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 SLC25A21

Basic gene info.	Gene symbol	SLC25A21
	Gene name	solute carrier family 25 (mitochondrial oxoadipate carrier), member 21
	Synonyms	ODC\|ODC1
	Cytomap	UCSC genome browser: 14q11.2
	Genomic location	chr14 :37147125-37641865
	Type of gene	protein-coding
	RefGenes	NM_001171170.1, NM_030631.3,
	Ensembl id	ENSG00000183032
	Description	mitochondrial 2-oxodicarboxylate carrieroxodicarboxylate carriersolute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21solute carrier family 25 member 21
	Modification date	20141207
dbXrefs	MIM : 607571
	HGNC : HGNC
	HPRD : 12124
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC25A21
	BioGPS: 89874
	Gene Expression Atlas: ENSG00000183032
	The Human Protein Atlas: ENSG00000183032
Pathway	NCI Pathway Interaction Database: SLC25A21
	KEGG: SLC25A21
	REACTOME: SLC25A21
	ConsensusPathDB
	Pathway Commons: SLC25A21
Metabolism	MetaCyc: SLC25A21
	HUMANCyc: SLC25A21
Regulation	Ensembl's Regulation: ENSG00000183032
	miRBase: chr14 :37,147,125-37,641,865
	TargetScan: NM_001171170
	cisRED: ENSG00000183032
Context	iHOP: SLC25A21
	cancer metabolism search in PubMed: SLC25A21
	UCL Cancer Institute: SLC25A21
Assigned class in ccmGDB	C

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Phenotypic Information for SLC25A21(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SLC25A21
	Familial Cancer Database: SLC25A21

* 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_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: SLC25A21
	MedGen: SLC25A21 (Human Medical Genetics with Condition)
	ClinVar: SLC25A21
Phenotype	MGI: SLC25A21 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SLC25A21

Mutations for SLC25A21

* 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

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- 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
large_intestine	SLC25A21	chr14	37610741	37610741	MIPOL1	chr14	37714136	37714136
liver	SLC25A21	chr14	37446216	37446216	SLC25A21	chr14	37454024	37454024
ovary	SLC25A21	chr14	37303585	37303605	SLC25A21	chr14	37303635	37303655
ovary	SLC25A21	chr14	37305646	37305666	SLC25A21	chr14	37306098	37306118
ovary	SLC25A21	chr14	37528480	37528500		chr14	37101794	37101814
ovary	SLC25A21	chr14	37608494	37608514	SLC25A21	chr14	37624185	37624205
pancreas	SLC25A21	chr14	37158550	37158570	BRMS1L	chr14	36329533	36329553
pancreas	SLC25A21	chr14	37372872	37372892		chr14	40471738	40471758

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 SLC25A21 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

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

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	8	1				2	2		26		2		3	1	1		3
GAIN (# sample)	7					2			26		2		3	1	1		2
LOSS (# sample)	1	1					2										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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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

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=20)	Stat. for Synonymous SNVs (# total SNVs=3)

Stat. for Deletions (# total SNVs=2)	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
chr14:37154057-37154057	p.I226T	3
chr14:37180638-37180638	p.W163*	2
chr14:37194791-37194791	p.R141Q	2
chr14:37194792-37194792	p.R141W	2
chr14:37153057-37153057	p.P272S	2
chr14:37203772-37203772	p.F70fs*20	2
chr14:37283130-37283130	p.M66L	2
chr14:37194883-37194883	p.?	1
chr14:37344201-37344201	p.E27K	1
chr14:37180645-37180645	p.E161*	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=2

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	3			2					2	1				7	4		3
# mutation		1	1	3			2					2	1				7	5		2
nonsynonymous SNV		1	1	2			2					1					7	4		2
synonymous SNV				1								1	1					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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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
chr14:37283178	p.R141W,SLC25A21	2
chr14:37194792	p.P272S,SLC25A21	2
chr14:37153057	p.P50S,SLC25A21	2
chr14:37283144	p.G152G,SLC25A21	1
chr14:37180580	p.A113V,SLC25A21	1
chr14:37180664	p.A113T,SLC25A21	1
chr14:37344171	p.G102E,SLC25A21	1
chr14:37180670	p.T84I,SLC25A21	1
chr14:37641501	p.R276R,SLC25A21	1
chr14:37153043	p.I76V,SLC25A21	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 SLC25A21 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 SLC25A21

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


ANKS4B,BAZ1A,LINC01559,PCNXL4,CHD8,CTAGE5,DTWD2, FANCM,LINC01184,GRIN2B,KIAA0391,MIPOL1,PAX9,POLE2, RALGAPA1,RDH11,REG4,SLC25A21,TRAPPC6B,TTLL5,ZNF253	ARMC1,NADK2,DCTN4,FAM120C,FAM47E,FBXO9,FRS2, MBTPS2,NRIP1,NT5DC1,PLA2G12A,RAB18,RAD21,TRMT10A, RHOT1,RNF170,SENP2,ARHGEF26,SLC25A21,SRPK2,UBE2W

ANXA13,CA8,CIB4,CIT,CKAP4,FAM174B,GALNT8, KIF19,MAK,MIPOL1,OPRD1,PCSK1,RAP1GAP,RHBDL3, SLAIN1,SLC25A21,SLC26A9,SPINK4,SSTR1,STXBP1,UGT2B4	ARL4D,C16orf45,CAB39L,CES1,CFL2,FBXO17,MORN5, MSRB3,MXRA7,NT5DC3,NUDT10,NUDT11,PDLIM3,PDLIM4, PTPLA,RASL12,RASSF8,SLC25A21,SOX15,ST3GAL3,TSPAN2

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 SLC25A21

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
DB00123	solute carrier family 25 (mitochondrial oxoadipate carrier), member 21	approved; nutraceutical	L-Lysine

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Cross referenced IDs for SLC25A21

* 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