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 IDH3A
Basic gene info.Gene symbolIDH3A
Gene nameisocitrate dehydrogenase 3 (NAD+) alpha
Synonyms-
CytomapUCSC genome browser: 15q25.1-q25.2
Genomic locationchr15 :78441718-78462884
Type of geneprotein-coding
RefGenesNM_005530.2,
Ensembl idENSG00000166411
DescriptionH-IDH alphaNAD(+)-specific ICDH subunit alphaNAD(H)-specific isocitrate dehydrogenase alpha subunitNAD+-specific ICDHisocitrate dehydrogenase (NAD+) alpha chainisocitrate dehydrogenase [NAD] subunit alpha, mitochondrialisocitric dehydrogenase subuni
Modification date20141207
dbXrefs MIM : 601149
HGNC : HGNC
HPRD : 03094
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IDH3A
BioGPS: 3419
Gene Expression Atlas: ENSG00000166411
The Human Protein Atlas: ENSG00000166411
PathwayNCI Pathway Interaction Database: IDH3A
KEGG: IDH3A
REACTOME: IDH3A
ConsensusPathDB
Pathway Commons: IDH3A
MetabolismMetaCyc: IDH3A
HUMANCyc: IDH3A
RegulationEnsembl's Regulation: ENSG00000166411
miRBase: chr15 :78,441,718-78,462,884
TargetScan: NM_005530
cisRED: ENSG00000166411
ContextiHOP: IDH3A
cancer metabolism search in PubMed: IDH3A
UCL Cancer Institute: IDH3A
Assigned class in ccmGDBC

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Phenotypic Information for IDH3A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: IDH3A
Familial Cancer Database: IDH3A
* 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: IDH3A
MedGen: IDH3A (Human Medical Genetics with Condition)
ClinVar: IDH3A
PhenotypeMGI: IDH3A (International Mouse Phenotyping Consortium)
PhenomicDB: IDH3A

Mutations for IDH3A
* 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 IDH3A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI571707IDH3A1187157846181678462002IDH3A185342157846151078461666
BE887604IDH3A2079157846165478461713IDH3A72386157846169278462006

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 # sample2                
GAIN (# sample)2                
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=17

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=23)
Stat. for Synonymous SNVs
(# total SNVs=20)
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
chr15:78441769-78441769p.S8S17
chr15:78455907-78455907p.D224N2
chr15:78458554-78458554p.L309L2
chr15:78458574-78458574p.R316H2
chr15:78453952-78453952p.H107Y2
chr15:78452509-78452509p.A84S1
chr15:78454015-78454015p.V128F1
chr15:78455916-78455916p.F227L1
chr15:78452522-78452522p.M88T1
chr15:78454029-78454029p.G132G1

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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
# sample 1 61 1    121  32 6
# mutation 1 61 1    121  32 5
nonsynonymous SNV 1 51      12   3  3
synonymous SNV   1  1      1   2 2
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
chr15:78458574p.S82L2
chr15:78452504p.R316H2
chr15:78453965p.V128F1
chr15:78455916p.D139E1
chr15:78453996p.D162A1
chr15:78457365p.T172T1
chr15:78454015p.K177K1
chr15:78458533p.A197A1
chr15:78454050p.R205W1
chr15:78458546p.L210L1

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 IDH3A 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 IDH3A

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

AAGAB,ADAM5,HYKK,ARIH1,BTBD1,DIS3L,DNAJA4,
FBXO22,FEM1B,HCN4,HMG20A,IDH3A,IREB2,MAP2K1,
MORF4L1,MTFMT,PSMA4,RAB11A,RCN2,SCAPER,WDR61
AK3,ANKRD40,ATPAF1,DLD,RMDN1,FEZ2,HOXA10,
HSDL2,HSPB6,IDH3A,QKI,RAD23B,RDX,RTN4,
SBDS,SETD3,SH3GLB1,STRADB,SUCLA2,UGP2,YWHAG

KNSTRN,CCNB1,CCNB2,CDC45,COX5A,FAM96A,FBXO22,
GRPEL1,IDH3A,KIF23,MAP2K1,MRPS11,MTFMT,NOP10,
PSMA4,PTGES3,RAB11A,RFC5,TIPIN,TPI1,ZWILCH
AAGAB,ATG4A,SPRYD7,CHUK,DDX39A,ERP44,GNG5,
H2AFY,IDH3A,KDELR2,LRRC59,MPDU1,PI4K2B,PNP,
PPP2CA,RAB11A,RAB1A,TCP1,TFG,TPM3,TXNDC17
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 IDH3A
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+) alphaapproved; nutraceuticalNADH


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Cross referenced IDs for IDH3A
* 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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