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 IDH3B
Basic gene info.Gene symbolIDH3B
Gene nameisocitrate dehydrogenase 3 (NAD+) beta
SynonymsH-IDHB|RP46
CytomapUCSC genome browser: 20p13
Genomic locationchr20 :2639660-2644865
Type of geneprotein-coding
RefGenesNM_001258384.1,
NM_006899.3,NM_174855.2,NM_174856.1,
Ensembl idENSG00000101365
DescriptionNAD(+)-specific ICDH subunit betaNAD+-specific ICDHNAD+-specific isocitrate dehydrogenase b subunitNAD+-specific isocitrate dehydrogenase betaisocitrate dehydrogenase [NAD] subunit beta, mitochondrialisocitrate dehydrogenase, NAD(+)-specific, mitocho
Modification date20141219
dbXrefs MIM : 604526
HGNC : HGNC
Ensembl : ENSG00000101365
HPRD : 05163
Vega : OTTHUMG00000031699
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IDH3B
BioGPS: 3420
Gene Expression Atlas: ENSG00000101365
The Human Protein Atlas: ENSG00000101365
PathwayNCI Pathway Interaction Database: IDH3B
KEGG: IDH3B
REACTOME: IDH3B
ConsensusPathDB
Pathway Commons: IDH3B
MetabolismMetaCyc: IDH3B
HUMANCyc: IDH3B
RegulationEnsembl's Regulation: ENSG00000101365
miRBase: chr20 :2,639,660-2,644,865
TargetScan: NM_001258384
cisRED: ENSG00000101365
ContextiHOP: IDH3B
cancer metabolism search in PubMed: IDH3B
UCL Cancer Institute: IDH3B
Assigned class in ccmGDBC

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Phenotypic Information for IDH3B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: IDH3B
Familial Cancer Database: IDH3B
* 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
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: IDH3B
MedGen: IDH3B (Human Medical Genetics with Condition)
ClinVar: IDH3B
PhenotypeMGI: IDH3B (International Mouse Phenotyping Consortium)
PhenomicDB: IDH3B

Mutations for IDH3B
* 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 IDH3B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG991562IDH3B272372026414242644189JUP238427173974011539776976
AF023265UBAC218713100038542100038628IDH3B7912782026390412644835
BI015407PSAP16170107358005273581743IDH3B1662432026407242640801
BQ366218MYT1L242263222421102242131IDH3B2496802026393032640772
DB143046IDH3B12112026402122644850IDH3B2083512026415172644136
AF023266UBAC218713100038542100038628IDH3B7913572026390412644835
U49283UBAC218713100038542100038628IDH3B7915952026390412644835

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=20)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr20:2639436-2639436p.I373M3
chr20:2641429-2641429p.P149S2
chr20:2640684-2640685p.E304fs*11
chr20:2641573-2641573p.S127F1
chr20:2640174-2640174p.G356G1
chr20:2640753-2640753p.L280V1
chr20:2644110-2644110p.N107D1
chr20:2640187-2640187p.V352A1
chr20:2641007-2641007p.L224V1
chr20:2644137-2644137p.E98K1

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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
# sample22    2 3  33   1314
# mutation22    2 3  33   1314
nonsynonymous SNV12      2  13   1213
synonymous SNV1     2 1  2     1 1
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
chr20:2640753p.L280V,IDH3B2
chr20:2641562p.R131W,IDH3B2
chr20:2641599p.E304Q,IDH3B1
chr20:2640407p.Y300Y,IDH3B1
chr20:2644110p.K207K,IDH3B1
chr20:2640677p.A198S,IDH3B1
chr20:2644347p.R196R,IDH3B1
chr20:2640681p.Q195P,IDH3B1
chr20:2644400p.H379D1
chr20:2640691p.P118P,IDH3B1

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 IDH3B 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 IDH3B

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

ATG101,TSR3,C20orf27,AP5S1,NDUFAF5,CENPB,DDRGK1,
DTYMK,IDH3B,ITPA,MRPS26,NDUFS6,NDUFS7,NOP56,
NSFL1C,PLEKHJ1,RBCK1,SNRPB,TIMM13,UBOX5,VPS16
BCKDHA,C21orf33,ECI1,EXOC3,HAX1,ICT1,IDH3B,
KEAP1,MAF1,MRPL2,MRPL38,MRPS18B,MRPS5,MRPS7,
NDUFB10,NDUFB9,NDUFV1,SPAG7,STK25,TACO1,WBSCR16

ANKEF1,C20orf27,AP5S1,NDUFAF5,CRLS1,CSNK2A1,DDRGK1,
FASTKD5,IDH3B,ITPA,MKKS,MRPS26,NOP56,NSFL1C,
PANK2,PCNA,PSMF1,SNRPB,TASP1,TRMT6,VPS16
ATP5A1,ATP5G1,CYC1,ERAL1,FBXW9,FH,IDH3B,
ITPA,MDH2,MRPL12,MRPL2,MRPL38,MRPS12,NDUFS3,
NDUFS6,POLDIP2,PPIA,TIMM13,UBAC1,UQCR10,UQCRC2
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 IDH3B
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157isocitrate dehydrogenase 3 (NAD+) betaapproved; nutraceuticalNADH


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Cross referenced IDs for IDH3B
* 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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