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 CBS

Basic gene info.	Gene symbol	CBS
	Gene name	cystathionine-beta-synthase
	Synonyms	HIP4
	Cytomap	UCSC genome browser: 21q22.3
	Genomic location	chr21 :44473300-44496472
	Type of gene	protein-coding
	RefGenes	NM_000071.2, NM_001178008.1,NM_001178009.1,
	Ensembl id	ENSG00000160200
	Description	beta-thionasecystathionine beta-synthasemethylcysteine synthaseserine sulfhydrase
	Modification date	20141222
dbXrefs	MIM : 613381
	HGNC : HGNC
	Ensembl : ENSG00000160200
	HPRD : 01994
	Vega : OTTHUMG00000086834
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CBS
	BioGPS: 875
	Gene Expression Atlas: ENSG00000160200
	The Human Protein Atlas: ENSG00000160200
Pathway	NCI Pathway Interaction Database: CBS
	KEGG: CBS
	REACTOME: CBS
	ConsensusPathDB
	Pathway Commons: CBS
Metabolism	MetaCyc: CBS
	HUMANCyc: CBS
Regulation	Ensembl's Regulation: ENSG00000160200
	miRBase: chr21 :44,473,300-44,496,472
	TargetScan: NM_000071
	cisRED: ENSG00000160200
Context	iHOP: CBS
	cancer metabolism search in PubMed: CBS
	UCL Cancer Institute: CBS
Assigned class in ccmGDB	C

Top

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

Cancer Description
Cancer	CGAP: CBS
	Familial Cancer Database: CBS

* 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
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM KEGG_CYSTEINE_AND_METHIONINE_METABOLISM KEGG_SELENOAMINO_ACID_METABOLISM REACTOME_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for CBS

* 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

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CBS 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
BE551948	B3GALNT1	1	286	3	160801673	160801958	CBS	287	517	21	44483505	44483735
BQ332259	CBS	1	264	21	44473660	44474372	SEMA4B	251	365	15	90752806	90752920
L25464	CBS	1	192	21	44474076	44478343	CBS	188	251	21	44474020	44474083

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=5

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=39)	Stat. for Synonymous SNVs (# total SNVs=21)

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
chr21:44488638-44488638	p.F99F	5
chr21:44488623-44488623	p.E104D	3
chr21:44485350-44485350	p.Y233Y	3
chr21:44480616-44480616	p.A360A	3
chr21:44476941-44476941	p.F508F	2
chr21:44478273-44478273	p.I483M	2
chr21:44483118-44483118	p.T300S	1
chr21:44492152-44492152	p.R51K	1
chr21:44476940-44476940	p.A509T	1
chr21:44485526-44485526	p.E213K	1

Top

SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

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	1	4	1		1					2	2		2		8	7		10
# mutation		2	1	4	1		1					2	3		2		8	6		13
nonsynonymous SNV		2		3	1							1	3		1		5	2		10
synonymous SNV			1	1			1					1			1		3	4		3

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
chr21:44488638	p.F99F,CBS	4
chr21:44478947	p.A452V,CBS	1
chr21:44482448	p.L287L,CBS	1
chr21:44485526	p.P88L,CBS	1
chr21:44488672	p.F443F,CBS	1
chr21:44478973	p.G284W,CBS	1
chr21:44482463	p.I84I,CBS	1
chr21:44485544	p.E440D,CBS	1
chr21:44488683	p.E283K,CBS	1
chr21:44478982	p.P273S,CBS	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 CBS 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 CBS

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


ASNS,AURKB,CBS,CDC20,CDC45,CDT1,CHAF1B, CTPS1,FAM64A,IFRD1,LMNB2,MCM5,MTHFD1L,PSAT1, PWP2,RRP1,SHMT2,ALYREF,TYMS,WDR4,YARS	AMN,APOC3,APOL4,TBATA,CBS,CHGA,CLSTN3, DBH,GABRD,GCDH,GLYCTK,LIME1,MEF2B,NDRG4, NTSR2,PDZD7,PHOX2B,SNORA14A,ST8SIA3,TH,TTC36

ETNPPL,NBEAP1,NCOR1P1,CBS,CCKBR,CETN1,CNTNAP4, CT45A2,DUSP9,EEF1A2,FBN3,FNDC5,GABRG3,GPR123, MAGEA10,OR10C1,OR4M2,PCDHB5,PLEKHG4B,STC2,TP53TG3B	ACE2,ALPI,ADIRF,CBS,SLC52A1,HEBP1,INPP5J, MMEL1,MSRA,NAALADL1,OIT3,PCK2,PKLR,PRAP1, PTGR1,SLC22A4,SLC5A11,TM4SF20,TM6SF2,AGMO,USH1G

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 CBS

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00114	cystathionine-beta-synthase	nutraceutical	Pyridoxal Phosphate
DB00118	cystathionine-beta-synthase	approved; nutraceutical	S-Adenosylmethionine
DB00133	cystathionine-beta-synthase	approved; nutraceutical	L-Serine
DB00151	cystathionine-beta-synthase	approved; nutraceutical	L-Cysteine
DB00165	cystathionine-beta-synthase	approved; nutraceutical	Pyridoxine
DB03014	cystathionine-beta-synthase	experimental	Heme
DB00175	cystathionine-beta-synthase	approved	Pravastatin
DB00563	cystathionine-beta-synthase	approved	Methotrexate
DB00158	cystathionine-beta-synthase	approved; nutraceutical	Folic Acid

Top

Cross referenced IDs for CBS

* 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