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 DDO
Basic gene info.Gene symbolDDO
Gene nameD-aspartate oxidase
SynonymsDASOX|DDO-1|DDO-2
CytomapUCSC genome browser: 6q21
Genomic locationchr6 :110713382-110736753
Type of geneprotein-coding
RefGenesNM_003649.2,
NM_004032.2,
Ensembl idENSG00000203797
DescriptionD-aspartate oxidase, DDOaspartic oxidase
Modification date20141207
dbXrefs MIM : 124450
HGNC : HGNC
Ensembl : ENSG00000203797
HPRD : 00498
Vega : OTTHUMG00000015360
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DDO
BioGPS: 8528
Gene Expression Atlas: ENSG00000203797
The Human Protein Atlas: ENSG00000203797
PathwayNCI Pathway Interaction Database: DDO
KEGG: DDO
REACTOME: DDO
ConsensusPathDB
Pathway Commons: DDO
MetabolismMetaCyc: DDO
HUMANCyc: DDO
RegulationEnsembl's Regulation: ENSG00000203797
miRBase: chr6 :110,713,382-110,736,753
TargetScan: NM_003649
cisRED: ENSG00000203797
ContextiHOP: DDO
cancer metabolism search in PubMed: DDO
UCL Cancer Institute: DDO
Assigned class in ccmGDBC

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

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

Mutations for DDO
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryDDOchr6110729308110729328chr6110704221110704241
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 DDO 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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=0)
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
chr6:110734556-110734556p.K65T2
chr6:110714054-110714054p.T345I2
chr6:110714065-110714065p.V341V2
chr6:110726086-110726086p.R145*2
chr6:110714129-110714129p.A320V2
chr6:110714304-110714304p.G262C2
chr6:110714205-110714205p.G295R2
chr6:110734521-110734521p.G77R2
chr6:110714313-110714313p.V259I2
chr6:110734538-110734538p.T71I1

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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
# sample   7  1 11 823  106 7
# mutation   7  1 11 923  136 7
nonsynonymous SNV   5     1 422  73 6
synonymous SNV   2  1 1  5 1  63 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
chr6:110714313p.V200I,DDO2
chr6:110714003p.P81S,DDO1
chr6:110729555p.V282V,DDO1
chr6:110734662p.K164K,DDO1
chr6:110714218p.T71I,DDO1
chr6:110714464p.G274G,DDO1
chr6:110714029p.R157I,DDO1
chr6:110729586p.T67P,DDO1
chr6:110736674p.V269L,DDO1
chr6:110714234p.V149V,DDO1

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 DDO 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 DDO

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

PITHD1,SZRD1,CALR,DDOST,DNAJB11,ENO1,KDM1A,
EMC1,KIAA2013,LYPLA2,MRTO4,P4HB,PDIA4,PDIA5,
PDIA6,PLOD1,PPIB,RCC2,RPN1,SEC61A1,SRM
AP1S1,APH1A,C11orf49,CAPN1,DDOST,EBNA1BP2,ERGIC3,
GMDS,H2AFY2,MBOAT7,NIPSNAP1,NPM3,PAFAH1B3,PRPF19,
RFC2,RNASEH2A,RUVBL1,SCAMP4,SLC35B2,STAP2,TMED3

AKR7A2,APITD1,C19orf10,PITHD1,SZRD1,MINOS1,KDF1,
CDC42,DDOST,EIF3I,ENO1,GPN2,HMGN2,EMC1,
MANF,MED18,MRTO4,NUDC,PPP1R8,SDF4,SDHB
APRT,BID,C19orf10,COPZ1,DDOST,ILF2,MTHFD2,
NPM3,NUDT5,NUF2,NUP37,PCNA,PDIA6,PPIB,
PRDX4,PYCR1,SNRPD3,SYNGR2,TMED3,TMED9,ZDHHC16
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 DDO


There's no related Drug.
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Cross referenced IDs for DDO
* 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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