62112155	62115571	ATG5	109	545	6	106634116	106634552
BE698729	CLNK	132	156	4	10602071	10602096	CCT4	153	218	2	62095716	62095781
X55330	CCT4	1	108	2	62095580	62095687	AGA	109	2150	4	178351924	178363591
CB243441	CCT4	14	163	2	62095560	62095709	CCT4	158	381	2	62095707	62096663
BM918916	CCT4	31	160	2	62100169	62100383	CCT4	159	239	2	62099409	62099630

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=7

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Somatic 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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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
chr2:62099331-62099331	p.E459D	4
chr2:62099332-62099332	p.E459G	3
chr2:62099658-62099658	p.V397V	2
chr2:62100176-62100176	p.A362A	2
chr2:62104536-62104536	p.K212K	2
chr2:62099450-62099450	p.A420P	1
chr2:62115590-62115590	p.G18D	1
chr2:62103241-62103241	p.K302N	1
chr2:62096668-62096668	p.L504F	1
chr2:62106140-62106140	p.H129R	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		2		14			1			1		5	1	3				4		2
# mutation		3		12			1			1		6	1	3				4		2
nonsynonymous SNV		1		8			1			1		5		2				3		1
synonymous SNV		2		4								1	1	1				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
chr2:62099332	p.E429G,CCT4	3
chr2:62099658	p.V367V,CCT4	2
chr2:62099626	p.R497W,CCT4	1
chr2:62106082	p.T357A,CCT4	1
chr2:62096610	p.E494K,CCT4	1
chr2:62099641	p.G264E,CCT4	1
chr2:62107456	p.R466Q,CCT4	1
chr2:62099221	p.P226P,CCT4	1
chr2:62107457	p.R453R,CCT4	1
chr2:62099259	p.K215K,CCT4	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 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

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


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

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 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