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 DDC
Basic gene info.Gene symbolDDC
Gene namedopa decarboxylase (aromatic L-amino acid decarboxylase)
SynonymsAADC
CytomapUCSC genome browser: 7p12.2
Genomic locationchr7 :50526133-50628768
Type of geneprotein-coding
RefGenesNM_000790.3,
NM_001082971.1,NM_001242886.1,NM_001242887.1,NM_001242888.1,
NM_001242889.1,NM_001242890.1,
Ensembl idENSG00000132437
Descriptionaromatic-L-amino-acid decarboxylase
Modification date20141211
dbXrefs MIM : 107930
HGNC : HGNC
Ensembl : ENSG00000132437
HPRD : 00145
Vega : OTTHUMG00000023353
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DDC
BioGPS: 1644
Gene Expression Atlas: ENSG00000132437
The Human Protein Atlas: ENSG00000132437
PathwayNCI Pathway Interaction Database: DDC
KEGG: DDC
REACTOME: DDC
ConsensusPathDB
Pathway Commons: DDC
MetabolismMetaCyc: DDC
HUMANCyc: DDC
RegulationEnsembl's Regulation: ENSG00000132437
miRBase: chr7 :50,526,133-50,628,768
TargetScan: NM_000790
cisRED: ENSG00000132437
ContextiHOP: DDC
cancer metabolism search in PubMed: DDC
UCL Cancer Institute: DDC
Assigned class in ccmGDBC

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Phenotypic Information for DDC(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DDC
Familial Cancer Database: DDC
* 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_HISTIDINE_METABOLISM
KEGG_TYROSINE_METABOLISM
KEGG_PHENYLALANINE_METABOLISM
KEGG_TRYPTOPHAN_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for DDC
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasDDCchr75057325650573276chr62949061829490638
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 DDC 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 # sample7312143 5 2  2741
GAIN (# sample)7311 43 4 2  273 
LOSS (# sample)   11   1      11
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=59)
Stat. for Synonymous SNVs
(# total SNVs=19)
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
chr7:50607722-50607722p.T69M3
chr7:50534976-50534976p.R393L3
chr7:50596945-50596945p.A177A2
chr7:50605614-50605614p.E127K2
chr7:50537776-50537776p.R379S2
chr7:50605624-50605624p.G123G2
chr7:50611760-50611760p.R8R2
chr7:50547491-50547491p.D339N2
chr7:50566900-50566900p.Y274Y2
chr7:50530997-50530997p.H459Y2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 62 5 3  584 1195 10
# mutation31 63 5 3  684 1225 13
nonsynonymous SNV31 43 5 3  462  115 12
synonymous SNV   2       222 111  1
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
chr7:50537852p.E89K,DDC2
chr7:50605614p.G85G,DDC2
chr7:50607722p.L275L,DDC2
chr7:50605624p.T69M,DDC2
chr7:50566900p.R315C,DDC1
chr7:50611607p.D193N,DDC1
chr7:50530953p.L95F,DDC1
chr7:50596925p.D59G,DDC1
chr7:50611693p.D395N,DDC1
chr7:50531071p.V304A,DDC1

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 DDC 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 DDC

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

AACS,ACSM1,AKR1D1,B3GAT1,C6orf223,DDC,FCN2,
GSTM5,GSTT2,GUSB,ISX,KCNA4,LOC91948,LST-3TM12,
MYOM2,PNLIPRP3,RNASE11,RNASE12,SLCO1B1,SULT1C3,TMPRSS9
ABCC12,ACSM1,ADCY10,AKR1D1,C15orf43,CTNNA2,DDC,
ELOVL7,EPS8L3,HIST1H2AG,HIST1H2BJ,HIST1H3G,IYD,LOC285692,
OR10A7,OR10S1,OR52E8,RIMS1,SLC12A3,SLC26A6,ZP2

AGMAT,AHCY,AIMP2,ASL,BZW2,MPLKIP,TMEM243,
MALSU1,YAE1D1,CCT6A,CHCHD2,CYCS,DDC,DDX56,
GGCT,HIBADH,LSM5,NUPL2,ORC5,TBRG4,ZNRF2
ACY1,CHN2,CLDN15,CYP2J2,DDC,DHRS4L2,EPHX2,
GOLT1A,HNF4G,LOC201651,LRRC28,MACC1,MMEL1,MS4A8,
MYO1A,OTC,PCK2,PTGR1,SLC2A9,SLC37A4,AGMO
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 DDC
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
DB00114dopa decarboxylase (aromatic L-amino acid decarboxylase)nutraceuticalPyridoxal Phosphate
DB00190dopa decarboxylase (aromatic L-amino acid decarboxylase)approvedCarbidopa
DB00126dopa decarboxylase (aromatic L-amino acid decarboxylase)approved; nutraceuticalVitamin C
DB00184dopa decarboxylase (aromatic L-amino acid decarboxylase)approvedNicotine
DB01235dopa decarboxylase (aromatic L-amino acid decarboxylase)approvedLevodopa
DB00988dopa decarboxylase (aromatic L-amino acid decarboxylase)approvedDopamine
DB00135dopa decarboxylase (aromatic L-amino acid decarboxylase)approved; nutraceuticalL-Tyrosine
DB00360dopa decarboxylase (aromatic L-amino acid decarboxylase)approved; investigationalTetrahydrobiopterin
DB00150dopa decarboxylase (aromatic L-amino acid decarboxylase)approved; nutraceuticalL-Tryptophan
DB01001dopa decarboxylase (aromatic L-amino acid decarboxylase)approvedSalbutamol


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Cross referenced IDs for DDC
* 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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