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 TBCB
Basic gene info.Gene symbolTBCB
Gene nametubulin folding cofactor B
SynonymsCG22|CKAP1|CKAPI
CytomapUCSC genome browser: 19q13.11-q13.12
Genomic locationchr19 :36605887-36616849
Type of geneprotein-coding
RefGenesNM_001281.2,
NM_001300971.1,
Ensembl idENSG00000105254
Descriptioncytoskeleton associated protein 1cytoskeleton-associated protein CKAPItubulin-folding cofactor Btubulin-specific chaperone B
Modification date20141207
dbXrefs MIM : 601303
HGNC : HGNC
Ensembl : ENSG00000105254
HPRD : 03196
Vega : OTTHUMG00000048143
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TBCB
BioGPS: 1155
Gene Expression Atlas: ENSG00000105254
The Human Protein Atlas: ENSG00000105254
PathwayNCI Pathway Interaction Database: TBCB
KEGG: TBCB
REACTOME: TBCB
ConsensusPathDB
Pathway Commons: TBCB
MetabolismMetaCyc: TBCB
HUMANCyc: TBCB
RegulationEnsembl's Regulation: ENSG00000105254
miRBase: chr19 :36,605,887-36,616,849
TargetScan: NM_001281
cisRED: ENSG00000105254
ContextiHOP: TBCB
cancer metabolism search in PubMed: TBCB
UCL Cancer Institute: TBCB
Assigned class in ccmGDBC

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

Mutations for TBCB
* 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
pancreasTBCBchr193661616736616167chr193661896436618964
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 TBCB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CD522326TBCB372193661665336616722SERPINB269721186155882261569752
AL561402TBCB1169193660638736606557EIF4EBP2160947107216411172181884
BP390379TBCB1283193661640736616833LOC7285542845005177311007177311223
DA235308TBCB1363193660638436611637B3GALNT13605913160804308160804539

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr19:36611618-36611618p.D89N2
chr19:36611634-36611634p.R94H2
chr19:36606528-36606528p.F22L1
chr19:36616667-36616667p.G240W1
chr19:36611653-36611653p.D100D1
chr19:36612584-36612584p.G171*1
chr19:36606539-36606539p.K26M1
chr19:36611654-36611654p.V101M1
chr19:36616392-36616392p.R196H1
chr19:36606546-36606546p.Y28Y1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   3    11  1 1 33 2
# mutation   3    11  1 1 33 3
nonsynonymous SNV        11  1 1 13 3
synonymous SNV   3            2   
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
chr19:36606509p.S16T1
chr19:36616392p.F22L1
chr19:36606528p.Y28Y1
chr19:36616592p.E70D1
chr19:36606546p.D80G1
chr19:36616597p.R94H1
chr19:36607038p.V101M1
chr19:36616633p.S102F1
chr19:36607067p.R103P1
chr19:36616654p.Y107F1

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 TBCB 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 TBCB

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

ALKBH6,DNPH1,CAPNS1,CCDC124,COX6B1,EXOSC5,HSPBP1,
LIN37,MIIP,MRPS12,POLR2I,RBM42,RPS16,SDHAF1,
TBCB,THAP8,TIMM50,TMEM147,U2AF1L4,USF2,YIF1B
ARF5,BAD,BCL7C,COPE,DGCR6L,DPM3,FBXL15,
GNB2,MPG,MRPL28,NME3,RALY,RBM42,ROMO1,
SCAND1,TBCB,TMUB1,TRAPPC5,UBE2J2,ZNF428,ZNF688

ALKBH6,ANAPC11,COX6B1,EXOSC5,JOSD2,MRPS12,NDUFA11,
NOSIP,PAFAH1B3,POLR2I,PRMT1,PSMD8,RBM42,RPS16,
SDHAF1,SNRPD2,TBCB,TIMM50,TMEM147,TMEM160,USF2
ARL2,C1orf122,CCDC23,DCTN3,DRAP1,EEF1D,FLOT1,
MRPL10,MRPL40,PIN1,PKIG,POLR2I,RPP21,SNAPIN,
SNX17,SSSCA1,STOML1,TBCB,UROD,VPS72,ZMAT5
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 TBCB


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