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 OXCT1
Basic gene info.Gene symbolOXCT1
Gene name3-oxoacid CoA transferase 1
SynonymsOXCT|SCOT
CytomapUCSC genome browser: 5p13.1
Genomic locationchr5 :41730166-41870791
Type of geneprotein-coding
RefGenesNM_000436.3,
Ensembl idENSG00000083720
Description3-oxoacid CoA-transferase 13-oxoacid-CoA transferase 1SCOT-ssomatic-type succinyl CoA:3-oxoacid CoA-transferasesomatic-type succinyl-CoA:3-oxoacid CoA-transferasesomatic-type succinyl-CoA:3-oxoacid-CoA-transferasesuccinyl CoA:3-oxoacid CoA transfera
Modification date20141207
dbXrefs MIM : 601424
HGNC : HGNC
Ensembl : ENSG00000083720
HPRD : 02001
Vega : OTTHUMG00000094783
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_OXCT1
BioGPS: 5019
Gene Expression Atlas: ENSG00000083720
The Human Protein Atlas: ENSG00000083720
PathwayNCI Pathway Interaction Database: OXCT1
KEGG: OXCT1
REACTOME: OXCT1
ConsensusPathDB
Pathway Commons: OXCT1
MetabolismMetaCyc: OXCT1
HUMANCyc: OXCT1
RegulationEnsembl's Regulation: ENSG00000083720
miRBase: chr5 :41,730,166-41,870,791
TargetScan: NM_000436
cisRED: ENSG00000083720
ContextiHOP: OXCT1
cancer metabolism search in PubMed: OXCT1
UCL Cancer Institute: OXCT1
Assigned class in ccmGDBC

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Phenotypic Information for OXCT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: OXCT1
Familial Cancer Database: OXCT1
* 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_BUTANOATE_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: OXCT1
MedGen: OXCT1 (Human Medical Genetics with Condition)
ClinVar: OXCT1
PhenotypeMGI: OXCT1 (International Mouse Phenotyping Consortium)
PhenomicDB: OXCT1

Mutations for OXCT1
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryOXCT1chr54179655341796573OXCT1chr54184088641840906
pancreasOXCT1chr54176509141765111chr53708812737088147
pancreasOXCT1chr54185198941852009chr54204395742043977
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 OXCT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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  2    3    2  1
GAIN (# sample)2  2    3    2  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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=45)
Stat. for Synonymous SNVs
(# total SNVs=14)
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
chr5:41850282-41850282p.?3
chr5:41853606-41853606p.R110H2
chr5:41850186-41850186p.S170S2
chr5:41805723-41805723p.V301I2
chr5:41739516-41739516p.Q499H2
chr5:41801144-41801144p.D360G2
chr5:41794170-41794170p.D395N2
chr5:41801159-41801159p.R355Q2
chr5:41803197-41803197p.Q342E2
chr5:41850261-41850261p.I145I2

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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
# sample1117  1 1  732  66 10
# mutation1116  1 1  832  68 10
nonsynonymous SNV 1 3  1    432  45 9
synonymous SNV1 14    1  4    23 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
chr5:41803250p.K418K2
chr5:41762297p.D395N2
chr5:41794170p.G324E2
chr5:41840595p.V301L1
chr5:41853606p.R110H1
chr5:41739521p.V498I1
chr5:41870407p.R285Q1
chr5:41794836p.I108L1
chr5:41840601p.G462E1
chr5:41853613p.E276D1

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 OXCT1 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 OXCT1

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

CA13,CLSPN,E2F3,EHBP1,ETV6,OTULIN,GNPTAB,
ICE1,KIF1B,KLF5,MSH2,MYO10,NUP155,OXCT1,
PDK1,PPM1L,SERPINB5,SKP2,TRIM2,ZFR,ZNF131
ABCD2,ABHD15,ACAA2,ACACB,ACSL1,ACVR1C,ADIPOQ,
AQP7,AQPEP,GPATCH11,CIDEC,HOGA1,GHR,GYG2,
LGALS12,MARC1,MTHFD1,OXCT1,PDE3B,PECR,PEX19

ALKBH5,FAM212B,CCDC109B,CYB5D1,FECH,HPSE,HSPA4L,
NKX3-1,OXCT1,PIAS2,RNF125,SAP30,THRAP3,TOP3A,
TRIM7,TYMS,UBR7,USP13,WDR76,ZBTB8A,ZNF232
C15orf41,CALU,CNTLN,IFT81,LOC221710,LRRC20,MDM1,
NUCKS1,OXCT1,PBX3,PHF19,RECQL,RIMKLB,RNF165,
SAE1,TACC1,TBC1D19,TNFAIP8L1,VPS45,WHAMMP2,ZMYND11
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 OXCT1
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
DB001393-oxoacid CoA transferase 1approved; nutraceuticalSuccinic acid
DB027313-oxoacid CoA transferase 1experimentalThimerosal


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Cross referenced IDs for OXCT1
* 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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