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 IDO1

Basic gene info.	Gene symbol	IDO1
	Gene name	indoleamine 2,3-dioxygenase 1
	Synonyms	IDO\|IDO-1\|INDO
	Cytomap	UCSC genome browser: 8p12-p11
	Genomic location	chr8 :39771327-39786309
	Type of gene	protein-coding
	RefGenes	NM_002164.5,
	Ensembl id	ENSG00000131203
	Description	indolamine 2,3 dioxygenaseindole 2,3-dioxygenaseindoleamine-pyrrole 2,3-dioxygenase
	Modification date	20141222
dbXrefs	MIM : 147435
	HGNC : HGNC
	HPRD : 00935
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_IDO1
	BioGPS: 3620
	Gene Expression Atlas: ENSG00000131203
	The Human Protein Atlas: ENSG00000131203
Pathway	NCI Pathway Interaction Database: IDO1
	KEGG: IDO1
	REACTOME: IDO1
	ConsensusPathDB
	Pathway Commons: IDO1
Metabolism	MetaCyc: IDO1
	HUMANCyc: IDO1
Regulation	Ensembl's Regulation: ENSG00000131203
	miRBase: chr8 :39,771,327-39,786,309
	TargetScan: NM_002164
	cisRED: ENSG00000131203
Context	iHOP: IDO1
	cancer metabolism search in PubMed: IDO1
	UCL Cancer Institute: IDO1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of IDO1 in cancer cell metabolism	1. Gostner JM, Becker K, Uberall F, Fuchs D (2015) The potential of targeting indoleamine 2,3-dioxygenase for cancer treatment. Expert Opin Ther Targets 19: 605-615. doi: 10.1517/14728222.2014.995092. go to article 2. Lee YK, Lee HB, Shin DM, Kang MJ, Yi EC, et al. (2014) Heme-binding-mediated negative regulation of the tryptophan metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1) by IDO2. Exp Mol Med 46: e121. doi: 10.1038/emm.2014.69. pmid: 4261913. go to article 3. Tang X, Lin CC, Spasojevic I, Iversen ES, Chi JT, et al. (2014) A joint analysis of metabolomics and genetics of breast cancer. Breast Cancer Res 16: 415. doi: 10.1186/s13058-014-0415-9. pmid: 4187326. go to article

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Phenotypic Information for IDO1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: IDO1
	Familial Cancer Database: IDO1

* 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_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: IDO1
	MedGen: IDO1 (Human Medical Genetics with Condition)
	ClinVar: IDO1
Phenotype	MGI: IDO1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: IDO1

Mutations for IDO1

* 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
pancreas	IDO1	chr8	39774237	39774257	PLAT	chr8	42034472	42034492

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 IDO1 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
BF917390	IDO1	12	263	8	39775666	39780127	IPO4	256	381	14	24658579	24658704
BF871880	EXOSC10	25	227	1	11132188	11134373	IDO1	215	402	8	39785479	39785666
BE172266	IDO1	103	126	8	39777650	39777673	NUFIP2	120	228	17	27582971	27583079

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=37)	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
chr8:39781028-39781028	p.R193Q	3
chr8:39780096-39780096	p.R155C	3
chr8:39785646-39785646	p.M385T	2
chr8:39775673-39775673	p.G84R	2
chr8:39782275-39782275	p.R231C	2
chr8:39776358-39776358	p.P110T	2
chr8:39785591-39785591	p.T367A	2
chr8:39785593-39785593	p.T367T	2
chr8:39782806-39782806	p.E258K	2
chr8:39776391-39776393	p.P122delP	1

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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=3

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				12	3		3		1			2	2	1			17	1	1	8
# mutation				12	3		3		1			2	2	1			18	1	1	8
nonsynonymous SNV				8	2		3		1			2	2	1			11	1	1	2
synonymous SNV				4	1												7			6

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
chr8:39775722	p.R100H	3
chr8:39780096	p.T367A	2
chr8:39782806	p.R155C	2
chr8:39785591	p.E258K	2
chr8:39781104	p.K61E	1
chr8:39775465	p.R193R	1
chr8:39782854	p.A331A	1
chr8:39785653	p.D72N	1
chr8:39782262	p.A204P	1
chr8:39775480	p.D333G	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 IDO1 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 IDO1

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


BATF2,CASP5,CCL8,CD274,CXCL10,CXCR2P1,FAM26F, GBP1,GBP5,IDO1,IDO2,IFNG,IL15RA,IRF1, KCNJ10,LAG3,LOC400759,SIGLEC10,TAP2,UBD,WARS	ADPRH,ATP6V1G3,CLRN3,DEFB119,DMRT1,DNASE1L3,FAM163A, GIPC3,GPR32,HTR2C,IDO1,IDO2,LRMP,OR4C6, PSG9,RPL13AP17,SAA1,SCGB2A1,SERPINB7,SNORA25,WARS

CIITA,CX3CL1,CXCL10,CXCL11,GBP1,GBP4,GJD3, HLA-DPA1,IDO1,IFIH1,JAK2,LAP3,LOC400696,LOC400759, ODF3B,OR3A4P,STAT1,TYMP,WARS,WDR49,ZNF683	APOL4,C3orf79,CD274,CXCL10,CXCL11,FCGR1A,FCGR1B, FCGR1C,IDO1,IDO2,IFIT3,IL27,LHX8,LOC400696, LOC400759,PER4,SCGB1D4,SEPT14,SOCS1,TNFSF13B,VAMP5

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 IDO1

There's no related Drug.

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Cross referenced IDs for IDO1

* 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