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 SLC25A10
Basic gene info.Gene symbolSLC25A10
Gene namesolute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10
SynonymsDIC
CytomapUCSC genome browser: 17q25.3
Genomic locationchr17 :79679370-79688042
Type of geneprotein-coding
RefGenesNM_001270888.1,
NM_001270953.1,NM_012140.4,
Ensembl idENSG00000262660
Descriptiondicarboxylate ion carriermitochondrial dicarboxylate carrier
Modification date20141207
dbXrefs MIM : 606794
HGNC : HGNC
Ensembl : ENSG00000183048
HPRD : 08424
Vega : OTTHUMG00000178173
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC25A10
BioGPS: 1468
Gene Expression Atlas: ENSG00000262660
The Human Protein Atlas: ENSG00000262660
PathwayNCI Pathway Interaction Database: SLC25A10
KEGG: SLC25A10
REACTOME: SLC25A10
ConsensusPathDB
Pathway Commons: SLC25A10
MetabolismMetaCyc: SLC25A10
HUMANCyc: SLC25A10
RegulationEnsembl's Regulation: ENSG00000262660
miRBase: chr17 :79,679,370-79,688,042
TargetScan: NM_001270888
cisRED: ENSG00000262660
ContextiHOP: SLC25A10
cancer metabolism search in PubMed: SLC25A10
UCL Cancer Institute: SLC25A10
Assigned class in ccmGDBC

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Phenotypic Information for SLC25A10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC25A10
Familial Cancer Database: SLC25A10
* 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_SULFUR_AMINO_ACID_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC25A10
MedGen: SLC25A10 (Human Medical Genetics with Condition)
ClinVar: SLC25A10
PhenotypeMGI: SLC25A10 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC25A10

Mutations for SLC25A10
* 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
pancreasSLC25A10chr177967963679679656SLC25A10chr177967980479679824
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 SLC25A10 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA998089EEF212741939841613985461SLC25A10275557177967948879682608

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=4

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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=10)
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
chr17:79687107-79687107p.*288C6
chr17:79682051-79682051p.T54T4
chr17:79682023-79682023p.T45R2
chr17:79682059-79682059p.I57N2
chr17:79686917-79686917p.K254N2
chr17:79682558-79682558p.R88R2
chr17:79682587-79682587p.P98H1
chr17:79686863-79686863p.G236G1
chr17:79679534-79679534p.P26P1
chr17:79682616-79682616p.V108F1

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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
# sample   11 1    431   4 4
# mutation   11 1    431   4 4
nonsynonymous SNV   1  1    43    4 2
synonymous SNV    1        1     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
chr17:79686897p.G257R,SLC25A102
chr17:79686863p.R50W,SLC25A101
chr17:79682037p.G264C,SLC25A101
chr17:79686876p.T54T,SLC25A101
chr17:79682051p.Q285H,SLC25A101
chr17:79686879p.I57S,SLC25A101
chr17:79682059p.F79F,SLC25A101
chr17:79686896p.R86L,SLC25A101
chr17:79682531p.T118M,SLC25A101
chr17:79682551p.V123V,SLC25A101

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 SLC25A10 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 SLC25A10

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

ANAPC11,ARHGDIA,ARL16,ASPSCR1,C17orf89,OXLD1,CCDC137,
CHMP6,DUS1L,GPS1,HGS,LRRC45,MRPL12,MRPL38,
PCYT2,PYCR1,RFNG,SIRT7,SLC25A10,STRA13,ALYREF
ACY1,BSG,C20orf27,CKB,DDT,FPGS,GCDH,
MESP1,MPST,PC,PCYT2,POLR2E,SCRN2,SHMT1,
SLC25A10,SLC25A1,SLC2A4RG,STAT5A,TALDO1,TMEM120A,TST

ATP5G1,BOLA3,UQCC3,C17orf89,CCDC137,DUS1L,GPS1,
HMBS,LRRC45,MRPL12,MRPL38,PHB,PTGES2,PYCR1,
SAC3D1,SLC25A10,SLC25A19,SLC25A39,THAP4,ALYREF,TOMM40
ABHD11,AGMAT,APEH,CCNI2,DCXR,DHRS13,DUS1L,
FGFR4,GOT1,GSS,MRPL12,MTFP1,PDSS1,SLC25A10,
SLC25A39,SLC35A4,TBRG4,TIMM13,TTLL12,TUFM,UQCRC1
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 SLC25A10
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
DB00139solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10approved; nutraceuticalSuccinic acid
DB00121solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10approved; nutraceuticalBiotin


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Cross referenced IDs for SLC25A10
* 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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