Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	SLC25A10
	Gene name	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10
	Synonyms	DIC
	Cytomap	UCSC genome browser: 17q25.3
	Genomic location	chr17 :79679370-79688042
	Type of gene	protein-coding
	RefGenes	NM_001270888.1, NM_001270953.1,NM_012140.4,
	Ensembl id	ENSG00000262660
	Description	dicarboxylate ion carriermitochondrial dicarboxylate carrier
	Modification date	20141207
dbXrefs	MIM : 606794
	HGNC : HGNC
	Ensembl : ENSG00000183048
	HPRD : 08424
	Vega : OTTHUMG00000178173
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC25A10
	BioGPS: 1468
	Gene Expression Atlas: ENSG00000262660
	The Human Protein Atlas: ENSG00000262660
Pathway	NCI Pathway Interaction Database: SLC25A10
	KEGG: SLC25A10
	REACTOME: SLC25A10
	ConsensusPathDB
	Pathway Commons: SLC25A10
Metabolism	MetaCyc: SLC25A10
	HUMANCyc: SLC25A10
Regulation	Ensembl's Regulation: ENSG00000262660
	miRBase: chr17 :79,679,370-79,688,042
	TargetScan: NM_001270888
	cisRED: ENSG00000262660
Context	iHOP: SLC25A10
	cancer metabolism search in PubMed: SLC25A10
	UCL Cancer Institute: SLC25A10
Assigned class in ccmGDB	C

Top

Phenotypic Information for SLC25A10(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: SLC25A10
	MedGen: SLC25A10 (Human Medical Genetics with Condition)
	ClinVar: SLC25A10
Phenotype	MGI: SLC25A10 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	SLC25A10	chr17	79679636	79679656	SLC25A10	chr17	79679804	79679824

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC25A10 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

DA998089

EEF2

274

3984161

3985461

SLC25A10

275

557

79679488

79682608

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

Top

SNV 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

Top

Somatic 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.

Top

Top 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 position	Mutation(aa)	Unique sampleID count
chr17:79687107-79687107	p.*288C	6
chr17:79682051-79682051	p.T54T	4
chr17:79682558-79682558	p.R88R	2
chr17:79682023-79682023	p.T45R	2
chr17:79682059-79682059	p.I57N	2
chr17:79686917-79686917	p.K254N	2
chr17:79687071-79687071	p.Q276H	1
chr17:79684474-79684474	p.Y194H	1
chr17:79682587-79682587	p.P98H	1
chr17:79686863-79686863	p.G236G	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample				1	1		1					4	3	1				4		4
# mutation				1	1		1					4	3	1				4		4
nonsynonymous SNV				1			1					4	3					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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr17:79686897	p.G257R,SLC25A10	2
chr17:79684472	p.R220G	1
chr17:79686863	p.A260T,SLC25A10	1
chr17:79682037	p.R50W,SLC25A10	1
chr17:79686876	p.G264C,SLC25A10	1
chr17:79682051	p.T54T,SLC25A10	1
chr17:79686879	p.Q285H,SLC25A10	1
chr17:79682059	p.I57S,SLC25A10	1
chr17:79686896	p.F79F,SLC25A10	1
chr17:79682531	p.R86L,SLC25A10	1

Other 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

Copy 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]

Top

Gene Expression for SLC25A10

Gene 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.

Differential 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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

Gene-Gene Network Information

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for SLC25A10

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00139	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	approved; nutraceutical	Succinic acid
DB00121	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	approved; nutraceutical	Biotin

Top

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