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 SLC25A11
Basic gene info.Gene symbolSLC25A11
Gene namesolute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), member 11
SynonymsOGC|SLC20A4
CytomapUCSC genome browser: 17p13.3
Genomic locationchr17 :4840425-4843462
Type of geneprotein-coding
RefGenesNM_001165417.1,
NM_001165418.1,NM_003562.4,
Ensembl idENSG00000108528
DescriptionOGCPmitochondrial 2-oxoglutarate/malate carrier proteinsolute carrier family 20 (oxoglutarate carrier), member 4solute carrier family 25 member 11
Modification date20141207
dbXrefs MIM : 604165
HGNC : HGNC
Ensembl : ENSG00000108528
HPRD : 05003
Vega : OTTHUMG00000099395
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC25A11
BioGPS: 8402
Gene Expression Atlas: ENSG00000108528
The Human Protein Atlas: ENSG00000108528
PathwayNCI Pathway Interaction Database: SLC25A11
KEGG: SLC25A11
REACTOME: SLC25A11
ConsensusPathDB
Pathway Commons: SLC25A11
MetabolismMetaCyc: SLC25A11
HUMANCyc: SLC25A11
RegulationEnsembl's Regulation: ENSG00000108528
miRBase: chr17 :4,840,425-4,843,462
TargetScan: NM_001165417
cisRED: ENSG00000108528
ContextiHOP: SLC25A11
cancer metabolism search in PubMed: SLC25A11
UCL Cancer Institute: SLC25A11
Assigned class in ccmGDBC

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Phenotypic Information for SLC25A11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC25A11
Familial Cancer Database: SLC25A11
* 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_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC25A11
MedGen: SLC25A11 (Human Medical Genetics with Condition)
ClinVar: SLC25A11
PhenotypeMGI: SLC25A11 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC25A11

Mutations for SLC25A11
* 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 SLC25A11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI480110SLC25A1127771748405994840655KLHL3601985136953559136953701

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
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
chr17:4841063-4841063p.A306A2
chr17:4841459-4841459p.A243T2
chr17:4841131-4841131p.P284S2
chr17:4841830-4841830p.E175Q2
chr17:4842250-4842250p.R90H2
chr17:4842372-4842372p.L77L2
chr17:4842102-4842102p.P139P1
chr17:4841055-4841055p.R309H1
chr17:4842408-4842408p.F65F1
chr17:4841351-4841351p.M252I1

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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 11 1   142   42 5
# mutation22 11 1   152   42 5
nonsynonymous SNV11 11      41   2  3
synonymous SNV11    1   111   22 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
chr17:4842372p.L66L,SLC25A112
chr17:4843164p.A255T,SLC25A111
chr17:4841131p.P65S,SLC25A111
chr17:4841830p.P233T,SLC25A111
chr17:4843185p.G63V,SLC25A111
chr17:4841132p.T232T,SLC25A111
chr17:4841845p.F55L,SLC25A111
chr17:4843194p.R220H,SLC25A111
chr17:4841169p.R39H,SLC25A111
chr17:4841850p.V214M,SLC25A111

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 SLC25A11 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 SLC25A11

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

C17orf59,ELP5,CTDNEP1,GPS2,NAA38,MED11,OVCA2,
PELP1,PFN1,PSMB6,RANGRF,RNASEK,RNF167,RNMTL1,
RPAIN,SAT2,SLC25A11,SPAG7,EMC6,TRAPPC1,WRAP53
AK1,ALDOA,COQ9,CTDNEP1,DYRK1B,ENDOG,MACROD1,
MDH2,LINC00116,NDUFB10,NDUFS2,NDUFS3,NDUFS7,RAD23A,
SIRT2,SLC25A11,TPI1,TRPT1,UBAC1,UQCR10,UQCRC1

ATPAF2,ELP5,C1QBP,COPS3,EIF4A1,EIF5A,EIF5AL1,
ELAC2,NAA38,MED11,MPDU1,OVCA2,PFN1,PSMB6,
RNF167,RNMTL1,SLC25A11,TIMM22,EMC6,WRAP53,YWHAE
C19orf70,CYC1,DCTPP1,FLAD1,ICT1,MRPL57,MRPL15,
MRPL27,MRPS12,MRPS16,MRPS7,SF3B5,SLC25A11,STOML2,
PAM16,TMEM223,TOMM22,TRUB2,TXN2,UBAC1,ZNF576
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 SLC25A11
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
DB00121solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), member 11approved; nutraceuticalBiotin


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Cross referenced IDs for SLC25A11
* 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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