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 SLC25A13
Basic gene info.Gene symbolSLC25A13
Gene namesolute carrier family 25 (aspartate/glutamate carrier), member 13
SynonymsARALAR2|CITRIN|CTLN2
CytomapUCSC genome browser: 7q21.3
Genomic locationchr7 :95749531-95951459
Type of geneprotein-coding
RefGenesNM_001160210.1,
NM_014251.2,NR_027662.1,
Ensembl idENSG00000004864
Descriptioncalcium-binding mitochondrial carrier protein Aralar2mitochondrial aspartate glutamate carrier 2solute carrier family 25, member 13 (citrin)
Modification date20141222
dbXrefs MIM : 603859
HGNC : HGNC
Ensembl : ENSG00000004864
HPRD : 04837
Vega : OTTHUMG00000023074
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC25A13
BioGPS: 10165
Gene Expression Atlas: ENSG00000004864
The Human Protein Atlas: ENSG00000004864
PathwayNCI Pathway Interaction Database: SLC25A13
KEGG: SLC25A13
REACTOME: SLC25A13
ConsensusPathDB
Pathway Commons: SLC25A13
MetabolismMetaCyc: SLC25A13
HUMANCyc: SLC25A13
RegulationEnsembl's Regulation: ENSG00000004864
miRBase: chr7 :95,749,531-95,951,459
TargetScan: NM_001160210
cisRED: ENSG00000004864
ContextiHOP: SLC25A13
cancer metabolism search in PubMed: SLC25A13
UCL Cancer Institute: SLC25A13
Assigned class in ccmGDBC

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Phenotypic Information for SLC25A13(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC25A13
Familial Cancer Database: SLC25A13
* 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_PROTEINS
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC25A13
MedGen: SLC25A13 (Human Medical Genetics with Condition)
ClinVar: SLC25A13
PhenotypeMGI: SLC25A13 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC25A13

Mutations for SLC25A13
* 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
There's no inter-chromosomal structural variation.
- 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
ovarySLC25A13chr79583607395836093CADPS2chr7122374949122374969
pancreasSLC25A13chr79585290895852928FLJ42280chr79612646596126485
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 SLC25A13 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA535064ZNF736122176377431163774531SLC25A1322155179582051795838290
BE072029SLC25A13113279578673695786868SLC25A1312731179578615295786336
BI480726CDK6129579235248392352566SLC25A138768679576645895767055

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 3 1   3  
GAIN (# sample)      1 3     3  
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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=72)
Stat. for Synonymous SNVs
(# total SNVs=24)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=3)

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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
chr7:95775866-95775866p.?32
chr7:95799433-95799433p.N412S7
chr7:95813609-95813609p.G386D2
chr7:95838255-95838255p.I121I2
chr7:95820501-95820501p.S225L2
chr7:95926239-95926239p.P14S2
chr7:95820524-95820524p.F217L2
chr7:95799390-95799390p.V426V2
chr7:95818905-95818905p.Y279C2
chr7:95799394-95799394p.S425L2

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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=7

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 6 191 2 31 74  196113
# mutation 6 131 2 31 84  199116
nonsynonymous SNV 4 101 2 3  64   77112
synonymous SNV 2 3     1 2   122 4
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
chr7:95799433p.N413S,SLC25A137
chr7:95799394p.R284H,SLC25A132
chr7:95820501p.G650G,SLC25A132
chr7:95820524p.S225L,SLC25A132
chr7:95818688p.F217L,SLC25A132
chr7:95750584p.S426L,SLC25A132
chr7:95775995p.V168M,SLC25A131
chr7:95822393p.S511F,SLC25A131
chr7:95750587p.R417S,SLC25A131
chr7:95813738p.E161E,SLC25A131

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 SLC25A13 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 SLC25A13

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

ANLN,ASNS,CENPI,DBF4,DLD,DNAJC2,EML4,
IFRD1,KCMF1,NUP205,PNO1,PPP3R1,PSMC2,PUS7,
RINT1,SLC25A13,SRPK1,SUV39H2,TRRAP,WDR43,YWHAG
CCDC138,CCDC160,CYP2R1,CYP51A1,F2RL1,GCNT2,IQGAP2,
LRRC8D,MANSC1,OAT,PAICS,QTRTD1,RFC3,RFWD3,
SEC23B,SLC15A2,SLC25A13,STIL,TMEM87B,XYLB,ZNF138

ANKIB1,ARPC1A,ASL,TMEM243,CBLL1,COG5,CRCP,
DDC,DLD,EIF4H,EXOC4,GATAD1,KRIT1,PEX1,
POM121,PUS7,SEMA3C,SLC25A13,TNPO3,VKORC1L1,ZSCAN25
ABCD3,ACTR2,MCU,FAR2,GJB2,IQGAP2,ITGB6,
LETM1,NDUFS2,NIPA2,PAPSS2,PDCD6IP,PGGT1B,PRSS12,
PTBP3,SLC25A13,SLC44A1,TGFA,UGDH,UGT1A10,UGT1A8
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 SLC25A13
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
DB00128solute carrier family 25 (aspartate/glutamate carrier), member 13approved; nutraceuticalL-Aspartic Acid


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Cross referenced IDs for SLC25A13
* 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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