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 ATP5B

Basic gene info.	Gene symbol	ATP5B
	Gene name	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide
	Synonyms	ATPMB\|ATPSB\|HEL-S-271
	Cytomap	UCSC genome browser: 12q13.13
	Genomic location	chr12 :57031958-57039852
	Type of gene	protein-coding
	RefGenes	NM_001686.3,
	Ensembl id	ENSG00000110955
	Description	ATP synthase subunit beta, mitochondrialepididymis secretory protein Li 271mitochondrial ATP synthase beta subunitmitochondrial ATP synthetase, beta subunit
	Modification date	20141207
dbXrefs	MIM : 102910
	HGNC : HGNC
	Ensembl : ENSG00000110955
	HPRD : 00044
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ATP5B
	BioGPS: 506
	Gene Expression Atlas: ENSG00000110955
	The Human Protein Atlas: ENSG00000110955
Pathway	NCI Pathway Interaction Database: ATP5B
	KEGG: ATP5B
	REACTOME: ATP5B
	ConsensusPathDB
	Pathway Commons: ATP5B
Metabolism	MetaCyc: ATP5B
	HUMANCyc: ATP5B
Regulation	Ensembl's Regulation: ENSG00000110955
	miRBase: chr12 :57,031,958-57,039,852
	TargetScan: NM_001686
	cisRED: ENSG00000110955
Context	iHOP: ATP5B
	cancer metabolism search in PubMed: ATP5B
	UCL Cancer Institute: ATP5B
Assigned class in ccmGDB	C

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Phenotypic Information for ATP5B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ATP5B
	Familial Cancer Database: ATP5B

* 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_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: ATP5B
	MedGen: ATP5B (Human Medical Genetics with Condition)
	ClinVar: ATP5B
Phenotype	MGI: ATP5B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ATP5B

Mutations for ATP5B

* 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 ATP5B 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
CA312538	ATP5B	18	86	12	57031962	57032030	ATP5B	83	135	12	57032029	57032081
AW852155	ATP5B	2	185	12	57033603	57033790	PTGES3	184	264	12	57076115	57076316
AW375766	HADH	8	290	4	108955685	108955967	ATP5B	285	399	12	57031962	57032076
BE676351	ATP5B	14	124	12	57031962	57032072	MSI2	111	443	17	55723353	55723686
BF819282	ATP5B	7	105	12	57036599	57037268	CLU	102	271	8	27462542	27462711
AA128804	UBE2T	1	56	1	202304725	202304780	ATP5B	48	107	12	57031962	57032021
CV344647	ATP5B	32	425	12	57037273	57038740	PTMA	421	527	2	232573311	232573417
BG258137	ATP5B	29	305	12	57036523	57037370	ATP5B	297	402	12	57031959	57032064
AK127078	FMN1	1	3310	15	33065737	33359029	ATP5B	3305	3812	12	57031962	57033823
BG179093	ATP5B	14	122	12	57033033	57033812	ATP5B	118	539	12	57031962	57033065

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=37)	Stat. for Synonymous SNVs (# total SNVs=12)

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
chr12:57038968-57038968	p.V99V	2
chr12:57037687-57037687	p.E181Q	2
chr12:57033832-57033832	p.I407V	2
chr12:57033894-57033894	p.S386L	2
chr12:57036523-57036523	p.D295D	2
chr12:57039674-57039674	p.S25L	2
chr12:57038681-57038681	p.Q123H	2
chr12:57037665-57037665	p.K188R	2
chr12:57036289-57036289	p.Q343*	1
chr12:57038732-57038732	p.S106S	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=4

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	2	1		10	1				2			5	2	3			2	9		7
# mutation	2	1		10	1				2			6	2	2			3	9		8
nonsynonymous SNV	1	1		7	1				1			3	2	1			3	4		5
synonymous SNV	1			3					1			3		1				5		3

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
chr12:57033004	p.K459Q	3
chr12:57036523	p.D295D	2
chr12:57038968	p.V99V	2
chr12:57037270	p.G237S	1
chr12:57039026	p.S386L	1
chr12:57033775	p.A224T	1
chr12:57036324	p.V384V	1
chr12:57037309	p.I187I	1
chr12:57039070	p.F507L	1
chr12:57033788	p.T375M	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 ATP5B 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 ATP5B

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


ATP5B,ATP5G3,CCT7,CS,GOT1,HSPA8,HSPA9, IMMT,MARS,MDH2,PA2G4,PGAM1,PRIM1,PTGES3, RACGAP1,RAN,SDHB,SHMT2,SLC25A3,SLC25A5,TIMELESS	ACAT1,ACO2,ALPK3,ATP5A1,ATP5B,ADCK3,CHCHD3, COX5A,FH,GYS1,HADHB,IMMT,MLYCD,NDUFS1, OGDH,PDHX,SDHA,SDHB,SLC2A4,UQCRC2,UQCRFS1

ATP5A1,ATP5B,C1QBP,COX6A1,CS,DLST,GAPDH, GOT1,IMMT,ME2,PCCB,PHB2,PSMD9,SCO1, SDHB,SHMT2,SLC25A3,TPI1,TSFM,TUBA1B,UQCRC1	ATP5A1,ATP5B,ATP5G3,C2orf47,COX5A,DBI,ETFA, GHITM,GOT1,HARBI1,HCCS,MYCBP,NDUFA9,NDUFS3, PSMD3,RTN4IP1,SCO1,SQRDL,UQCRC1,UQCRC2,UQCRFS1

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 ATP5B

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
DB04216	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	experimental	Quercetin
DB07384	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	experimental	1-ACETYL-2-CARBOXYPIPERIDINE
DB07394	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	experimental	AUROVERTIN B
DB08399	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	experimental	PICEATANNOL
DB08629	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	experimental	N1-(2-AMINO-4-METHYLPENTYL)OCTAHYDRO-PYRROLO[1,2-A] PYRIMIDINE

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Cross referenced IDs for ATP5B

* 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