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 SLC25A4
Basic gene info.Gene symbolSLC25A4
Gene namesolute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4
Synonyms1|AAC1|ANT|ANT 1|ANT1|MTDPS12|PEO2|PEO3|T1
CytomapUCSC genome browser: 4q35
Genomic locationchr4 :186064416-186071538
Type of geneprotein-coding
RefGenesNM_001151.3,
Ensembl idENSG00000151729
DescriptionADP,ATP carrier protein 1ADP,ATP carrier protein, heart/skeletal muscleADP/ATP translocase 1adenine nucleotide translocator 1 (skeletal muscle)heart/skeletal muscle ATP/ADP translocatorsolute carrier family 25 member 4
Modification date20141207
dbXrefs MIM : 103220
HGNC : HGNC
Ensembl : ENSG00000151729
HPRD : 00058
Vega : OTTHUMG00000134299
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC25A4
BioGPS: 291
Gene Expression Atlas: ENSG00000151729
The Human Protein Atlas: ENSG00000151729
PathwayNCI Pathway Interaction Database: SLC25A4
KEGG: SLC25A4
REACTOME: SLC25A4
ConsensusPathDB
Pathway Commons: SLC25A4
MetabolismMetaCyc: SLC25A4
HUMANCyc: SLC25A4
RegulationEnsembl's Regulation: ENSG00000151729
miRBase: chr4 :186,064,416-186,071,538
TargetScan: NM_001151
cisRED: ENSG00000151729
ContextiHOP: SLC25A4
cancer metabolism search in PubMed: SLC25A4
UCL Cancer Institute: SLC25A4
Assigned class in ccmGDBC

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Phenotypic Information for SLC25A4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC25A4
Familial Cancer Database: SLC25A4
* 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_INTEGRATION_OF_ENERGY_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC25A4
MedGen: SLC25A4 (Human Medical Genetics with Condition)
ClinVar: SLC25A4
PhenotypeMGI: SLC25A4 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC25A4

Mutations for SLC25A4
* 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 SLC25A4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
N45527SLC25A422714186068524186068790POGZ2684421151418819151418993

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)                 
LOSS (# sample)      1          
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=21)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr4:186068077-186068077p.G283G2
chr4:186066261-186066261p.R152H2
chr4:186067969-186067969p.A247A1
chr4:186064595-186064595p.K23N1
chr4:186066130-186066130p.Q108Q1
chr4:186066316-186066316p.L170L1
chr4:186068023-186068023p.E265E1
chr4:186064596-186064596p.T24S1
chr4:186066138-186066138p.R111H1
chr4:186066328-186066328p.Y174Y1

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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 6    2   11  13 5
# mutation 1 5    2   11  13 7
nonsynonymous SNV 1 3    2    1   2 4
synonymous SNV   2        1   11 3
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
chr4:186068077p.G283G2
chr4:186066261p.R152H2
chr4:186065961p.F67S1
chr4:186066369p.S242C1
chr4:186066006p.E265E1
chr4:186066370p.L68L1
chr4:186066010p.R80C1
chr4:186066382p.R80H1
chr4:186066044p.F89F1
chr4:186066922p.R111H1

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 SLC25A4 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 SLC25A4

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

ATP6AP1,BCAT2,BLVRB,HID1,LRRC73,CDKN2AIPNL,DAK,
DCXR,DDRGK1,ELMO3,GABARAPL2,HEXIM2,MRFAP1,NECAB3,
NOL3,P4HTM,PARD6A,RAB17,SLC25A4,SLC27A4,UFSP2
ABRA,ART1,C10orf71,CACNG1,DHRS7C,ENO3,FBP2,
FBXO40,FITM1,HSPB3,MB,MYBPH,MYL3,MYO18B,
MYOZ1,MYPN,PYGM,SLC25A4,TMEM38A,TNNC2,TRIM54

ABHD10,ATP5A1,ATP5B,ATP5G3,C4orf27,CASP3,COPS4,
FH,GOT1,HSPA4L,MDH1,NDUFA6,NDUFC1,NDUFS4,
RPL22L1,RWDD4,SDHA,SDHB,SLC25A4,UFSP2,UQCRC1
BAG2,CPED1,CAB39L,CCDC69,CFL2,DSTN,MORN5,
MSRB3,MXRA7,PDLIM3,PDLIM4,PLN,PPP1R14A,PPP3CB,
PSD,PTPLA,RAB12,REEP1,SLC25A4,SLMAP,TEAD2
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 SLC25A4
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
DB00171solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4approved; nutraceuticalAdenosine triphosphate
DB00720solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4approved; investigationalClodronate
DB01736solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4experimental[3-(Dodecanoylamino)Propyl](Hydroxy)Dimethylammonium
DB02426solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4experimentalCarboxyatractyloside
DB03429solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4experimentalCardiolipin
DB04178solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4experimentalDi-Stearoyl-3-Sn-Phosphatidylcholine


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Cross referenced IDs for SLC25A4
* 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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