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 IDH1

Basic gene info.	Gene symbol	IDH1
	Gene name	isocitrate dehydrogenase 1 (NADP+), soluble
	Synonyms	HEL-216\|HEL-S-26\|IDCD\|IDH\|IDP\|IDPC\|PICD
	Cytomap	UCSC genome browser: 2q33.3
	Genomic location	chr2 :209100952-209119806
	Type of gene	protein-coding
	RefGenes	NM_001282386.1, NM_001282387.1,NM_005896.3,
	Ensembl id	ENSG00000138413
	Description	NADP(+)-specific ICDHNADP-dependent isocitrate dehydrogenase, cytosolicNADP-dependent isocitrate dehydrogenase, peroxisomalepididymis luminal protein 216epididymis secretory protein Li 26isocitrate dehydrogenase [NADP] cytoplasmicoxalosuccinate deca
	Modification date	20141222
dbXrefs	MIM : 147700
	HGNC : HGNC
	Ensembl : ENSG00000138413
	HPRD : 00984
	Vega : OTTHUMG00000132943
Protein	UniProt: O75874 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_IDH1
	BioGPS: 3417
	Gene Expression Atlas: ENSG00000138413
	The Human Protein Atlas: ENSG00000138413
Pathway	NCI Pathway Interaction Database: IDH1
	KEGG: IDH1
	REACTOME: IDH1
	ConsensusPathDB
	Pathway Commons: IDH1
Metabolism	MetaCyc: IDH1
	HUMANCyc: IDH1
Regulation	Ensembl's Regulation: ENSG00000138413
	miRBase: chr2 :209,100,952-209,119,806
	TargetScan: NM_001282386
	cisRED: ENSG00000138413
Context	iHOP: IDH1
	cancer metabolism search in PubMed: IDH1
	UCL Cancer Institute: IDH1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of IDH1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_GLUTATHIONE_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_PEROXISOMAL_LIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
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.
Disease	KEGG Disease: IDH1
	MedGen: IDH1 (Human Medical Genetics with Condition)
	ClinVar: IDH1
Phenotype	MGI: IDH1 (International Mouse Phenotyping Consortium)
Phenotype	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.

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 IDH1 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
CN423757	IDH1	1	89	2	209103827	209103915	NCL	85	305	2	232326411	232326631
BU153261	IDH1	94	480	2	209104672	209108329	RPS24	471	772	10	79795397	79800459
AW001546	IDH1	1	242	2	209100954	209101195	MBOAT2	239	557	2	9077895	9078213
BC065703	CCNYL1	1	426	2	208576416	208576841	IDH1	424	1672	2	209100951	209104729

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=7408

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Somatic 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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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
chr2:209113112-209113112	p.R132H	4057
chr2:209113113-209113113	p.R132C	896
chr2:209108317-209108317	p.V178I	9
chr2:209113112-209113113	p.R132S	7
chr2:209113298-209113298	p.G70D	6
chr2:209113192-209113192	p.G105G	5
chr2:209113208-209113208	p.R100Q	5
chr2:209113210-209113210	p.I99M	5
chr2:209113111-209113112	p.R132H	4
chr2:209116179-209116179	p.P33S	3

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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=169

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	2	3		19	15		2		1		19	3	2	1		1	14	3		6
# mutation	2	3		16	2		2		1		2	4	2	1		1	5	3		7
nonsynonymous SNV	2	2		14	2		2		1		2	3	2	1		1	4	2		4
synonymous SNV		1		2								1					1	1		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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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
chr2:209113112	p.R132H,IDH1	171
chr2:209113113	p.R132C,IDH1	42
chr2:209116179	p.V71A,IDH1	3
chr2:209113295	p.P33S,IDH1	3
chr2:209113111	p.R132R,IDH1	2
chr2:209108295	p.M291I,IDH1	1
chr2:209113170	p.R119W,IDH1	1
chr2:209104604	p.I5V,IDH1	1
chr2:209108305	p.I251I,IDH1	1
chr2:209113177	p.I113V,IDH1	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 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

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


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

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 IDH1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	O75874; -.
Chemistry	ChEMBL	CHEMBL2007625; -.
Organism-specific databases	PharmGKB	PA29630; -.
Organism-specific databases	CTD	3417; -.

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
DB01727	isocitrate dehydrogenase 1 (NADP+), soluble	experimental	Isocitric Acid
DB03461	isocitrate dehydrogenase 1 (NADP+), soluble	experimental	2'-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