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 IVD
Basic gene info.Gene symbolIVD
Gene nameisovaleryl-CoA dehydrogenase
SynonymsACAD2
CytomapUCSC genome browser: 15q14-q15
Genomic locationchr15 :40697685-40713512
Type of geneprotein-coding
RefGenesNM_001159508.1,
NM_002225.3,
Ensembl idENSG00000128928
Descriptionisovaleryl CoA dehydrogenaseisovaleryl Coenzyme A dehydrogenaseisovaleryl-CoA dehydrogenase, mitochondrial
Modification date20141211
dbXrefs MIM : 607036
HGNC : HGNC
Ensembl : ENSG00000128928
HPRD : 09516
Vega : OTTHUMG00000129984
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IVD
BioGPS: 3712
Gene Expression Atlas: ENSG00000128928
The Human Protein Atlas: ENSG00000128928
PathwayNCI Pathway Interaction Database: IVD
KEGG: IVD
REACTOME: IVD
ConsensusPathDB
Pathway Commons: IVD
MetabolismMetaCyc: IVD
HUMANCyc: IVD
RegulationEnsembl's Regulation: ENSG00000128928
miRBase: chr15 :40,697,685-40,713,512
TargetScan: NM_001159508
cisRED: ENSG00000128928
ContextiHOP: IVD
cancer metabolism search in PubMed: IVD
UCL Cancer Institute: IVD
Assigned class in ccmGDBC

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

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

Mutations for IVD
* 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 IVD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA232469IVD186154070345940703544IVD81197154070290940703487
BM797058IVD1103154071135840711460PTGES994349132500840132501175
AI928420IVD1375154071313040713505MALAT1372456116526792365268007
AA618569IVD1374154071313040713505MALAT1371523116526785565268007

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
There's no copy number variation information in COSMIC data for this gene.

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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr15:40699846-40699846p.T55A5
chr15:40707160-40707160p.V289G2
chr15:40707606-40707606p.M298I2
chr15:40710373-40710373p.R398*2
chr15:40702862-40702862p.H111Y2
chr15:40710412-40710412p.E411K2
chr15:40702940-40702940p.I137V2
chr15:40708319-40708319p.A338T1
chr15:40698041-40698041p.T8P1
chr15:40702942-40702942p.I137I1

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  5  1 1  522 137 2
# mutation1  2  1 1  522 148 2
nonsynonymous SNV1  2  1 1  4 2 124 1
synonymous SNV           12   24 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
chr15:40699846p.T55A5
chr15:40698128p.T223T,IVD1
chr15:40703542p.P37S,IVD1
chr15:40708319p.K232K,IVD1
chr15:40698147p.N43T,IVD1
chr15:40703543p.Q54K1
chr15:40708362p.D254V,IVD1
chr15:40699843p.A270T,IVD1
chr15:40703778p.K78K1
chr15:40708545p.A270V,IVD1

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 IVD 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 IVD

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

ARFIP2,BBS4,FAM174B,RMDN3,FOXA1,IVD,KIAA0319L,
LCMT2,MFAP1,MOAP1,MPI,FAN1,NDUFAF1,P4HTM,
PNPLA4,SPG11,SUOX,TADA2B,TMEM25,TTC8,VPS39
AACS,ACSL3,ADAM2,B3GAT1,DHCR7,DHRS2,FDFT1,
GGT1,HIST1H4H,HPGD,IDI1,IVD,LONP2,MPV17L,
MVK,PNLIPRP3,PPEF1,SERHL2,SERHL,SULT1C3,UGT2B28

AQR,BAHD1,HYPK,CDAN1,EIF2AK4,RMDN3,FAM98B,
GALK2,INO80,IVD,LOC729082,MPI,PAK6,PDIA3,
PDIA3P1,PPIP5K1,RPAP1,RPUSD2,RTF1,SFXN2,SPATA5L1
BEND3,C19orf57,EPHB2,FKTN,FOXA1,IVD,LIMD1,
LRPPRC,MLEC,MRPS25,PLAGL1,PPM1H,PROM2,RPS10P7,
SLC12A2,SUPV3L1,TARS2,TAS1R3,TP53,TRPM5,VGLL4
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 IVD
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
DB03147isovaleryl-CoA dehydrogenaseexperimentalFlavin-Adenine Dinucleotide
DB04036isovaleryl-CoA dehydrogenaseexperimentalCoenzyme a Persulfide
DB00121isovaleryl-CoA dehydrogenaseapproved; nutraceuticalBiotin
DB00149isovaleryl-CoA dehydrogenaseapproved; nutraceuticalL-Leucine


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Cross referenced IDs for IVD
* 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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