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 symbolIDH2
Gene nameisocitrate dehydrogenase 2 (NADP+), mitochondrial
SynonymsD2HGA2|ICD-M|IDH|IDHM|IDP|IDPM|mNADP-IDH
CytomapUCSC genome browser: 15q26.1
Genomic locationchr15 :90627211-90645708
Type of geneprotein-coding
RefGenesNM_001289910.1,
NM_001290114.1,NM_002168.3,
Ensembl idENSG00000182054
DescriptionNADP(+)-specific ICDHisocitrate dehydrogenase [NADP], mitochondrialoxalosuccinate decarboxylase
Modification date20141207
dbXrefs MIM : 147650
HGNC : HGNC
HPRD : 00973
ProteinUniProt: P48735
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IDH2
BioGPS: 3418
Gene Expression Atlas: ENSG00000182054
The Human Protein Atlas: ENSG00000182054
PathwayNCI Pathway Interaction Database: IDH2
KEGG: IDH2
REACTOME: IDH2
ConsensusPathDB
Pathway Commons: IDH2
MetabolismMetaCyc: IDH2
HUMANCyc: IDH2
RegulationEnsembl's Regulation: ENSG00000182054
miRBase: chr15 :90,627,211-90,645,708
TargetScan: NM_001289910
cisRED: ENSG00000182054
ContextiHOP: IDH2
cancer metabolism search in PubMed: IDH2
UCL Cancer Institute: IDH2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of IDH2 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLUTATHIONE_METABOLISM
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

check002.gifOthers
OMIM 147650; gene.
613657; phenotype.
Orphanet 163634; Maffucci syndrome.
296; Enchondromatosis.
79315; D-2-hydroxyglutaric aciduria.
DiseaseKEGG Disease: IDH2
MedGen: IDH2 (Human Medical Genetics with Condition)
ClinVar: IDH2
PhenotypeMGI: IDH2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows IDH2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA091237IDH2192159063067090630761IDH293261159063159190631849
Z28531IDH2180159062740890627487KIF1C742791749270834927289
U52144RPS111176195000276950002945IDH21681591159062721090633860
AV658020IDH21179159063760290637780IDH2176349159063902190639248

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

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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=966

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check002.gifSomatic 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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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
chr15:90631934-90631934p.R140Q436
chr15:90631838-90631838p.R172K204
chr15:90631837-90631837p.R172S29
chr15:90631839-90631839p.R172G23
chr15:90631935-90631935p.R140W12
chr15:90631841-90631841p.G171D5
chr15:90631879-90631879p.P158P2
chr15:90631880-90631880p.P158L2
chr15:90631881-90631881p.P158T2
chr15:90634848-90634848p.K48N2

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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=16

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   18    1 2011   22 6
# mutation   14    1 221   22 7
nonsynonymous SNV   11    1 211   22 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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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
chr15:90631934p.R10Q,IDH217
chr15:90631838p.R42K,IDH210
chr15:90631837p.R42S,IDH23
chr15:90631879p.A286V,IDH22
chr15:90631880p.P28P,IDH22
chr15:90628072p.P28L,IDH22
chr15:90628080p.I311T,IDH21
chr15:90630742p.P83P,IDH21
chr15:90628113p.D57V,IDH21
chr15:90630804p.K283K,IDH21

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 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

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

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
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 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



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