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 SLC25A12
Basic gene info.Gene symbolSLC25A12
Gene namesolute carrier family 25 (aspartate/glutamate carrier), member 12
SynonymsAGC1|ARALAR
CytomapUCSC genome browser: 2q24
Genomic locationchr2 :172639914-172750816
Type of geneprotein-coding
RefGenesNM_003705.4,
NR_047549.1,
Ensembl idENSG00000115840
Descriptionaraceli hiperlargacalcium binding mitochondrial carrier superfamily member Aralar1calcium-binding mitochondrial carrier protein Aralar1mitochondrial aspartate glutamate carrier 1solute carrier family 25 (mitochondrial carrier, Aralar), member 12
Modification date20141207
dbXrefs MIM : 603667
HGNC : HGNC
Ensembl : ENSG00000115840
HPRD : 04719
Vega : OTTHUMG00000134290
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC25A12
BioGPS: 8604
Gene Expression Atlas: ENSG00000115840
The Human Protein Atlas: ENSG00000115840
PathwayNCI Pathway Interaction Database: SLC25A12
KEGG: SLC25A12
REACTOME: SLC25A12
ConsensusPathDB
Pathway Commons: SLC25A12
MetabolismMetaCyc: SLC25A12
HUMANCyc: SLC25A12
RegulationEnsembl's Regulation: ENSG00000115840
miRBase: chr2 :172,639,914-172,750,816
TargetScan: NM_003705
cisRED: ENSG00000115840
ContextiHOP: SLC25A12
cancer metabolism search in PubMed: SLC25A12
UCL Cancer Institute: SLC25A12
Assigned class in ccmGDBC

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Phenotypic Information for SLC25A12(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC25A12
Familial Cancer Database: SLC25A12
* 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: SLC25A12
MedGen: SLC25A12 (Human Medical Genetics with Condition)
ClinVar: SLC25A12
PhenotypeMGI: SLC25A12 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC25A12

Mutations for SLC25A12
* 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
ovarySLC25A12chr2172748795172748815chr2174838757174838777
ovarySLC25A12chr2172748802172748822chr2174838764174838784
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 SLC25A12 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF947427SPATS13437464427660244276941SLC25A123686602172650608172650899
AW845689SLC25A121892172675216172675307SLC25A12845562172678638172679110

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)             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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=51)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=3)
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
chr2:172648071-172648071p.I492S4
chr2:172641950-172641950p.R624H3
chr2:172712358-172712358p.G104A2
chr2:172749752-172749752p.R10Q2
chr2:172641848-172641848p.P658Q2
chr2:172666787-172666787p.?2
chr2:172712428-172712428p.E81K2
chr2:172641902-172641902p.R640K2
chr2:172690472-172690472p.?2
chr2:172671641-172671641p.S334S2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample3 114  1 11 731  5618
# mutation3 113  1 11 731  5618
nonsynonymous SNV3  11  1 11 621  1517
synonymous SNV  12       11   41 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
chr2:172666181p.R624H2
chr2:172641950p.E200D2
chr2:172693643p.R414W2
chr2:172749752p.R10Q2
chr2:172647961p.S662Y1
chr2:172712451p.T462M1
chr2:172641836p.F253F1
chr2:172690559p.P658P1
chr2:172647993p.R453H1
chr2:172725232p.L239L1

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 SLC25A12 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 SLC25A12

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

ANKAR,ZFAND4,BBS5,C1orf21,CFAP69,SPATA6L,CACNA1D,
CCDC28A,CYBRD1,DIXDC1,DLX2,DNAH7,DYNC1I2,HAT1,
KIF13B,NOSTRIN,OSBPL1A,SIK3,SLC25A12,SPATA6,ZC3H6
AMPD1,ASB12,ASB14,ASB4,CA14,CAPN3,CMYA5,
CTXN3,FLJ41941,IDI2,JPH1,KCNQ5,MYLK3,MYLK4,
MYOM3,OBSCN,PKIA,PRKCQ,SLC25A12,TXLNB,MSS51

C1orf95,C3orf18,CEP68,DNAJC27,EPC2,EXTL2,FASTKD1,
GTDC1,LYRM7,MARCH7,METTL8,PLEKHA3,PRKCE,RBM43,
RCOR3,SCRN3,SLC25A12,SRGAP3,TFCP2L1,TOR1AIP1,ZC3H8
BVES,CALD1,CSRP1,CTXN1,DES,DNAJB5,HSPB8,
ILK,LMO3,MYL9,MYLK,PDLIM7,PNCK,SLC25A12,
SMTN,TAGLN,THBS4,TPM1,TPM2,TSPAN2,TUBA1A
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 SLC25A12
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 12approved; nutraceuticalL-Aspartic Acid


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Cross referenced IDs for SLC25A12
* 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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