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 IDH2

Basic gene info.	Gene symbol	IDH2
	Gene name	isocitrate dehydrogenase 2 (NADP+), mitochondrial
	Synonyms	D2HGA2\|ICD-M\|IDH\|IDHM\|IDP\|IDPM\|mNADP-IDH
	Cytomap	UCSC genome browser: 15q26.1
	Genomic location	chr15 :90627211-90645708
	Type of gene	protein-coding
	RefGenes	NM_001289910.1, NM_001290114.1,NM_002168.3,
	Ensembl id	ENSG00000182054
	Description	NADP(+)-specific ICDHisocitrate dehydrogenase [NADP], mitochondrialoxalosuccinate decarboxylase
	Modification date	20141207
dbXrefs	MIM : 147650
	HGNC : HGNC
	HPRD : 00973
Protein	UniProt: P48735 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_IDH2
	BioGPS: 3418
	Gene Expression Atlas: ENSG00000182054
	The Human Protein Atlas: ENSG00000182054
Pathway	NCI Pathway Interaction Database: IDH2
	KEGG: IDH2
	REACTOME: IDH2
	ConsensusPathDB
	Pathway Commons: IDH2
Metabolism	MetaCyc: IDH2
	HUMANCyc: IDH2
Regulation	Ensembl's Regulation: ENSG00000182054
	miRBase: chr15 :90,627,211-90,645,708
	TargetScan: NM_001289910
	cisRED: ENSG00000182054
Context	iHOP: IDH2
	cancer metabolism search in PubMed: IDH2
	UCL Cancer Institute: IDH2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of IDH2 in cancer cell metabolism	1. Cairns RA, Mak TW (2013) Oncogenic isocitrate dehydrogenase mutations: mechanisms, models, and clinical opportunities. Cancer Discov 3: 730-741. doi: 10.1158/2159-8290.CD-13-0083. go to article 2. Shim EH, Livi CB, Rakheja D, Tan J, Benson D, et al. (2014) L-2-Hydroxyglutarate: an epigenetic modifier and putative oncometabolite in renal cancer. Cancer Discov 4: 1290-1298. doi: 10.1158/2159-8290.CD-13-0696. pmid: 4286872. go to article 3. Lu C, Venneti S, Akalin A, Fang F, Ward PS, et al. (2013) Induction of sarcomas by mutant IDH2. Genes Dev 27: 1986-1998. doi: 10.1101/gad.226753.113. pmid: 3792475. go to article 4. Akbay EA, Moslehi J, Christensen CL, Saha S, Tchaicha JH, et al. (2014) D-2-hydroxyglutarate produced by mutant IDH2 causes cardiomyopathy and neurodegeneration in mice. Genes Dev 28: 479-490. doi: 10.1101/gad.231233.113. pmid: 3950345. go to article 5. Kats LM, Reschke M, Taulli R, Pozdnyakova O, Burgess K, et al. (2014) Proto-oncogenic role of mutant IDH2 in leukemia initiation and maintenance. Cell Stem Cell 14: 329-341. doi: 10.1016/j.stem.2013.12.016. pmid: 4380188. go to article

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Phenotypic Information for IDH2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: IDH2
	Familial Cancer Database: IDH2

* 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 LAML ⁶, GBM ⁷,	Therapeutic Vulnerabilities in Cancer⁸

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,
6 http://www.nejm.org/doi/full/10.1056/NEJMoa1301689,
7 http://www.nejm.org/doi/full/10.1056/NEJMoa1402121,
8Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_GLUTATHIONE_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

Others
OMIM	147650; gene. 613657; phenotype.
Orphanet	163634; Maffucci syndrome. 296; Enchondromatosis. 79315; D-2-hydroxyglutaric aciduria.
Disease	KEGG Disease: IDH2
	MedGen: IDH2 (Human Medical Genetics with Condition)
	ClinVar: IDH2
Phenotype	MGI: IDH2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: IDH2

Mutations for IDH2

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows IDH2 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
AA091237	IDH2	1	92	15	90630670	90630761	IDH2	93	261	15	90631591	90631849
Z28531	IDH2	1	80	15	90627408	90627487	KIF1C	74	279	17	4927083	4927289
U52144	RPS11	1	176	19	50002769	50002945	IDH2	168	1591	15	90627210	90633860
AV658020	IDH2	1	179	15	90637602	90637780	IDH2	176	349	15	90639021	90639248

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

There's no copy number variation information in COSMIC data for this gene.

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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=966

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=1471)	Stat. for Synonymous SNVs (# total SNVs=12)

Stat. for Deletions (# total SNVs=1)	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
chr15:90631934-90631934	p.R140Q	436
chr15:90631838-90631838	p.R172K	204
chr15:90631837-90631837	p.R172S	29
chr15:90631839-90631839	p.R172G	23
chr15:90631935-90631935	p.R140W	12
chr15:90631841-90631841	p.G171D	5
chr15:90631879-90631879	p.P158P	2
chr15:90631880-90631880	p.P158L	2
chr15:90631881-90631881	p.P158T	2
chr15:90634848-90634848	p.K48N	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=16

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				18					1		20	1	1				2	2		6
# mutation				14					1		2	2	1				2	2		7
nonsynonymous SNV				11					1		2	1	1				2	2		5
synonymous SNV				4								1								2

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
chr15:90631934	p.R10Q,IDH2	17
chr15:90631838	p.R42K,IDH2	10
chr15:90631837	p.R42S,IDH2	3
chr15:90631879	p.A286V,IDH2	2
chr15:90631880	p.P28P,IDH2	2
chr15:90628072	p.P28L,IDH2	2
chr15:90628080	p.I311T,IDH2	1
chr15:90630742	p.P83P,IDH2	1
chr15:90628113	p.D57V,IDH2	1
chr15:90630804	p.K283K,IDH2	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 IDH2 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 IDH2

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


AP3S2,AVEN,TICRR,GDPGP1,CIB1,COX5A,ECE2, ETFA,GGCT,IDH2,MRPL46,MRPS11,NGRN,NOP10, POR,PSMA4,VIMP,SEMA4B,SNRPA1,TRPV6,TTLL13	ADPRHL1,ALDOA,PERM1,CACNB1,CCDC28B,FEM1A,GAMT, GOT1,GOT2,HS3ST5,HSPA2,IDH2,IPO13,JSRP1, MYL6B,MYOM2,RNF123,RTN2,SH2B2,VDAC1,WDR62

ACOT7,CENPM,CLN6,COMMD4,COX5A,ENO1,FEN1, IDH2,MCAT,MCM5,MESP1,MMAB,MPI,MRPS11, POC1A,DESI1,RCC1,SLC25A10,TK1,TXN2,ZWINT	DPCD,DRAP1,EMD,FTSJ2,GLIPR2,GMPR,IDH2, KCNQ2,LDHB,MLH1,NUP62,OXCT1,PHF19,PPP2R4, RECQL,RHBDD1,SKA2,SLC25A28,TUBB,USP5,ZNF771

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 IDH2

There's no related Drug.

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Cross referenced IDs for IDH2

* 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