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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for DDO |
Basic gene info. | Gene symbol | DDO |
Gene name | D-aspartate oxidase | |
Synonyms | DASOX|DDO-1|DDO-2 | |
Cytomap | UCSC genome browser: 6q21 | |
Genomic location | chr6 :110713382-110736753 | |
Type of gene | protein-coding | |
RefGenes | NM_003649.2, NM_004032.2, | |
Ensembl id | ENSG00000203797 | |
Description | D-aspartate oxidase, DDOaspartic oxidase | |
Modification date | 20141207 | |
dbXrefs | MIM : 124450 | |
HGNC : HGNC | ||
Ensembl : ENSG00000203797 | ||
HPRD : 00498 | ||
Vega : OTTHUMG00000015360 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_DDO | |
BioGPS: 8528 | ||
Gene Expression Atlas: ENSG00000203797 | ||
The Human Protein Atlas: ENSG00000203797 | ||
Pathway | NCI Pathway Interaction Database: DDO | |
KEGG: DDO | ||
REACTOME: DDO | ||
ConsensusPathDB | ||
Pathway Commons: DDO | ||
Metabolism | MetaCyc: DDO | |
HUMANCyc: DDO | ||
Regulation | Ensembl's Regulation: ENSG00000203797 | |
miRBase: chr6 :110,713,382-110,736,753 | ||
TargetScan: NM_003649 | ||
cisRED: ENSG00000203797 | ||
Context | iHOP: DDO | |
cancer metabolism search in PubMed: DDO | ||
UCL Cancer Institute: DDO | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for DDO(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: DDO |
Familial Cancer Database: DDO |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
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KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: DDO |
MedGen: DDO (Human Medical Genetics with Condition) | |
ClinVar: DDO | |
Phenotype | MGI: 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. |
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- Statistics for Tissue and Mutation type | Top |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | DDO | chr6 | 110729308 | 110729328 | chr6 | 110704221 | 110704241 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DDO 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 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=43) | (# total SNVs=16) |
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(# total SNVs=3) | (# total SNVs=0) |
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* 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 |
chr6:110734521-110734521 | p.G77R | 2 |
chr6:110714313-110714313 | p.V259I | 2 |
chr6:110734556-110734556 | p.K65T | 2 |
chr6:110714054-110714054 | p.T345I | 2 |
chr6:110714065-110714065 | p.V341V | 2 |
chr6:110726086-110726086 | p.R145* | 2 |
chr6:110714129-110714129 | p.A320V | 2 |
chr6:110714304-110714304 | p.G262C | 2 |
chr6:110714205-110714205 | p.G295R | 2 |
chr6:110736689-110736689 | p.D21Y | 1 |
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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 |   |   |   | 7 |   |   | 1 |   | 1 | 1 |   | 8 | 2 | 3 |   |   | 10 | 6 |   | 7 |
# mutation |   |   |   | 7 |   |   | 1 |   | 1 | 1 |   | 9 | 2 | 3 |   |   | 13 | 6 |   | 7 |
nonsynonymous SNV |   |   |   | 5 |   |   |   |   |   | 1 |   | 4 | 2 | 2 |   |   | 7 | 3 |   | 6 |
synonymous SNV |   |   |   | 2 |   |   | 1 |   | 1 |   |   | 5 |   | 1 |   |   | 6 | 3 |   | 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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* 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 |
chr6:110714313 | p.V200I,DDO | 2 |
chr6:110714324 | p.A291V,DDO | 1 |
chr6:110726085 | p.G196V,DDO | 1 |
chr6:110714134 | p.L103I,DDO | 1 |
chr6:110734560 | p.A290A,DDO | 1 |
chr6:110714395 | p.V172V,DDO | 1 |
chr6:110729542 | p.H82Y,DDO | 1 |
chr6:110714170 | p.V282V,DDO | 1 |
chr6:110734612 | p.K164K,DDO | 1 |
chr6:110714419 | p.P81S,DDO | 1 |
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* 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. |
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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 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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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 |
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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 |
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* 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 |
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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 |
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