Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 TBCD

Basic gene info.	Gene symbol	TBCD
	Gene name	tubulin folding cofactor D
	Synonyms	SSD-1\|tfcD
	Cytomap	UCSC genome browser: 17q25.3
	Genomic location	chr17 :80709939-80901062
	Type of gene	protein-coding
	RefGenes	NM_005993.4, NM_001033052.1,
	Ensembl id	ENSG00000141556
	Description	beta-tubulin cofactor Dtubulin-folding cofactor Dtubulin-specific chaperone D
	Modification date	20141207
dbXrefs	MIM : 604649
	HGNC : HGNC
	Ensembl : ENSG00000141556
	HPRD : 05227
	Vega : OTTHUMG00000177878
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TBCD
	BioGPS: 6904
	Gene Expression Atlas: ENSG00000141556
	The Human Protein Atlas: ENSG00000141556
Pathway	NCI Pathway Interaction Database: TBCD
	KEGG: TBCD
	REACTOME: TBCD
	ConsensusPathDB
	Pathway Commons: TBCD
Metabolism	MetaCyc: TBCD
	HUMANCyc: TBCD
Regulation	Ensembl's Regulation: ENSG00000141556
	miRBase: chr17 :80,709,939-80,901,062
	TargetScan: NM_005993
	cisRED: ENSG00000141556
Context	iHOP: TBCD
	cancer metabolism search in PubMed: TBCD
	UCL Cancer Institute: TBCD
Assigned class in ccmGDB	C

Top

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

Cancer Description
Cancer	CGAP: TBCD
	Familial Cancer Database: TBCD

* 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: TBCD
	MedGen: TBCD (Human Medical Genetics with Condition)
	ClinVar: TBCD
Phenotype	MGI: TBCD (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TBCD

Mutations for TBCD

* 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

Top

- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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	TBCD	chr17	80759982	80760002		chr17	31248611	31248631
pancreas	TBCD	chr17	80767171	80767191	NFATC2	chr20	50039704	50039724

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 TBCD 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
BG009392	TBCD	61	156	17	80790096	80790191	AKR1B1	148	340	7	134134452	134135632
AI205530	TBCD	27	300	17	80731233	80731506	TBCD	282	408	17	80732972	80733095
BF922050	TBCD	16	267	17	80887004	80887343	NEAT1	250	440	11	65195157	65195344
AI336944	TBCD	34	307	17	80731233	80731506	TBCD	289	459	17	80732928	80733095
BF931286	TBCD	1	291	17	80863861	80879419	SGCD	276	295	5	156077901	156077920

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=0

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=0)	Stat. for Synonymous SNVs (# total SNVs=0)
There's no ns-snv.	There's no s-snv.
Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

Top

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

Top

SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

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	3	6		6	1		4		4	2		8	9	2		1	8	12	1	18
# mutation	3	6		7	1		4		4	2		10	8	2		1	9	11	1	19
nonsynonymous SNV	2	6		5			2		2	1		9	4	2			6	6		14
synonymous SNV	1			2	1		2		2	1		1	4			1	3	5	1	5

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])

Top

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
chr17:80847546	p.A823V	2
chr17:80884364	p.P434P	2
chr17:80772794	p.A584V	2
chr17:80878488	p.R476C	2
chr17:80861301	p.P164P	2
chr17:80828207	p.S491S	2
chr17:80726352	p.A512A	2
chr17:80828254	p.V699I	2
chr17:80758865	p.D201E	1
chr17:80863819	p.A415V	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 TBCD 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]

Top

Gene Expression for TBCD

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


ARHGDIA,OGFOD3,C17orf62,C17orf70,CCDC137,CSNK1D,FN3K, FN3KRP,FOXK2,GPS1,HGS,LRRC45,NPLOC4,RPTOR, SIRT7,SLC25A10,SLC26A11,STRA13,TBCD,TSEN54,WDR45B	ADCK4,ARFGAP1,CCDC137,CLCN7,COMT,CORO1B,CTDP1, DGKQ,DUS1L,GAK,HDAC10,HGS,LRRC45,NCLN, NDOR1,PIGQ,PNKP,RANGAP1,RHBDD3,TBCD,ZNF598

ARHGDIA,CEP131,OGFOD3,C17orf53,C17orf70,CCDC137,DDX54, DUS1L,EFTUD2,FOXK2,HEXDC,HGS,KPNB1,LRRC45, POLD1,RPTOR,SLC25A10,SLC25A19,SRP68,TBCD,UBE2O	CAD,CDH24,CHTF18,CIT,DOHH,EIF3B,IQGAP3, KHSRP,LMNB2,MED24,MYBBP1A,NOC2L,NRGN,NUP188, PFAS,RANGAP1,SMPD4,TBCD,TELO2,TMEM201,VARS

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for TBCD

There's no related Drug.

Top

Cross referenced IDs for TBCD

* 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