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 IDO2
Basic gene info.Gene symbolIDO2
Gene nameindoleamine 2,3-dioxygenase 2
SynonymsINDOL1
CytomapUCSC genome browser: 8p11.21
Genomic locationchr8 :39792473-39873910
Type of geneprotein-coding
RefGenesNM_194294.2,
Ensembl idENSG00000188676
DescriptionIDO-2indoleamine 2,3-dioxygenase-like 1 proteinindoleamine 2,3-dioxygenase-like protein 1indoleamine-pyrrole 2,3 dioxygenase-like 1indoleamine-pyrrole 2,3-dioxygenase-like protein 1
Modification date20141211
dbXrefs MIM : 612129
HGNC : HGNC
Ensembl : ENSG00000188676
HPRD : 14113
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IDO2
BioGPS: 169355
Gene Expression Atlas: ENSG00000188676
The Human Protein Atlas: ENSG00000188676
PathwayNCI Pathway Interaction Database: IDO2
KEGG: IDO2
REACTOME: IDO2
ConsensusPathDB
Pathway Commons: IDO2
MetabolismMetaCyc: IDO2
HUMANCyc: IDO2
RegulationEnsembl's Regulation: ENSG00000188676
miRBase: chr8 :39,792,473-39,873,910
TargetScan: NM_194294
cisRED: ENSG00000188676
ContextiHOP: IDO2
cancer metabolism search in PubMed: IDO2
UCL Cancer Institute: IDO2
Assigned class in ccmGDBC

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Phenotypic Information for IDO2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: IDO2
Familial Cancer Database: IDO2
* 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: IDO2
MedGen: IDO2 (Human Medical Genetics with Condition)
ClinVar: IDO2
PhenotypeMGI: IDO2 (International Mouse Phenotyping Consortium)
PhenomicDB: IDO2

Mutations for IDO2
* 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
pancreasIDO2chr83979305539793055chr84026187840261878
pancreasIDO2chr83985128939851309IDO2chr83982820039828220
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 IDO2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG007180AQPEP51675115314559115314720IDO215836283981070839810912

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 # sample11  2  6 5 1  11  
GAIN (# sample)11  2  5 3 1  11  
LOSS (# sample)      1 2        
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=39)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr8:39872860-39872860p.I321I2
chr8:39862881-39862881p.R235W2
chr8:39871208-39871208p.G282C2
chr8:39871214-39871214p.R284C2
chr8:39840263-39840263p.T136T2
chr8:39872789-39872789p.D298N2
chr8:39806779-39806779p.S32F2
chr8:39872801-39872801p.P302S2
chr8:39845390-39845390p.G150G2
chr8:39872805-39872805p.S303F2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 6    3  432  155 8
# mutation12 6    3  442  195 11
nonsynonymous SNV11 6    3  422  123 6
synonymous SNV 1          2   72 5
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
chr8:39872860p.I334I2
chr8:39871208p.T149T2
chr8:39871214p.G295C2
chr8:39806779p.G163G2
chr8:39872789p.R297C2
chr8:39840263p.S45F2
chr8:39845390p.D311N2
chr8:39871174p.G106A1
chr8:39836668p.R248R1
chr8:39872851p.R331R1

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 IDO2 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 IDO2

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

C21orf62,CSF2RB,CXCR2P1,CXCR6,FAM26F,FASLG,FCAMR,
IDO2,IFNG,IL21R,IL2RG,KCNJ10,LAG3,PDCD1,
PRF1,SIGLEC10,SLA2,STAT4,TBX21,TNFSF14,ZNF80
AIM2,BTLA,DCANP1,CCR4,CCR7,CD1A,CD80,
DPPA4,EOMES,FAM129C,IDO2,IL21R,KLHL6,LOC283663,
MIAT,MIR155HG,PARP15,PTPN7,SP140,TIFAB,TIGIT

ARHGAP9,BTLA,CCR7,CD28,CD3E,GVINP1,IDO2,
IKZF1,ITK,JAK3,TESPA1,MAP4K1,NLRC3,P2RY10,
PPP1R16B,RASAL3,STAT4,TBC1D10C,TRAF3IP3,ZAP70,ZNF831
APOL4,C3orf79,CASP1,CD274,CXCL10,CXCL11,FBXO6,
FCGR1A,FCGR1B,FCGR1C,GBP1,HAPLN3,IDO1,IDO2,
IFIT3,IL18BP,IL27,LOC400696,LOC400759,SOCS1,WARS
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 IDO2


There's no related Drug.
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Cross referenced IDs for IDO2
* 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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