Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 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)

Cancer 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/

Metabolic Pathway Description
KEGG_TRYPTOPHAN_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
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)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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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'.

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)

Related fusion transcripts : go to Chitars2.0

* 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

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr7:44684936-44684936	p.R81fs*19	5
chr7:44664045-44664045	p.Q35K	4
chr7:44663949-44663949	p.H3Y	2
chr7:44739760-44739760	p.F817F	2
chr7:44747514-44747514	p.T996T	2
chr7:44736635-44736635	p.G675S	2
chr7:44687328-44687328	p.A163T	2
chr7:44736044-44736044	p.D596D	2
chr7:44734097-44734097	p.I530I	2
chr7:44737812-44737812	p.R794S	2

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SNV 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 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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr7:44736044	p.R790S,OGDH	2
chr7:44714840	p.R910Q,OGDH	2
chr7:44734097	p.I526I,OGDH	2
chr7:44746932	p.D592D,OGDH	2
chr7:44737336	p.F333F,OGDH	2
chr7:44737812	p.R767R,OGDH	2
chr7:44741208	p.N373S,OGDH	1
chr7:44664106	p.Y481Y,OGDH	1
chr7:44721375	p.D608Y,OGDH	1
chr7:44737016	p.L774L,OGDH	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2816; -.
Organism-specific databases	PharmGKB	PA31910; -.
Organism-specific databases	CTD	4967; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* 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

: Open all cross reference information