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 CBS
Basic gene info.Gene symbolCBS
Gene namecystathionine-beta-synthase
SynonymsHIP4
CytomapUCSC genome browser: 21q22.3
Genomic locationchr21 :44473300-44496472
Type of geneprotein-coding
RefGenesNM_000071.2,
NM_001178008.1,NM_001178009.1,
Ensembl idENSG00000160200
Descriptionbeta-thionasecystathionine beta-synthasemethylcysteine synthaseserine sulfhydrase
Modification date20141222
dbXrefs MIM : 613381
HGNC : HGNC
Ensembl : ENSG00000160200
HPRD : 01994
Vega : OTTHUMG00000086834
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CBS
BioGPS: 875
Gene Expression Atlas: ENSG00000160200
The Human Protein Atlas: ENSG00000160200
PathwayNCI Pathway Interaction Database: CBS
KEGG: CBS
REACTOME: CBS
ConsensusPathDB
Pathway Commons: CBS
MetabolismMetaCyc: CBS
HUMANCyc: CBS
RegulationEnsembl's Regulation: ENSG00000160200
miRBase: chr21 :44,473,300-44,496,472
TargetScan: NM_000071
cisRED: ENSG00000160200
ContextiHOP: CBS
cancer metabolism search in PubMed: CBS
UCL Cancer Institute: CBS
Assigned class in ccmGDBC

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Phenotypic Information for CBS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CBS
MedGen: CBS (Human Medical Genetics with Condition)
ClinVar: CBS
PhenotypeMGI: CBS (International Mouse Phenotyping Consortium)
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.

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 CBS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE551948B3GALNT112863160801673160801958CBS287517214448350544483735
BQ332259CBS1264214447366044474372SEMA4B251365159075280690752920
L25464CBS1192214447407644478343CBS188251214447402044474083

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)1                
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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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=5

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check002.gifSomatic 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.

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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
chr21:44488638-44488638p.F99F5
chr21:44488623-44488623p.E104D3
chr21:44485350-44485350p.Y233Y3
chr21:44480616-44480616p.A360A3
chr21:44476941-44476941p.F508F2
chr21:44478273-44478273p.I483M2
chr21:44479065-44479065p.R413C1
chr21:44485590-44485590p.T191T1
chr21:44482445-44482445p.I339F1
chr21:44488617-44488617p.?1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2141 1    22 2 87 10
# mutation 2141 1    23 2 86 13
nonsynonymous SNV 2 31      13 1 52 10
synonymous SNV  11  1    1  1 34 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])

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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
chr21:44488638p.F99F,CBS4
chr21:44483156p.A340T,CBS1
chr21:44486375p.G153R,CBS1
chr21:44479374p.L338M,CBS1
chr21:44492180p.I143I,CBS1
chr21:44483167p.A544A,CBS1
chr21:44474014p.T333A,CBS1
chr21:44486415p.A130V,CBS1
chr21:44479399p.F542F,CBS1
chr21:44492252p.Y308Y,CBS1

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 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]

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Gene Expression for CBS

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

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
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 CBS
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00114cystathionine-beta-synthasenutraceuticalPyridoxal Phosphate
DB00118cystathionine-beta-synthaseapproved; nutraceuticalS-Adenosylmethionine
DB00133cystathionine-beta-synthaseapproved; nutraceuticalL-Serine
DB00151cystathionine-beta-synthaseapproved; nutraceuticalL-Cysteine
DB00165cystathionine-beta-synthaseapproved; nutraceuticalPyridoxine
DB03014cystathionine-beta-synthaseexperimentalHeme
DB00175cystathionine-beta-synthaseapprovedPravastatin
DB00563cystathionine-beta-synthaseapprovedMethotrexate
DB00158cystathionine-beta-synthaseapproved; nutraceuticalFolic Acid


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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



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