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 IDH1
Basic gene info.Gene symbolIDH1
Gene nameisocitrate dehydrogenase 1 (NADP+), soluble
SynonymsHEL-216|HEL-S-26|IDCD|IDH|IDP|IDPC|PICD
CytomapUCSC genome browser: 2q33.3
Genomic locationchr2 :209100952-209119806
Type of geneprotein-coding
RefGenesNM_001282386.1,
NM_001282387.1,NM_005896.3,
Ensembl idENSG00000138413
DescriptionNADP(+)-specific ICDHNADP-dependent isocitrate dehydrogenase, cytosolicNADP-dependent isocitrate dehydrogenase, peroxisomalepididymis luminal protein 216epididymis secretory protein Li 26isocitrate dehydrogenase [NADP] cytoplasmicoxalosuccinate deca
Modification date20141222
dbXrefs MIM : 147700
HGNC : HGNC
Ensembl : ENSG00000138413
HPRD : 00984
Vega : OTTHUMG00000132943
ProteinUniProt: O75874
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IDH1
BioGPS: 3417
Gene Expression Atlas: ENSG00000138413
The Human Protein Atlas: ENSG00000138413
PathwayNCI Pathway Interaction Database: IDH1
KEGG: IDH1
REACTOME: IDH1
ConsensusPathDB
Pathway Commons: IDH1
MetabolismMetaCyc: IDH1
HUMANCyc: IDH1
RegulationEnsembl's Regulation: ENSG00000138413
miRBase: chr2 :209,100,952-209,119,806
TargetScan: NM_001282386
cisRED: ENSG00000138413
ContextiHOP: IDH1
cancer metabolism search in PubMed: IDH1
UCL Cancer Institute: IDH1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of IDH1 in cancer cell metabolism1. Grassian AR, Parker SJ, Davidson SM, Divakaruni AS, Green CR, et al. (2014) IDH1 mutations alter citric acid cycle metabolism and increase dependence on oxidative mitochondrial metabolism. Cancer Res 74: 3317-3331. doi: 10.1158/0008-5472.CAN-14-0772-T. go to article
2. Esmaeili M, Hamans BC, Navis AC, van Horssen R, Bathen TF, et al. (2014) IDH1 R132H mutation generates a distinct phospholipid metabolite profile in glioma. Cancer Res 74: 4898-4907. doi: 10.1158/0008-5472.CAN-14-0008. go to article
3. Izquierdo-Garcia JL, Viswanath P, Eriksson P, Cai L, Radoul M, et al. (2015) IDH1 Mutation Induces Reprogramming of Pyruvate Metabolism. Cancer Res. doi: 10.1158/0008-5472.CAN-15-0840. go to article
4. Schumacher T, Bunse L, Pusch S, Sahm F, Wiestler B, et al. (2014) A vaccine targeting mutant IDH1 induces antitumour immunity. Nature 512: 324-327. doi: 10.1038/nature13387. go to article
5. Hirata M, Sasaki M, Cairns RA, Inoue S, Puviindran V, et al. (2015) Mutant IDH is sufficient to initiate enchondromatosis in mice. Proc Natl Acad Sci U S A 112: 2829-2834. doi: 10.1073/pnas.1424400112. pmid: 4352794. go to article

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Phenotypic Information for IDH1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: IDH1
Familial Cancer Database: IDH1
* 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 GBM 6, LAML 7, MM 8, SKCM 9, GBM 10,

Therapeutic Vulnerabilities in Cancer11

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.sciencedirect.com/science/article/pii/S0092867413012087,
7 http://www.nejm.org/doi/full/10.1056/NEJMoa1301689,
8 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
9 http://www.sciencedirect.com/science/article/pii/S0092867415006340,
10 http://www.nejm.org/doi/full/10.1056/NEJMoa1402121,
11Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_GLUTATHIONE_METABOLISM
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE
REACTOME_PEROXISOMAL_LIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 137800; phenotype.
147700; gene.
Orphanet 163634; Maffucci syndrome.
251576; Gliosarcoma.
251579; Giant cell glioblastoma.
296; Enchondromatosis.
99646; Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria.
DiseaseKEGG Disease: IDH1
MedGen: IDH1 (Human Medical Genetics with Condition)
ClinVar: IDH1
PhenotypeMGI: IDH1 (International Mouse Phenotyping Consortium)
PhenomicDB: IDH1

Mutations for IDH1
* 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 IDH1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN423757IDH11892209103827209103915NCL853052232326411232326631
BU153261IDH1944802209104672209108329RPS24471772107979539779800459
AW001546IDH112422209100954209101195MBOAT2239557290778959078213
BC065703CCNYL114262208576416208576841IDH142416722209100951209104729

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          
GAIN (# sample)                 
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=7408

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=7619)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr2:209113112-209113112p.R132H4057
chr2:209113113-209113113p.R132C896
chr2:209108317-209108317p.V178I9
chr2:209113112-209113113p.R132S7
chr2:209113298-209113298p.G70D6
chr2:209113192-209113192p.G105G5
chr2:209113208-209113208p.R100Q5
chr2:209113210-209113210p.I99M5
chr2:209113111-209113112p.R132H4
chr2:209116179-209116179p.P33S3

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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=169

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample23 1915 2 1 19321 1143 6
# mutation23 162 2 1 2421 153 7
nonsynonymous SNV22 142 2 1 2321 142 4
synonymous SNV 1 2       1    11 3
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
chr2:209113112p.R132H,IDH1171
chr2:209113113p.R132C,IDH142
chr2:209116179p.V71A,IDH13
chr2:209113295p.P33S,IDH13
chr2:209113111p.R132R,IDH12
chr2:209108281p.L359F,IDH11
chr2:209113152p.K345K,IDH11
chr2:209103949p.G70G,IDH11
chr2:209116173p.F334I,IDH11
chr2:209108295p.I130M,IDH11

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 IDH1 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 IDH1

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

APOD,CASP10,CCNYL1,RHOV___CHP1,CYP2J2,EGF,G6PD,
GALNT3,GGT1,IDH1,LIMCH1,NDUFS1,RETSAT,SCP2,
SGPP2,SLC31A1,SPINK8,SRD5A3,ST6GALNAC1,TMEM86A,ZNF652
ABHD15,ACADL,ACSL1,ACSS3,BNIP3L,RHOV___CHP1,CIDEC,
CYB5A,EYS,FAH,FBXO27,GYG2,HEPACAM,IDH1,
LGALS12,LPL,MARC1,PCCA,PECR,THRSP,TMEM135

ACAT2,ATP5G3,C2orf47,CASP6,DBI,IDH1,IDI1,
MDH1,MRPL1,MRPL19,MRPL35,MRPL42,MRPL44,MVK,
PPCS,PRDX3,RDH11,SC5D,SDHD,SUCLG1,TMEM135
ADH1C,BCL2L15,CD46,COX15,EHHADH,EIF2AK1,GJB1,
IDH1,MCCC2,MEST,AP5M1,NDUFS1,PEX11A,PHKB,
SH2D4A,SKAP2,SUCLG2,SULT1B1,TMEM184C,UGT1A8,UGT8
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 IDH1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB O75874; -.
ChemistryChEMBL CHEMBL2007625; -.
Organism-specific databasesPharmGKB PA29630; -.
Organism-specific databasesCTD 3417; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01727isocitrate dehydrogenase 1 (NADP+), solubleexperimentalIsocitric Acid
DB03461isocitrate dehydrogenase 1 (NADP+), solubleexperimental2'-Monophosphoadenosine 5'-Diphosphoribose


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Cross referenced IDs for IDH1
* 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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