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 OXCT1

Basic gene info.	Gene symbol	OXCT1
	Gene name	3-oxoacid CoA transferase 1
	Synonyms	OXCT\|SCOT
	Cytomap	UCSC genome browser: 5p13.1
	Genomic location	chr5 :41730166-41870791
	Type of gene	protein-coding
	RefGenes	NM_000436.3,
	Ensembl id	ENSG00000083720
	Description	3-oxoacid CoA-transferase 13-oxoacid-CoA transferase 1SCOT-ssomatic-type succinyl CoA:3-oxoacid CoA-transferasesomatic-type succinyl-CoA:3-oxoacid CoA-transferasesomatic-type succinyl-CoA:3-oxoacid-CoA-transferasesuccinyl CoA:3-oxoacid CoA transfera
	Modification date	20141207
dbXrefs	MIM : 601424
	HGNC : HGNC
	Ensembl : ENSG00000083720
	HPRD : 02001
	Vega : OTTHUMG00000094783
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_OXCT1
	BioGPS: 5019
	Gene Expression Atlas: ENSG00000083720
	The Human Protein Atlas: ENSG00000083720
Pathway	NCI Pathway Interaction Database: OXCT1
	KEGG: OXCT1
	REACTOME: OXCT1
	ConsensusPathDB
	Pathway Commons: OXCT1
Metabolism	MetaCyc: OXCT1
	HUMANCyc: OXCT1
Regulation	Ensembl's Regulation: ENSG00000083720
	miRBase: chr5 :41,730,166-41,870,791
	TargetScan: NM_000436
	cisRED: ENSG00000083720
Context	iHOP: OXCT1
	cancer metabolism search in PubMed: OXCT1
	UCL Cancer Institute: OXCT1
Assigned class in ccmGDB	C

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Phenotypic Information for OXCT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: OXCT1
	Familial Cancer Database: OXCT1

* 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
KEGG_BUTANOATE_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: OXCT1
	MedGen: OXCT1 (Human Medical Genetics with Condition)
	ClinVar: OXCT1
Phenotype	MGI: OXCT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: OXCT1

Mutations for OXCT1

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
ovary	OXCT1	chr5	41796553	41796573	OXCT1	chr5	41840886	41840906
pancreas	OXCT1	chr5	41765091	41765111		chr5	37088127	37088147
pancreas	OXCT1	chr5	41851989	41852009		chr5	42043957	42043977

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 OXCT1 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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=45)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr5:41850282-41850282	p.?	3
chr5:41803197-41803197	p.Q342E	2
chr5:41850261-41850261	p.I145I	2
chr5:41853594-41853594	p.S114L	2
chr5:41853606-41853606	p.R110H	2
chr5:41850186-41850186	p.S170S	2
chr5:41805723-41805723	p.V301I	2
chr5:41739516-41739516	p.Q499H	2
chr5:41801144-41801144	p.D360G	2
chr5:41794170-41794170	p.D395N	2

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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	1	7			1		1			7	3	2			6	6		10
# mutation	1	1	1	6			1		1			8	3	2			6	8		10
nonsynonymous SNV		1		3			1					4	3	2			4	5		9
synonymous SNV	1		1	4					1			4					2	3		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
chr5:41762297	p.G324E	2
chr5:41794170	p.K418K	2
chr5:41803250	p.D395N	2
chr5:41850186	p.T372N	1
chr5:41762295	p.S170S	1
chr5:41862746	p.R18R	1
chr5:41805770	p.L363L	1
chr5:41850248	p.A150T	1
chr5:41862794	p.S9S	1
chr5:41807445	p.R355Q	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 OXCT1 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 OXCT1

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


CA13,CLSPN,E2F3,EHBP1,ETV6,OTULIN,GNPTAB, ICE1,KIF1B,KLF5,MSH2,MYO10,NUP155,OXCT1, PDK1,PPM1L,SERPINB5,SKP2,TRIM2,ZFR,ZNF131	ABCD2,ABHD15,ACAA2,ACACB,ACSL1,ACVR1C,ADIPOQ, AQP7,AQPEP,GPATCH11,CIDEC,HOGA1,GHR,GYG2, LGALS12,MARC1,MTHFD1,OXCT1,PDE3B,PECR,PEX19

ALKBH5,FAM212B,CCDC109B,CYB5D1,FECH,HPSE,HSPA4L, NKX3-1,OXCT1,PIAS2,RNF125,SAP30,THRAP3,TOP3A, TRIM7,TYMS,UBR7,USP13,WDR76,ZBTB8A,ZNF232	C15orf41,CALU,CNTLN,IFT81,LOC221710,LRRC20,MDM1, NUCKS1,OXCT1,PBX3,PHF19,RECQL,RIMKLB,RNF165, SAE1,TACC1,TBC1D19,TNFAIP8L1,VPS45,WHAMMP2,ZMYND11

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 OXCT1

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	3-oxoacid CoA transferase 1	approved; nutraceutical	Succinic acid
DB02731	3-oxoacid CoA transferase 1	experimental	Thimerosal

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Cross referenced IDs for OXCT1

* 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