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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for OGDH |
Basic gene info. | Gene symbol | OGDH |
Gene name | oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) | |
Synonyms | AKGDH|E1k|OGDC | |
Cytomap | UCSC genome browser: 7p14-p13 | |
Genomic location | chr7 :44646120-44716195 | |
Type of gene | protein-coding | |
RefGenes | NM_001003941.2, NM_001165036.1,NM_002541.3, | |
Ensembl id | ENSG00000105953 | |
Description | 2-oxoglutarate dehydrogenase complex component E12-oxoglutarate dehydrogenase, mitochondrialOGDC-E1oxoglutarate decarboxylaseoxoglutarate dehydrogenase (succinyl-transferring) | |
Modification date | 20141207 | |
dbXrefs | MIM : 613022 | |
HGNC : HGNC | ||
Ensembl : ENSG00000105953 | ||
HPRD : 08938 | ||
Vega : OTTHUMG00000155304 | ||
Protein | UniProt: Q02218 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_OGDH | |
BioGPS: 4967 | ||
Gene Expression Atlas: ENSG00000105953 | ||
The Human Protein Atlas: ENSG00000105953 | ||
Pathway | NCI Pathway Interaction Database: OGDH | |
KEGG: OGDH | ||
REACTOME: OGDH | ||
ConsensusPathDB | ||
Pathway Commons: OGDH | ||
Metabolism | MetaCyc: OGDH | |
HUMANCyc: OGDH | ||
Regulation | Ensembl's Regulation: ENSG00000105953 | |
miRBase: chr7 :44,646,120-44,716,195 | ||
TargetScan: NM_001003941 | ||
cisRED: ENSG00000105953 | ||
Context | iHOP: OGDH | |
cancer metabolism search in PubMed: OGDH | ||
UCL Cancer Institute: OGDH | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for OGDH(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: OGDH |
Familial Cancer Database: OGDH |
* This gene is included in those cancer gene databases. |
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_TRYPTOPHAN_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
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OMIM | 613022; gene. |
Orphanet | 31; Oxoglutaricaciduria. |
Disease | KEGG Disease: OGDH |
MedGen: OGDH (Human Medical Genetics with Condition) | |
ClinVar: OGDH | |
Phenotype | MGI: OGDH (International Mouse Phenotyping Consortium) |
PhenomicDB: OGDH |
Mutations for OGDH |
* 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 | OGDH | chr7 | 44679453 | 44679473 | OGDH | chr7 | 44680190 | 44680210 |
ovary | OGDH | chr7 | 44715975 | 44715995 | CAMK2B | chr7 | 44304432 | 44304452 |
pancreas | OGDH | chr7 | 44663202 | 44663222 | OGDH | chr7 | 44663086 | 44663106 |
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 OGDH 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 |
BF851199 | DCTN1 | 17 | 114 | 2 | 74598245 | 74598703 | OGDH | 109 | 205 | 7 | 44748019 | 44748115 | |
BF367739 | OGDH | 1 | 231 | 7 | 44676177 | 44676407 | PAN3-AS1 | 227 | 388 | 13 | 28713182 | 28748527 | |
BE164304 | OGDH | 33 | 105 | 7 | 44676764 | 44676838 | OGDH | 101 | 193 | 7 | 44676616 | 44676708 | |
BF367733 | OGDH | 1 | 231 | 7 | 44676177 | 44676407 | PAN3-AS1 | 227 | 387 | 13 | 28713182 | 28748526 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   | |||
GAIN (# sample) |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |
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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Stat. for Non-Synonymous SNVs (# total SNVs=61) | (# total SNVs=35) |
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(# total SNVs=6) | (# 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 |
chr7:44684936-44684936 | p.R81fs*19 | 5 |
chr7:44664045-44664045 | p.Q35K | 4 |
chr7:44736044-44736044 | p.D596D | 2 |
chr7:44734097-44734097 | p.I530I | 2 |
chr7:44737812-44737812 | p.R794S | 2 |
chr7:44714840-44714840 | p.F333F | 2 |
chr7:44737043-44737043 | p.N709S | 2 |
chr7:44663949-44663949 | p.H3Y | 2 |
chr7:44747514-44747514 | p.T996T | 2 |
chr7:44739760-44739760 | p.F817F | 2 |
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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 | 6 | 5 | 2 | 19 | 3 |   | 7 |   | 6 | 2 |   | 13 | 6 | 4 |   |   | 17 | 10 | 1 | 15 |
# mutation | 7 | 5 | 2 | 18 | 3 |   | 7 |   | 6 | 2 |   | 14 | 6 | 4 |   |   | 17 | 10 | 1 | 21 |
nonsynonymous SNV | 4 | 4 | 2 | 9 |   |   | 4 |   | 2 | 2 |   | 9 | 3 | 4 |   |   | 9 | 7 | 1 | 14 |
synonymous SNV | 3 | 1 |   | 9 | 3 |   | 3 |   | 4 |   |   | 5 | 3 |   |   |   | 8 | 3 |   | 7 |
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 |
chr7:44714840 | p.R767R,OGDH | 2 |
chr7:44736044 | p.R790S,OGDH | 2 |
chr7:44734097 | p.R910Q,OGDH | 2 |
chr7:44746932 | p.I526I,OGDH | 2 |
chr7:44737336 | p.F333F,OGDH | 2 |
chr7:44737812 | p.D592D,OGDH | 2 |
chr7:44664106 | p.Y57N,OGDH | 1 |
chr7:44741208 | p.G874E,OGDH | 1 |
chr7:44747273 | p.R208C,OGDH | 1 |
chr7:44687313 | p.R970Q,OGDH | 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 OGDH |
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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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ACTL6B,AP3B2,APLP1,CRMP1,AMER3,GNG4,KCNH2, UNC79,OGDHL,PCSK1,PHF21B,PSD,PTPRN,RUNDC3A, SCG3,SNAP25,SYN1,SYP,SYT4,TMEM145,UNC13A | ABCB9,ASCL2,C11orf85,C2orf50,C2orf54,RHPN1-AS1,THEM6, CALML5,CPA6,RIPPLY3,ENTPD8,FAM110A,KLHL35,MAPK8IP2, MCHR1,OGDHL,PCSK1N,PYCRL,TRIB3,ABHD11-AS1,WNT3A | ||||
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CHRNA2,DLX6AS,ERP27,GPR83,GPR98,KCTD16,KNG1, KRT36,KRT38,LCN10,MYL3,NAV2,OGDHL,TGM5, TMPRSS6,UGT2A3,UGT2B7,UNC13C,USH1G,VSTM2B,ZNF660 | AEBP1,AFAP1L2,ARHGAP20,BMX,CHAT,CORO2B,EMX2, EMX2OS,GSPT2,HOXD3,HOXD8,HTR3E,KLK13,MAN1C1, MEGF9,MFGE8,OGDHL,PCDHGA9,SH2D7,TMEM150C,TSPYL1 |
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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 OGDH |
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DB Category | DB Name | DB's ID and Url link |
Chemistry | ChEMBL | CHEMBL2816; -. |
Organism-specific databases | PharmGKB | PA31910; -. |
Organism-specific databases | CTD | 4967; -. |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00157 | oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) | approved; nutraceutical | NADH | ![]() | ![]() |
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Cross referenced IDs for OGDH |
* 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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