Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolIDO1
Gene nameindoleamine 2,3-dioxygenase 1
SynonymsIDO|IDO-1|INDO
CytomapUCSC genome browser: 8p12-p11
Genomic locationchr8 :39771327-39786309
Type of geneprotein-coding
RefGenesNM_002164.5,
Ensembl idENSG00000131203
Descriptionindolamine 2,3 dioxygenaseindole 2,3-dioxygenaseindoleamine-pyrrole 2,3-dioxygenase
Modification date20141222
dbXrefs MIM : 147435
HGNC : HGNC
HPRD : 00935
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IDO1
BioGPS: 3620
Gene Expression Atlas: ENSG00000131203
The Human Protein Atlas: ENSG00000131203
PathwayNCI Pathway Interaction Database: IDO1
KEGG: IDO1
REACTOME: IDO1
ConsensusPathDB
Pathway Commons: IDO1
MetabolismMetaCyc: IDO1
HUMANCyc: IDO1
RegulationEnsembl's Regulation: ENSG00000131203
miRBase: chr8 :39,771,327-39,786,309
TargetScan: NM_002164
cisRED: ENSG00000131203
ContextiHOP: IDO1
cancer metabolism search in PubMed: IDO1
UCL Cancer Institute: IDO1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of IDO1 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_TRYPTOPHAN_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: IDO1
MedGen: IDO1 (Human Medical Genetics with Condition)
ClinVar: IDO1
PhenotypeMGI: IDO1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasIDO1chr83977423739774257PLATchr84203447242034492
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows IDO1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF917390IDO11226383977566639780127IPO4256381142465857924658704
BF871880EXOSC102522711113218811134373IDO121540283978547939785666
BE172266IDO110312683977765039777673NUFIP2120228172758297127583079

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)        1        
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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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=4

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check002.gifSomatic 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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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
chr8:39780096-39780096p.R155C3
chr8:39781028-39781028p.R193Q3
chr8:39785646-39785646p.M385T2
chr8:39775673-39775673p.G84R2
chr8:39782275-39782275p.R231C2
chr8:39776358-39776358p.P110T2
chr8:39785591-39785591p.T367A2
chr8:39785593-39785593p.T367T2
chr8:39782806-39782806p.E258K2
chr8:39776414-39776414p.D128E1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   123 3 1  221  17118
# mutation   123 3 1  221  18118
nonsynonymous SNV   82 3 1  221  11112
synonymous SNV   41           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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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
chr8:39775722p.R100H3
chr8:39780096p.T367A2
chr8:39782806p.R155C2
chr8:39785591p.E258K2
chr8:39781060p.L169L1
chr8:39782841p.V269V1
chr8:39775406p.D34N1
chr8:39776385p.V170V1
chr8:39785599p.C272F1
chr8:39781071p.L49L1

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 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

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

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
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 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



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