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

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 SLC25A1

Basic gene info.	Gene symbol	SLC25A1
	Gene name	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1
	Synonyms	CTP\|D2L2AD\|SEA\|SLC20A3
	Cytomap	UCSC genome browser: 22q11.21
	Genomic location	chr22 :19163087-19166338
	Type of gene	protein-coding
	RefGenes	NM_001256534.1, NM_001287387.1,NM_005984.4,NR_046298.2,
	Ensembl id	ENSG00000268928
	Description	citrate transport proteinsolute carrier family 20 (mitochondrial citrate transporter), member 3tricarboxylate carrier proteintricarboxylate transport protein, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 190315
	HGNC : HGNC
	Ensembl : ENSG00000100075
	HPRD : 01832
	Vega : OTTHUMG00000150123
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC25A1
	BioGPS: 6576
	Gene Expression Atlas: ENSG00000268928
	The Human Protein Atlas: ENSG00000268928
Pathway	NCI Pathway Interaction Database: SLC25A1
	KEGG: SLC25A1
	REACTOME: SLC25A1
	ConsensusPathDB
	Pathway Commons: SLC25A1
Metabolism	MetaCyc: SLC25A1
	HUMANCyc: SLC25A1
Regulation	Ensembl's Regulation: ENSG00000268928
	miRBase: chr22 :19,163,087-19,166,338
	TargetScan: NM_001256534
	cisRED: ENSG00000268928
Context	iHOP: SLC25A1
	cancer metabolism search in PubMed: SLC25A1
	UCL Cancer Institute: SLC25A1
Assigned class in ccmGDB	C

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Phenotypic Information for SLC25A1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: SLC25A1
	MedGen: SLC25A1 (Human Medical Genetics with Condition)
	ClinVar: SLC25A1
Phenotype	MGI: SLC25A1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC25A1 related fusion information.

ID	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
D16945	SLC25A1	1	162	22	19164171	19164653	HSPA13	159	405	21	15743529	15743768
CD614306	JUN	14	431	1	59249297	59249716	SLC25A1	428	639	22	19164999	19165212
CD614310	SLC25A1	1	347	22	19164999	19165347	JUN	344	691	1	59249365	59249716
CD614312	JUN	16	435	1	59249297	59249716	SLC25A1	432	696	22	19164999	19165266
CD614307	JUN	15	434	1	59249297	59249716	SLC25A1	431	714	22	19164999	19165289
BC016877	CBL	11	2128	11	119175363	119177480	SLC25A1	2128	3100	22	19163094	19164441
CD614308	SLC25A1	1	339	22	19164999	19165339	JUN	336	659	1	59249388	59249716
AA086119	PLXNB1	29	168	3	48445291	48445430	SLC25A1	169	472	22	19163746	19164455
CD614309	JUN	15	434	1	59249297	59249716	SLC25A1	431	719	22	19164999	19165289
AI394736	SLC25A1	10	129	22	19163094	19163213	FMNL3	126	427	12	50069340	50069641
CD614314	JUN	13	433	1	59249297	59249716	SLC25A1	430	654	22	19164999	19165288
CD614313	SLC25A1	1	348	22	19164999	19165347	JUN	345	612	1	59249452	59249716
CA427923	SLC25A1	40	280	22	19163483	19163722	SLC25A1	273	587	22	19164105	19165262

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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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=2

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Somatic 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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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
chr22:19164123-19164123	p.T239S	2
chr22:19164157-19164157	p.G227G	2
chr22:19166130-19166130	p.K19K	1
chr22:19163667-19163667	p.L304L	1
chr22:19164411-19164411	p.S193S	1
chr22:19163733-19163733	p.R282R	1
chr22:19164667-19164667	p.F164L	1
chr22:19163745-19163745	p.G278G	1
chr22:19164682-19164682	p.P159P	1
chr22:19163948-19163950	p.K269delK	1

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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	1						1				1			1	2		4
# mutation	1	2	1	1						1				1			1	2		4
nonsynonymous SNV	1	1	1															1		2
synonymous SNV		1		1						1				1			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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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
chr22:19163745	p.Q272Q,SLC25A1	1
chr22:19165323	p.A260A,SLC25A1	1
chr22:19163960	p.G244R,SLC25A1	1
chr22:19165368	p.K223Q,SLC25A1	1
chr22:19163996	p.F207F,SLC25A1	1
chr22:19166130	p.S200S,SLC25A1	1
chr22:19164129	p.F171L,SLC25A1	1
chr22:19164192	p.P166P,SLC25A1	1
chr22:19164390	p.Q161H,SLC25A1	1
chr22:19164411	p.L132P,SLC25A1	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 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

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))

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CNV 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

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


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

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

: Open all plots for all cancer types

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Interacting 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

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
DB00121	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1	approved; nutraceutical	Biotin

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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