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 SLC25A1
Basic gene info.Gene symbolSLC25A1
Gene namesolute carrier family 25 (mitochondrial carrier; citrate transporter), member 1
SynonymsCTP|D2L2AD|SEA|SLC20A3
CytomapUCSC genome browser: 22q11.21
Genomic locationchr22 :19163087-19166338
Type of geneprotein-coding
RefGenesNM_001256534.1,
NM_001287387.1,NM_005984.4,NR_046298.2,
Ensembl idENSG00000268928
Descriptioncitrate transport proteinsolute carrier family 20 (mitochondrial citrate transporter), member 3tricarboxylate carrier proteintricarboxylate transport protein, mitochondrial
Modification date20141207
dbXrefs MIM : 190315
HGNC : HGNC
Ensembl : ENSG00000100075
HPRD : 01832
Vega : OTTHUMG00000150123
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC25A1
BioGPS: 6576
Gene Expression Atlas: ENSG00000268928
The Human Protein Atlas: ENSG00000268928
PathwayNCI Pathway Interaction Database: SLC25A1
KEGG: SLC25A1
REACTOME: SLC25A1
ConsensusPathDB
Pathway Commons: SLC25A1
MetabolismMetaCyc: SLC25A1
HUMANCyc: SLC25A1
RegulationEnsembl's Regulation: ENSG00000268928
miRBase: chr22 :19,163,087-19,166,338
TargetScan: NM_001256534
cisRED: ENSG00000268928
ContextiHOP: SLC25A1
cancer metabolism search in PubMed: SLC25A1
UCL Cancer Institute: SLC25A1
Assigned class in ccmGDBC

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Phenotypic Information for SLC25A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC25A1
Familial Cancer Database: SLC25A1
* 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_LIPIDS_AND_LIPOPROTEINS
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC25A1
MedGen: SLC25A1 (Human Medical Genetics with Condition)
ClinVar: SLC25A1
PhenotypeMGI: SLC25A1 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC25A1

Mutations for SLC25A1
* 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 SLC25A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=11)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr22:19164157-19164157p.G227G2
chr22:19164123-19164123p.T239S2
chr22:19165692-19165692p.Q52H1
chr22:19163654-19163654p.K309E1
chr22:19164192-19164192p.K216Q1
chr22:19166130-19166130p.K19K1
chr22:19163667-19163667p.L304L1
chr22:19164411-19164411p.S193S1
chr22:19163733-19163733p.R282R1
chr22:19164667-19164667p.F164L1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1111     1   1  12 4
# mutation1211     1   1  12 4
nonsynonymous SNV111              1 2
synonymous SNV 1 1     1   1  11 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
chr22:19164697p.K19K1
chr22:19163733p.R289R,SLC25A11
chr22:19165307p.G285G,SLC25A11
chr22:19163745p.Q272Q,SLC25A11
chr22:19165323p.A260A,SLC25A11
chr22:19163960p.G244R,SLC25A11
chr22:19165368p.K223Q,SLC25A11
chr22:19163996p.F207F,SLC25A11
chr22:19166130p.S200S,SLC25A11
chr22:19164129p.F171L,SLC25A11

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 SLC25A1 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 SLC25A1

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

ACO2,ATXN10,BCL2L13,DRG1,ST13P4,FOXRED2,L3MBTL2,
MRPL40,NDUFA6,NHP2L1,NUP50,PHF5A,RNF185,SAMM50,
SLC25A17,SNAP29,ST13,SYNGR1,TOMM22,XPNPEP3,XRCC6
AGA,BUB3,C14orf1,TMEM241,C3orf14,CYP2R1,CYP51A1,
HSD17B7,HSPB11,MYCBP,PEX3,PIP4K2C,PPA2,PPAPDC2,
PTPLAD1,RNF103,SERP1,SLC25A17,TMEM33,SARAF,TMEM87B

ADSL,BID,CDC45,CENPM,DGCR6L,DRG1,MRPL40,
NDUFA6,NHP2L1,PHF5A,POLR2F,RANBP1,RBX1,SLC25A17,
SNRPD3,TOMM22,TXN2,UBE2L3,UFD1L,UQCR10,XRCC6
DTD2,CMC2,TEFM,CCDC58,CHAC2,COX18,DCAF13,
HSPA14,MEMO1,MRPL1,MRPL42,MRPS35,PTRH2,TRMT10C,
RINT1,SLC25A17,SRPRB,TAF9,TOMM22,UTP18,WDR12
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 SLC25A1
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; citrate transporter), member 1approved; nutraceuticalBiotin


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Cross referenced IDs for SLC25A1
* 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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