Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 TBCC
Basic gene info.Gene symbolTBCC
Gene nametubulin folding cofactor C
SynonymsCFC
CytomapUCSC genome browser: 6p21.1
Genomic locationchr6 :42712233-42713884
Type of geneprotein-coding
RefGenesNM_003192.2,
Ensembl idENSG00000124659
Descriptiontubulin-folding cofactor Ctubulin-specific chaperone C
Modification date20141207
dbXrefs MIM : 602971
HGNC : HGNC
Ensembl : ENSG00000124659
HPRD : 04276
Vega : OTTHUMG00000014704
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TBCC
BioGPS: 6903
Gene Expression Atlas: ENSG00000124659
The Human Protein Atlas: ENSG00000124659
PathwayNCI Pathway Interaction Database: TBCC
KEGG: TBCC
REACTOME: TBCC
ConsensusPathDB
Pathway Commons: TBCC
MetabolismMetaCyc: TBCC
HUMANCyc: TBCC
RegulationEnsembl's Regulation: ENSG00000124659
miRBase: chr6 :42,712,233-42,713,884
TargetScan: NM_003192
cisRED: ENSG00000124659
ContextiHOP: TBCC
cancer metabolism search in PubMed: TBCC
UCL Cancer Institute: TBCC
Assigned class in ccmGDBC

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

Mutations for TBCC
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TBCC related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ670175TBCC143964271253142712968TNFRSF12A4405651630720583072183
BQ052721ISG201107158918227189182642TBCC10837464271344742713713
BE349632TBCC824964271223642712477ELMO124745173695437236954576

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
There's no copy number variation information in COSMIC data for this gene.

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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=21)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr6:42713803-42713803p.S3S3
chr6:42712887-42712887p.D309H1
chr6:42713214-42713214p.E200Q1
chr6:42713543-42713543p.R90P1
chr6:42712914-42712914p.D300N1
chr6:42713228-42713228p.E195V1
chr6:42713552-42713552p.A87E1
chr6:42712916-42712916p.I299T1
chr6:42713244-42713244p.E190*1
chr6:42713573-42713573p.S80L1

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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
# sample23 4   11  23 1  112
# mutation43 4   11  23 1  112
nonsynonymous SNV33 4   1   21 1  1 1
synonymous SNV1       1   2     11
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
chr6:42713803p.S3S2
chr6:42712938p.E247Q1
chr6:42713552p.E200Q1
chr6:42712981p.K172N1
chr6:42713573p.P159S1
chr6:42713039p.F137F1
chr6:42713641p.A122A1
chr6:42713073p.Q121H1
chr6:42713653p.A329A1
chr6:42713214p.R90P1

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 TBCC 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 TBCC

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

BYSL,OARD1,CCND3,CUL7,FLJ41941,KLC4,KLHDC3,
SKOR1,MED20,MRPL2,NFYA,OLIG1,OLIG2,POLR1C,
RPL7L1,SLC29A1,TBCC,TJAP1,TOMM6,UCMA,USP49
ATP5G2,BANF1,CLP1,IMP3,LCMT1,LSM2,MAD2L1BP,
MRPL57,MRPL18,MRPL9,NHP2L1,PDXP,RNF5,SCNM1,
SNRPC,TBCC,THAP11,TMEM203,UBL7,ZCCHC3,ZNRD1

ABT1,ASF1A,KLHDC3,LSM2,LYRM4,MAD2L1BP,MEA1,
MRPL14,MRPS10,POLR1C,PPIL1,NELFE,RPS10,RPS18,
SNRPC,TAF11,TBCC,TMEM14C,TOMM6,UBL5,ZNRD1
AAMP,BAK1,BCL2L10,CASP3,CXCR2P1,DAO,HARBI1,
HCCS,IFI27L1,NCR1,NT5C3A,RRAGC,SNORA72,SOD1,
TBCC,TDRD7,TMEM54,TMSB4XP8,TRIM31,UBB,USF1
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 TBCC


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