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 DBH
Basic gene info.Gene symbolDBH
Gene namedopamine beta-hydroxylase (dopamine beta-monooxygenase)
SynonymsDBM
CytomapUCSC genome browser: 9q34
Genomic locationchr9 :136501484-136524466
Type of geneprotein-coding
RefGenesNM_000787.3,
Ensembl idENSG00000123454
Descriptiondopamine beta-hydroxylase
Modification date20141222
dbXrefs MIM : 609312
HGNC : HGNC
Ensembl : ENSG00000123454
HPRD : 01963
Vega : OTTHUMG00000020878
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DBH
BioGPS: 1621
Gene Expression Atlas: ENSG00000123454
The Human Protein Atlas: ENSG00000123454
PathwayNCI Pathway Interaction Database: DBH
KEGG: DBH
REACTOME: DBH
ConsensusPathDB
Pathway Commons: DBH
MetabolismMetaCyc: DBH
HUMANCyc: DBH
RegulationEnsembl's Regulation: ENSG00000123454
miRBase: chr9 :136,501,484-136,524,466
TargetScan: NM_000787
cisRED: ENSG00000123454
ContextiHOP: DBH
cancer metabolism search in PubMed: DBH
UCL Cancer Institute: DBH
Assigned class in ccmGDBC

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Phenotypic Information for DBH(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DBH
Familial Cancer Database: DBH
* 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_TYROSINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for DBH
* 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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryDBHchr9136508337136508357DBHchr9136508545136508565
ovaryDBHchr9136521852136521872MAPK8IP3chr1618202161820236
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 DBH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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         1      
GAIN (# sample)1         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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=63)
Stat. for Synonymous SNVs
(# total SNVs=35)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr9:136508616-136508616p.V276I6
chr9:136518097-136518097p.T470T3
chr9:136508597-136508597p.C269C3
chr9:136508598-136508598p.A270T3
chr9:136505114-136505114p.E162E3
chr9:136517406-136517406p.P458P3
chr9:136508639-136508639p.C283C2
chr9:136507497-136507497p.P219S2
chr9:136508583-136508583p.E265K2
chr9:136509395-136509395p.R326I2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample231135 4 2  7251 189 12
# mutation231124 4 2  7251 1710 15
nonsynonymous SNV22 61 3 2  5241 94 9
synonymous SNV 1163 1    2 1  86 6
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
chr9:136508583p.E265K2
chr9:136516782p.C269C2
chr9:136508597p.L76L2
chr9:136501721p.G281R2
chr9:136508631p.I406I2
chr9:136522203p.G107G1
chr9:136501680p.P219S1
chr9:136505046p.C295C1
chr9:136509385p.A408T1
chr9:136507481p.V26V1

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 DBH 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 DBH

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

APCS,APOA2,APOA4,ASGR2,C3P1,C8A,C9,
CREB3L3,CRP,DBH,F2,FABP1,FGF23,HP,
ITIH1,ITIH3,MT1B,SERPINA7,SLC17A2,SULT2A1,TM4SF5
ACSM2A,ACSM2B,AMN,APOC3,APOL4,TBATA,CHGA,
CHGB,CPO,DBH,NDRG4,NTSR2,ORM1,ORM2,
PDZD7,PHOX2B,SLC18A1,SNORA14A,ST8SIA3,TH,TTC36

AMBN,CACNA1S,CALML3,CST5,DBH,ENTPD3,FGF8,
KLK14,KRT31,LIPM,MUCL1,NELL2,RPTN,S100A3,
SERPINI1,SEZ6L,SNAP91,SPAG6,SST,TCHHL1,TULP2
ATM,C3orf62,CDYL2,CNTRL,DBH,EML6,GRAPL,
KCNMB3,KDM2B,LOC100131691,LTB4R,LTB4R2,NFATC2,QSOX2,
RBM6,RPL32P3,SLC4A8,THRAP3,TTN,USP49,ZNF335
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 DBH
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
DB00126dopamine beta-hydroxylase (dopamine beta-monooxygenase)approved; nutraceuticalVitamin C
DB00822dopamine beta-hydroxylase (dopamine beta-monooxygenase)approvedDisulfiram
DB00988dopamine beta-hydroxylase (dopamine beta-monooxygenase)approvedDopamine
DB00184dopamine beta-hydroxylase (dopamine beta-monooxygenase)approvedNicotine
DB00135dopamine beta-hydroxylase (dopamine beta-monooxygenase)approved; nutraceuticalL-Tyrosine
DB00360dopamine beta-hydroxylase (dopamine beta-monooxygenase)approved; investigationalTetrahydrobiopterin
DB00368dopamine beta-hydroxylase (dopamine beta-monooxygenase)approvedNorepinephrine
DB01235dopamine beta-hydroxylase (dopamine beta-monooxygenase)approvedLevodopa
DB01156dopamine beta-hydroxylase (dopamine beta-monooxygenase)approvedBupropion


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Cross referenced IDs for DBH
* 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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