Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 OGDH
Basic gene info.Gene symbolOGDH
Gene nameoxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)
SynonymsAKGDH|E1k|OGDC
CytomapUCSC genome browser: 7p14-p13
Genomic locationchr7 :44646120-44716195
Type of geneprotein-coding
RefGenesNM_001003941.2,
NM_001165036.1,NM_002541.3,
Ensembl idENSG00000105953
Description2-oxoglutarate dehydrogenase complex component E12-oxoglutarate dehydrogenase, mitochondrialOGDC-E1oxoglutarate decarboxylaseoxoglutarate dehydrogenase (succinyl-transferring)
Modification date20141207
dbXrefs MIM : 613022
HGNC : HGNC
Ensembl : ENSG00000105953
HPRD : 08938
Vega : OTTHUMG00000155304
ProteinUniProt: Q02218
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_OGDH
BioGPS: 4967
Gene Expression Atlas: ENSG00000105953
The Human Protein Atlas: ENSG00000105953
PathwayNCI Pathway Interaction Database: OGDH
KEGG: OGDH
REACTOME: OGDH
ConsensusPathDB
Pathway Commons: OGDH
MetabolismMetaCyc: OGDH
HUMANCyc: OGDH
RegulationEnsembl's Regulation: ENSG00000105953
miRBase: chr7 :44,646,120-44,716,195
TargetScan: NM_001003941
cisRED: ENSG00000105953
ContextiHOP: OGDH
cancer metabolism search in PubMed: OGDH
UCL Cancer Institute: OGDH
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 613022; gene.
Orphanet 31; Oxoglutaricaciduria.
DiseaseKEGG Disease: OGDH
MedGen: OGDH (Human Medical Genetics with Condition)
ClinVar: OGDH
PhenotypeMGI: 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.

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
ovaryOGDHchr74467945344679473OGDHchr74468019044680210
ovaryOGDHchr74471597544715995CAMK2Bchr74430443244304452
pancreasOGDHchr74466320244663222OGDHchr74466308644663106
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 OGDH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF851199DCTN11711427459824574598703OGDH10920574474801944748115
BF367739OGDH123174467617744676407PAN3-AS1227388132871318228748527
BE164304OGDH3310574467676444676838OGDH10119374467661644676708
BF367733OGDH123174467617744676407PAN3-AS1227387132871318228748526

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 # 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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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=61)
Stat. for Synonymous SNVs
(# total SNVs=35)
Stat. for Deletions
(# total SNVs=6)
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
chr7:44684936-44684936p.R81fs*195
chr7:44664045-44664045p.Q35K4
chr7:44663949-44663949p.H3Y2
chr7:44747514-44747514p.T996T2
chr7:44739760-44739760p.F817F2
chr7:44687328-44687328p.A163T2
chr7:44736635-44736635p.G675S2
chr7:44736044-44736044p.D596D2
chr7:44734097-44734097p.I530I2
chr7:44737812-44737812p.R794S2

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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
# sample652193 7 62 1364  1710115
# mutation752183 7 62 1464  1710121
nonsynonymous SNV4429  4 22 934  97114
synonymous SNV31 93 3 4  53   83 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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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
chr7:44737812p.F333F,OGDH2
chr7:44714840p.D592D,OGDH2
chr7:44736044p.R767R,OGDH2
chr7:44734097p.R790S,OGDH2
chr7:44746932p.R910Q,OGDH2
chr7:44737336p.I526I,OGDH2
chr7:44714122p.R839R,OGDH1
chr7:44734156p.S159P,OGDH1
chr7:44739836p.V965V,OGDH1
chr7:44663986p.G301S,OGDH1

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 OGDH 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 OGDH

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

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

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
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 OGDH
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2816; -.
Organism-specific databasesPharmGKB PA31910; -.
Organism-specific databasesCTD 4967; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)approved; nutraceuticalNADH


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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

: Open all cross reference information



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